Contacts of the helix formed by residues 111 - 136 (chain G) in PDB entry 3IYD
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ASP 111 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G PRO 5.4 3.6 - - - +
109G ASN* 3.0 19.7 + - - +
110G PRO* 1.3 81.6 - - + +
112G ILE* 1.3 60.8 + - - +
114G MET* 3.0 22.1 + - - +
115G ARG* 3.2 37.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 112 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G THR* 4.9 9.0 - - + +
13G TRP* 4.8 7.9 - - + +
14G PHE* 3.5 42.8 - - + -
69G PHE* 4.9 9.6 - - + -
102G PHE* 3.6 21.1 - - + -
105G LEU* 4.1 17.3 - - + +
106G ILE* 4.2 13.5 - - + -
109G ASN* 3.2 29.4 + - + +
111G ASP* 1.3 78.0 - - - +
113G LEU* 1.3 66.8 + - - +
115G ARG* 3.3 8.1 + - - +
116G LEU* 3.3 17.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 113 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75G LEU* 4.9 5.4 - - + -
76G PHE* 4.7 13.2 - - + -
102G PHE* 4.6 9.4 - - + -
106G ILE* 3.7 46.2 - - + -
110G PRO 3.1 9.7 + - - +
112G ILE* 1.3 80.8 - - - +
114G MET* 1.3 59.4 + - - +
115G ARG 3.1 0.9 - - - -
116G LEU* 4.6 7.0 - - + +
117G SER* 3.0 51.3 + - - +
110H PRO* 4.8 13.9 - - + +
113H LEU* 4.7 18.6 - - + +
114H MET* 4.5 17.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 114 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110G PRO 3.2 10.1 + - - +
111G ASP* 3.0 23.0 + - - +
113G LEU* 1.3 77.0 - - - +
115G ARG* 1.3 59.8 + - - +
117G SER* 4.5 1.2 - - - -
118G ALA* 3.2 23.8 + - - +
75H LEU* 4.0 9.0 - - + +
76H PHE* 3.4 45.1 - - + +
103H ARG* 5.5 9.6 - - + +
106H ILE* 5.0 15.0 - - + -
113H LEU* 4.0 24.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 115 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G PRO* 4.9 18.0 - - - +
10G THR* 3.3 40.9 + - + +
69G PHE* 5.1 3.4 - - + -
111G ASP* 3.2 35.4 + - - +
112G ILE* 3.6 9.9 - - - +
113G LEU 3.1 0.4 - - - -
114G MET* 1.3 81.8 - - - +
116G LEU* 1.3 64.1 + - - +
117G SER 3.3 0.2 - - - -
118G ALA* 3.1 18.6 + - - +
119G GLN* 3.3 17.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 116 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39G LEU* 4.4 9.4 - - + -
69G PHE* 3.5 45.9 - - + -
72G GLU* 3.6 39.0 - - + +
75G LEU* 4.1 15.0 - - + -
76G PHE* 6.1 1.6 - - + -
102G PHE* 4.0 25.1 - - + -
112G ILE 3.3 12.4 + - - +
113G LEU* 3.7 7.2 + - + +
115G ARG* 1.3 77.5 - - - +
117G SER* 1.3 63.1 + - - +
118G ALA 3.1 1.1 + - - -
119G GLN* 3.3 10.7 + - + +
120G MET* 3.3 22.2 + - - +
123G ARG* 5.5 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 117 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76G PHE* 4.1 5.0 - - - -
113G LEU* 3.0 37.6 + - - +
114G MET* 5.0 0.7 - - - -
116G LEU* 1.3 76.3 - - - +
118G ALA* 1.3 59.7 + - - +
119G GLN 3.5 0.2 - - - -
120G MET* 3.8 21.4 + - - +
121G ALA 4.1 0.9 + - - -
76H PHE* 3.1 41.5 - - - -
113H LEU* 5.2 3.2 - - - +
117H SER* 3.5 21.5 + - - -
120H MET* 4.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 118 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G MET 3.2 21.0 + - - +
115G ARG* 3.1 10.3 + - - +
116G LEU 3.1 0.6 - - - -
117G SER* 1.3 78.6 - - - +
119G GLN* 1.3 63.9 + - + +
120G MET 3.2 0.4 - - - -
121G ALA* 3.4 17.5 + - - +
122G ARG* 4.0 4.3 + - - +
76H PHE* 3.7 25.3 - - + +
77H GLU* 6.0 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 119 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G THR* 5.2 6.3 + - - -
67G GLY 3.3 20.9 + - - -
68G ASP* 4.0 5.6 + - - -
69G PHE* 3.2 36.7 + - - -
115G ARG* 3.3 12.5 + - - +
116G LEU* 3.3 6.9 + - + +
118G ALA* 1.3 73.4 - - + +
120G MET* 1.3 62.1 + - + +
121G ALA 3.1 6.0 + - - -
122G ARG* 3.3 7.7 + - - +
123G ARG* 3.1 53.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 120 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72G GLU* 4.1 26.2 - - + +
73G LEU* 3.8 27.6 - - + -
76G PHE* 3.8 36.1 - - + -
116G LEU* 3.3 20.4 - - + +
117G SER* 3.9 14.8 - - - +
118G ALA 3.2 0.6 - - - -
119G GLN* 1.3 77.9 - - + +
121G ALA* 1.3 61.0 + - - +
122G ARG 3.5 0.2 - - - -
123G ARG* 4.0 8.4 - - - +
124G LEU* 3.3 23.4 + - - +
117H SER* 4.2 9.4 - - - +
120H MET* 4.1 31.4 - - + +
121H ALA 4.3 0.7 - - - +
124H LEU* 5.3 6.2 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G SER 4.1 0.2 + - - -
118G ALA 3.4 12.9 + - - +
119G GLN 3.1 0.6 - - - -
120G MET* 1.3 78.3 - - - +
122G ARG* 1.3 63.8 + - - +
124G LEU* 3.5 8.5 + - - +
125G GLN* 3.3 25.1 + - - +
73H LEU* 3.6 36.1 - - + +
76H PHE* 4.1 20.4 - - + -
80H GLN* 6.4 0.4 - - - +
120H MET* 3.9 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 122 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118G ALA 4.0 3.7 + - - +
119G GLN* 3.3 11.4 + - - +
121G ALA* 1.3 76.3 - - - +
123G ARG* 1.3 65.9 + - + +
125G GLN* 3.0 32.5 + - - +
126G VAL* 3.1 38.2 + - + +
129G GLU* 5.9 1.0 + - - -
77H GLU* 5.5 2.2 + - - -
80H GLN* 4.9 14.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 123 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64G LEU* 4.5 15.4 - - + +
68G ASP* 3.4 15.2 - - - +
69G PHE* 2.9 47.7 + - - +
72G GLU* 3.0 33.6 + - - -
116G LEU* 5.5 0.6 - - - +
119G GLN* 3.1 39.5 + - - +
120G MET* 4.2 7.1 - - - +
122G ARG* 1.3 78.7 - - + +
124G LEU* 1.3 60.5 + - - +
126G VAL* 3.3 10.2 - - + +
127G THR* 2.8 32.6 + - - -
679G CMP 4.0 32.7 + - + -
124H LEU* 3.9 12.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 124 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G MET 3.3 16.7 + - - +
121G ALA 3.7 6.5 - - - +
122G ARG 3.2 0.6 - - - -
123G ARG* 1.3 77.6 - - - +
125G GLN* 1.3 59.9 + - + +
127G THR* 4.3 1.2 - - - -
128G SER* 2.8 30.4 + - - +
72H GLU* 5.4 2.0 - - - +
73H LEU* 4.5 20.6 - - + -
120H MET* 4.7 15.7 - - + +
123H ARG* 3.3 49.6 - - + +
124H LEU* 3.9 20.2 - - + +
127H THR* 5.0 1.3 - - - +
680H CMP 4.5 26.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 125 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121G ALA* 3.3 16.6 + - - +
122G ARG* 3.0 41.0 + - - +
124G LEU* 1.3 78.2 - - + +
126G VAL* 1.3 60.8 + - + +
127G THR 3.1 1.6 - - - -
128G SER* 3.1 5.4 + - - -
129G GLU* 2.9 46.7 + - + +
73H LEU* 3.3 35.4 - - + +
80H GLN* 5.7 2.2 + - - -
83H SER* 4.4 18.1 - - - -
680H CMP 5.1 1.5 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 126 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G SER* 4.9 21.3 - - - +
64G LEU* 6.6 0.2 - - + -
122G ARG* 3.1 31.6 + - + +
123G ARG* 3.3 21.8 - - + +
125G GLN* 1.3 75.8 - - + +
127G THR* 1.3 66.2 + - - +
129G GLU* 3.8 12.3 + - - +
130G LYS* 3.3 21.3 + - - +
679G CMP 5.1 3.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 127 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G LEU* 5.7 3.1 - - + -
123G ARG 2.8 20.0 + - - -
124G LEU 4.5 1.8 - - - -
125G GLN 3.1 0.4 - - - -
126G VAL* 1.3 80.0 - - - +
128G SER* 1.3 63.4 + - - +
130G LYS* 3.3 18.7 + - + +
131G VAL* 3.6 10.6 - - - +
679G CMP 3.0 28.0 + - - +
124H LEU* 3.7 11.4 - - + +
127H THR* 3.7 21.1 - - + +
128H SER* 3.5 28.0 - - - +
131H VAL* 4.7 3.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124G LEU* 2.8 22.9 + - - +
125G GLN* 3.1 6.6 + - - -
127G THR* 1.3 77.0 - - - +
129G GLU* 1.3 65.2 + - - +
131G VAL* 3.2 16.3 + - - +
132G GLY* 3.6 2.8 + - - -
61H LEU* 3.4 39.9 - - - +
127H THR* 4.1 17.1 + - - +
680H CMP 3.2 21.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122G ARG* 5.9 0.5 + - - -
125G GLN* 2.9 33.4 + - - +
126G VAL* 4.2 11.0 - - - +
128G SER* 1.3 76.0 - - - +
130G LYS* 1.3 63.9 + - - +
131G VAL 3.2 0.2 - - - -
132G GLY* 3.4 8.2 + - - +
133G ASN* 3.2 26.6 + - - +
51H ILE* 6.1 8.1 - - + -
61H LEU* 5.3 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G MET* 4.5 10.1 - - - -
60G ILE 4.1 10.2 + - - -
61G LEU* 3.9 42.0 + - + +
126G VAL 3.3 14.0 + - - +
127G THR* 3.3 13.9 + - - +
128G SER 3.1 0.8 - - - -
129G GLU* 1.3 78.8 - - - +
131G VAL* 1.3 62.5 + - - +
133G ASN* 3.4 27.1 + - + +
134G LEU* 3.7 17.2 - - - +
175G ILE* 3.2 33.9 + - - +
176G VAL* 5.3 0.4 - - - +
131H VAL* 4.7 7.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 131 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127G THR 3.6 15.3 - - - +
128G SER* 3.5 9.2 - - - +
129G GLU 3.2 0.4 - - - -
130G LYS* 1.3 76.3 - - - +
132G GLY* 1.3 64.1 + - - +
134G LEU* 3.1 25.5 + - - +
135G ALA* 3.8 4.0 + - - +
59H MET* 3.9 17.9 - - + -
61H LEU* 5.3 2.5 - - + -
127H THR* 4.1 15.9 - - + +
130H LYS* 5.6 4.5 - - + -
131H VAL* 3.6 24.7 - - + +
134H LEU* 3.8 27.7 - - + +
174H GLN 5.1 2.2 - - - +
175H ILE 5.3 0.4 - - - +
177H GLY* 6.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 132 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128G SER 3.6 5.0 + - - -
129G GLU* 3.4 7.9 + - - -
130G LYS 3.4 0.6 - - - -
131G VAL* 1.3 79.7 - - - +
133G ASN* 1.3 63.8 + - - +
134G LEU 3.1 0.2 - - - -
135G ALA* 3.1 1.4 + - - -
136G PHE* 3.1 42.3 + - - +
137G LEU* 5.9 0.2 - - - -
51H ILE* 6.2 2.2 - - - -
59H MET* 3.9 20.1 - - - +
61H LEU* 6.0 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 133 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129G GLU* 3.2 19.8 + - - +
130G LYS* 3.6 26.0 + - + +
131G VAL 3.1 0.6 - - - -
132G GLY* 1.3 78.4 - - - +
134G LEU* 1.3 62.5 + - + +
135G ALA 3.3 1.1 - - - -
136G PHE 4.5 0.9 - - - -
137G LEU* 3.4 31.6 + - + +
142G ARG* 3.2 29.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G MET* 4.1 16.6 - - + -
130G LYS* 3.7 17.9 - - - +
131G VAL* 3.1 11.4 + - + +
133G ASN* 1.3 83.1 - - + +
135G ALA* 1.3 59.1 + - - +
137G LEU 4.8 2.9 - - - -
142G ARG* 3.3 20.3 + - - +
176G VAL* 3.3 29.6 - - - +
177G GLY* 5.2 0.7 - - - -
131H VAL* 3.7 32.3 - - + +
134H LEU* 4.1 30.0 - - + +
135H ALA* 5.1 2.7 - - + -
177H GLY* 4.7 10.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 135 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131G VAL* 4.2 7.2 - - + +
132G GLY 3.1 7.8 + - - +
133G ASN 3.3 0.6 + - - -
134G LEU* 1.3 80.5 - - - +
136G PHE* 1.3 73.6 + - + +
137G LEU 4.6 1.3 + - - -
57H LYS* 5.9 2.3 - - - +
59H MET* 4.5 14.1 - - + -
173H GLY 5.5 0.9 - - - +
177H GLY* 4.2 24.5 - - - -
178H CYS* 5.0 6.5 + - - +
84J A 5.4 3.1 - - - +
85J T 4.2 10.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 136 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132G GLY* 3.1 29.5 + - - +
135G ALA* 1.3 83.3 - - + +
137G LEU* 1.3 77.8 + - + +
138G ASP* 3.7 2.1 + - - +
51H ILE* 5.6 4.0 - - + -
52H LYS 5.9 1.1 - - - -
53H ASP* 3.5 37.7 - - + -
54H GLU* 5.7 2.2 - - - +
57H LYS* 3.7 27.6 - - + -
58H GLU 4.0 8.1 - - - -
59H MET* 3.7 44.6 - - + -
84J A 5.4 0.7 - - - +
85J T 4.5 11.1 + - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il