Contacts of the helix formed by residues 108 - 130 (chain G) in PDB entry 4HHM
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 108 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106G ALA* 3.3 2.0 - - + +
107G ASN* 1.3 75.6 - - - +
109G ARG* 1.3 64.9 + - - +
110G ASP* 3.8 15.5 - - - +
111G VAL* 3.3 21.3 + - + +
112G ARG* 3.4 16.3 + - - +
334H ARG* 2.7 53.8 + - - +
337H GLN* 3.5 9.8 + - - +
368H ARG* 2.9 21.0 + - - +
370H MET* 3.9 10.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 109 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107G ASN 3.4 2.2 + - - -
108G ASP* 1.3 68.5 - - - +
110G ASP* 1.3 66.7 + - - +
112G ARG* 3.0 37.0 + - - +
113G ARG* 3.1 52.0 + - + +
337H GLN* 2.8 22.6 - - + +
340H GLU* 4.7 10.1 - - - -
341H PRO 3.2 21.4 + - - -
342H THR* 3.3 14.1 + - - +
343H ALA* 4.6 2.0 - - - +
344H ALA* 4.6 5.9 - - - +
345H ASP* 3.8 12.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 110 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108G ASP* 3.8 9.3 - - - +
109G ARG* 1.3 78.8 - - - +
111G VAL* 1.3 87.4 + - - +
113G ARG* 3.4 11.2 + - - +
114G TYR* 2.9 29.6 + - - +
337H GLN* 4.6 1.7 - - - +
355H THR 5.1 4.9 - - - +
356H ALA* 5.3 1.9 - - - -
360H PHE* 3.6 27.9 - - + -
368H ARG* 3.7 19.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 111 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98G VAL* 3.8 35.4 - - + +
99G PHE* 3.9 13.8 - - + -
102G GLY 3.8 10.5 - - - +
103G ALA 4.6 0.2 - - - +
106G ALA* 3.8 20.6 - - + -
108G ASP* 3.5 21.8 - - + +
109G ARG 3.1 0.6 - - - -
110G ASP* 1.3 96.1 + - - +
112G ARG* 1.3 55.8 + - - +
114G TYR* 3.2 7.9 + - + +
115G ALA* 2.8 28.1 + - - +
360H PHE* 4.3 4.9 - - + -
365H ALA* 4.6 6.1 - - + +
368H ARG* 4.7 2.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 112 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
103G ALA 3.3 19.7 - - - +
104G PHE* 3.1 25.5 - - - +
105G THR* 4.2 1.8 - - - +
106G ALA* 2.9 27.7 + - + +
107G ASN 2.7 30.7 + - - -
108G ASP 3.4 3.8 - - - +
109G ARG* 3.0 32.9 + - - +
111G VAL* 1.3 75.6 - - - +
113G ARG* 1.3 63.0 + - - +
115G ALA* 3.3 4.0 + - - +
116G LEU* 3.2 26.2 + - + +
157G ARG* 3.4 13.3 - - - +
337H GLN 3.0 13.8 + - - -
338H LEU* 4.0 2.6 - - - +
340H GLU 2.7 29.9 + - - -
341H PRO 4.1 1.2 + - - -
342H THR* 2.9 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 113 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109G ARG* 3.1 52.4 + - - +
110G ASP* 3.7 9.6 - - - +
112G ARG* 1.3 73.0 - - - +
114G TYR* 1.3 67.5 + - - +
116G LEU* 3.2 6.3 + - - +
117G ARG* 3.1 26.3 + - - +
342H THR* 3.0 37.3 + - + +
343H ALA* 3.7 7.7 - - - +
345H ASP* 3.7 22.4 + - - -
349H ALA 4.4 0.2 + - - -
350H LEU* 3.7 32.9 - - + +
353H ASP* 2.7 42.5 + - - +
355H THR* 4.9 1.6 + - - -
356H ALA* 3.9 10.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 114 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G PHE* 3.4 30.9 - + - -
98G VAL* 4.3 11.7 - - + -
99G PHE* 3.5 34.5 - + - -
110G ASP 2.9 18.1 + - - +
111G VAL 3.4 3.8 - - - +
113G ARG* 1.3 78.5 - - - +
115G ALA* 1.3 56.1 + - - +
117G ARG* 3.3 1.7 + - - +
118G LYS* 2.9 39.5 + - + +
356H ALA* 3.4 20.6 + - - +
357H TYR* 4.0 29.1 - + - -
360H PHE* 3.5 31.2 - + + -
362H VAL* 3.9 20.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 115 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93G LEU* 3.7 13.2 - - + +
99G PHE* 3.5 21.1 - - + -
103G ALA* 3.8 25.6 - - + -
104G PHE* 3.9 6.5 - - + -
111G VAL 2.8 15.7 + - - +
112G ARG 3.5 7.2 - - - +
113G ARG 3.2 0.4 - - - -
114G TYR* 1.3 79.2 - - - +
116G LEU* 1.3 59.3 + - - +
118G LYS* 3.5 0.6 + - - -
119G THR* 2.9 28.9 + - - -
----------------------------------------------------------
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
----------------------------------------------------------
104G PHE* 3.7 21.8 - - + -
112G ARG 3.2 12.9 + - - +
113G ARG* 3.2 8.1 + - - +
115G ALA* 1.3 73.2 - - - +
117G ARG* 1.3 60.6 + - - +
119G THR* 3.2 3.4 + - - -
120G ILE* 2.8 38.7 + - + +
161G ALA* 3.5 33.7 - - + +
164G LEU* 3.6 31.9 - - + -
165G LEU* 4.1 14.6 - - + -
342H THR* 3.6 24.7 - - + -
350H LEU* 3.8 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 117 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G ARG 3.1 13.8 + - - +
114G TYR 3.7 5.8 - - - +
116G LEU* 1.3 76.7 - - - +
118G LYS* 1.3 63.0 + - - +
120G ILE* 3.3 6.1 + - - +
121G ARG* 2.9 25.6 + - - +
350H LEU* 3.0 44.7 + - + -
351H LEU* 3.2 38.9 + - - +
353H ASP 3.0 22.4 + - - -
356H ALA* 3.5 14.1 - - - +
357H TYR* 3.8 27.3 - - + +
358H GLU* 4.1 19.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 118 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G ASP* 2.8 30.7 + - - +
56G ASP* 3.0 18.6 + - - -
61G PHE* 3.6 30.1 - - - -
91G THR* 4.1 2.7 - - + +
92G ASN 2.8 24.9 + - - +
93G LEU* 4.0 16.8 - - + -
96G HIS* 6.4 0.2 - - - -
99G PHE* 4.2 12.6 - - + -
114G TYR* 2.9 31.7 + - + +
115G ALA* 3.8 5.4 - - - +
117G ARG* 1.3 77.3 - - - +
119G THR* 1.3 63.7 - - - +
121G ARG* 3.4 5.2 + - - +
122G ASN* 3.4 17.0 + - - +
357H TYR* 4.6 12.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 119 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91G THR* 3.6 19.8 + - - +
93G LEU* 3.4 22.6 - - + +
104G PHE* 3.6 9.5 - - + -
115G ALA 2.9 15.3 + - - -
116G LEU 3.5 7.9 - - - -
117G ARG 3.2 0.2 - - - -
118G LYS* 1.3 74.6 - - - +
120G ILE* 1.3 67.3 + - - +
122G ASN* 3.0 6.4 + - - +
123G ILE* 3.0 22.9 + - + +
134G TYR* 3.8 14.5 + - + -
165G LEU* 3.9 29.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 120 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G LEU* 2.8 33.4 + - + +
117G ARG* 3.3 8.7 + - - +
119G THR* 1.3 71.7 - - - +
121G ARG* 1.3 64.9 + - - +
123G ILE* 3.1 18.4 + - - +
124G ASP* 3.3 14.8 + - - +
164G LEU* 5.4 2.0 - - + +
165G LEU* 3.8 20.9 - - + -
168G TYR* 3.4 42.8 - - + +
347H LEU* 4.1 26.9 - - + -
350H LEU* 5.0 4.7 - - + -
351H LEU* 4.2 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63G ALA 5.4 5.3 + - - -
65G ASP* 3.2 27.5 + - - +
68G ARG* 3.4 58.4 + - - +
117G ARG 2.9 15.8 + - - +
118G LYS* 3.6 8.3 - - - +
119G THR 3.2 0.2 - - - -
120G ILE* 1.3 79.2 - - - +
122G ASN* 1.3 61.4 + - - +
124G ASP* 3.4 19.0 + - - +
125G LEU 3.5 6.8 + - - -
357H TYR* 3.0 36.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 122 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G PHE* 3.7 12.7 - - - -
55G ASP* 3.2 34.1 - - + +
59G ILE* 5.3 0.2 - - - +
68G ARG* 4.9 3.2 + - - +
89G ALA* 4.4 0.2 - - - +
90G THR 2.8 30.5 + - - +
91G THR* 4.3 1.6 - - - +
118G LYS 3.4 7.5 + - - +
119G THR 3.0 4.4 + - - +
121G ARG* 1.3 74.6 - - - +
123G ILE* 1.3 67.4 + - - +
124G ASP 3.1 1.8 - - - -
125G LEU* 3.0 25.1 + - - +
126G ALA* 2.9 21.8 + - - +
134G TYR* 3.0 21.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 123 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119G THR* 3.0 20.5 + - + +
120G ILE* 3.1 12.1 + - - +
122G ASN* 1.3 75.7 - - - +
124G ASP* 1.3 65.3 + - - +
126G ALA* 3.0 13.0 + - - +
127G VAL* 3.1 13.3 + - + +
134G TYR* 3.8 26.2 - - + -
165G LEU* 3.9 22.2 - - + +
168G TYR* 4.5 8.5 - - + -
169G VAL* 4.0 13.7 - - + -
174G TYR* 3.9 25.6 - - + -
176G ILE* 4.5 9.9 - - + -
178G PHE* 3.7 29.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 124 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120G ILE* 3.3 13.3 + - - +
121G ARG* 3.6 12.9 - - - +
122G ASN 3.1 0.8 - - - -
123G ILE* 1.3 77.4 - - - +
125G LEU* 1.3 62.0 + - - +
127G VAL* 3.1 5.5 + - - +
128G GLU* 3.1 21.2 + - - +
168G TYR* 2.7 26.0 + - - -
174G TYR* 2.5 37.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 125 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G PHE* 4.1 16.6 - - + -
58G LEU* 4.3 4.3 - - + -
59G ILE* 3.6 31.4 - - + -
68G ARG* 4.0 22.0 - - - +
69G GLU* 6.2 0.2 - - - +
72G VAL* 4.3 18.2 - - + -
121G ARG 3.5 2.2 + - - -
122G ASN* 3.0 27.0 + - - +
124G ASP* 1.3 78.6 - - - +
126G ALA* 1.3 58.0 + - - +
128G GLU* 3.6 21.5 + - - +
129G LEU* 3.1 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 126 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G PHE* 5.3 1.1 - - - -
89G ALA* 3.6 26.9 - - + -
122G ASN 2.9 12.0 + - - +
123G ILE 3.0 13.7 + - - +
125G LEU* 1.3 77.1 - - - +
127G VAL* 1.3 57.7 + - - +
129G LEU* 3.4 3.3 + - - -
130G GLY 3.0 7.3 + - - -
131G ALA* 2.8 36.3 + - + +
134G TYR* 3.9 11.7 - - + -
176G ILE* 4.0 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 127 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123G ILE* 3.1 12.9 + - + +
124G ASP 3.1 6.7 + - - +
126G ALA* 1.3 73.0 - - - +
128G GLU* 1.3 65.4 + - - +
130G GLY* 3.3 11.5 + - - +
131G ALA 4.5 4.7 - - - +
174G TYR* 3.4 59.2 - - + +
175G ASP 5.6 1.8 - - - +
176G ILE* 5.0 9.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69G GLU* 4.0 19.8 - - - +
72G VAL* 5.1 2.0 - - - +
76G ARG* 3.3 35.6 + - - +
124G ASP 3.1 12.9 + - - +
125G LEU* 3.8 24.3 - - - +
126G ALA 3.3 0.2 - - - -
127G VAL* 1.3 80.4 - - - +
129G LEU* 1.3 62.2 + - + +
130G GLY 3.5 0.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 129 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53G PHE* 3.5 36.3 - - + -
58G LEU* 4.5 2.7 - - + -
72G VAL* 5.6 5.8 - - + +
75G PHE* 3.9 28.9 - - + -
76G ARG* 4.0 26.0 - - + +
79G LEU* 4.8 10.9 - - + +
86G VAL* 4.4 26.2 + - + +
125G LEU* 3.1 32.7 + - + +
126G ALA* 3.4 5.1 + - - +
128G GLU* 1.3 76.3 - - - +
130G GLY* 1.3 59.6 + - - +
131G ALA 3.5 0.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 130 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86G VAL 4.0 4.8 - - - +
87G PRO* 5.3 1.0 - - - +
126G ALA 3.0 3.8 + - - -
127G VAL 3.3 8.4 + - - -
128G GLU 3.2 4.6 - - - -
129G LEU* 1.3 79.8 - - - +
131G ALA* 1.3 64.4 + - - +
132G LYS* 3.1 30.1 + - - +
----------------------------------------------------------
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