Contacts of the helix formed by residues 103 - 123 (chain G) in PDB entry 1KYO
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 LEU 103 (chain G).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46G ASP* 2.8 30.1 + - + +
49G ILE* 4.9 0.4 - - + -
56G MET* 3.6 37.0 - - + -
59G ALA* 4.3 4.0 - - + -
60G LEU* 3.8 33.0 - - + +
63G LEU* 3.4 28.9 - - + -
71G ARG* 4.9 1.6 - - - +
102G TYR* 1.3 88.3 - - + +
104G LEU* 1.3 66.5 + - - +
105G PRO 3.4 0.2 - - - -
106G TYR* 2.9 25.2 + - + +
107G ILE* 3.2 19.2 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379C TYR* 4.1 29.8 - - + +
382C ARG* 5.6 1.3 - - - +
383C VAL* 4.9 1.8 - - + -
385C LYS* 5.3 7.4 - - - +
5G PHE* 4.0 31.0 - - + +
9G ALA* 5.4 0.2 - - + -
46G ASP* 3.0 10.5 + - - +
101G PRO* 3.7 30.5 - - + +
103G LEU* 1.3 75.4 - - - +
105G PRO* 1.3 71.0 - - + +
107G ILE* 3.0 11.9 + - + +
108G LEU* 3.0 50.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 105 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101G PRO 3.3 17.3 - - - +
102G TYR* 3.8 13.0 - - - +
103G LEU 3.5 1.1 - - - -
104G LEU* 1.3 94.1 - - + +
106G TYR* 1.3 70.3 - - + +
108G LEU* 3.4 9.1 + - + +
109G GLU* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 106 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59G ALA* 4.1 24.1 - - + +
62G ARG* 3.5 35.3 + - + +
63G LEU* 3.7 20.6 - - + -
64G PRO* 2.9 28.7 - - + +
102G TYR 3.5 20.2 - - - -
103G LEU* 2.9 14.6 + - + +
105G PRO* 1.3 82.8 - - + +
107G ILE* 1.3 64.4 + - - +
109G GLU* 3.3 18.3 + - - +
110G ALA* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 107 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G PHE* 3.5 39.5 - - + -
49G ILE* 3.6 30.3 - - + -
55G ILE* 4.2 10.0 - - + +
56G MET* 3.8 18.2 - - + -
59G ALA* 4.1 18.8 - - + -
103G LEU* 3.2 11.6 + - + +
104G LEU* 3.0 20.4 + - + +
106G TYR* 1.3 77.0 - - - +
108G LEU* 1.3 52.0 + - - +
110G ALA* 3.1 7.7 + - - +
111G GLU* 2.8 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 108 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385C LYS* 4.7 11.9 - - - +
5G PHE* 3.6 38.8 - - + +
6G THR* 3.6 15.5 + - - +
9G ALA* 4.3 12.8 - - + -
104G LEU* 3.0 43.1 + - + +
105G PRO* 3.8 7.2 - - + +
107G ILE* 1.3 73.6 - - - +
109G GLU* 1.3 68.7 + - - +
111G GLU* 3.6 5.4 - - - +
112G ALA* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 109 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ARG* 5.1 7.8 + - - +
105G PRO 3.0 14.1 + - - +
106G TYR* 3.4 24.0 - - - +
108G LEU* 1.3 76.5 - - - +
110G ALA* 1.3 65.5 + - - +
112G ALA* 3.9 3.4 - - - +
113G ALA* 3.0 25.6 + - + +
115M LYS* 3.0 35.8 + - - +
117M HIS* 3.9 25.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 110 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G ILE* 3.7 23.9 - - + +
58G THR* 4.1 25.6 - - + -
59G ALA* 5.1 1.3 - - - +
62G ARG* 4.6 8.5 - - - +
106G TYR 3.0 12.9 + - - +
107G ILE* 3.4 8.7 - - - +
109G GLU* 1.3 78.3 - - - +
111G GLU* 1.3 61.2 + - - +
113G ALA* 3.4 7.4 + - - +
114G ALA* 3.0 23.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 111 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G SER* 3.5 12.9 - - - -
5G PHE* 2.9 40.4 + - - -
6G THR* 2.8 38.7 + - - +
55G ILE* 4.1 20.6 - - + +
107G ILE* 2.8 30.9 + - + +
108G LEU* 3.6 6.5 - - - +
109G GLU 3.2 0.2 - - - -
110G ALA* 1.3 73.8 - - - +
112G ALA* 1.3 58.2 + - - +
114G ALA* 3.0 7.4 + - - +
115G LYS* 2.9 26.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 112 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G THR* 4.6 5.8 + - + +
108G LEU 3.1 14.6 + - - +
109G GLU* 3.9 3.1 - - - +
111G GLU* 1.3 76.5 - - - +
113G ALA* 1.3 64.6 + - - +
115G LYS* 3.2 11.0 + - - +
116G GLU* 3.1 24.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 113 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62G ARG* 5.4 6.5 - - - +
109G GLU* 3.0 20.0 + - + +
110G ALA* 3.5 10.1 - - - +
112G ALA* 1.3 75.5 - - - +
114G ALA* 1.3 61.2 - - - +
116G GLU* 3.5 10.5 + - - +
117G LYS* 3.2 22.5 + - - +
65M LEU* 5.0 1.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 114 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G ILE* 4.2 15.7 - - + -
110G ALA 3.0 12.7 + - - +
111G GLU* 3.0 10.6 + - - +
113G ALA* 1.3 76.2 - - - +
115G LYS* 1.3 58.9 + - - +
117G LYS* 3.4 7.9 + - - +
118G ASP* 2.9 31.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 115 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G THR* 6.2 3.4 - - - -
111G GLU 2.9 12.4 + - - +
112G ALA* 3.2 15.9 + - + +
114G ALA* 1.3 77.9 - - - +
116G GLU* 1.3 55.4 + - - +
118G ASP* 3.2 11.4 - - + +
119G GLU* 2.9 51.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 116 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112G ALA 3.1 11.4 + - - +
113G ALA* 3.6 12.4 - - - +
114G ALA 3.2 0.2 - - - -
115G LYS* 1.3 73.3 - - - +
117G LYS* 1.3 58.7 + - - +
118G ASP 3.0 1.1 - - - -
119G GLU* 2.8 13.7 + - + +
120G LEU* 2.7 52.7 + - + +
63M SER* 2.8 36.1 + - - -
65M LEU* 4.5 7.0 - - + +
66M LYS* 3.8 19.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 117 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113G ALA 3.2 11.5 + - - +
114G ALA* 3.4 11.6 + - - +
116G GLU* 1.3 79.7 - - - +
118G ASP* 1.3 65.4 + - - +
120G LEU* 3.4 2.1 + - - +
121G ASP* 3.1 54.0 + - - +
303L ASP* 3.4 26.3 + - - -
65M LEU* 3.6 27.4 - - + +
69M ARG* 4.6 9.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 118 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114G ALA 2.9 18.2 + - - +
115G LYS* 3.2 13.2 - - + +
117G LYS* 1.3 84.1 - - + +
119G GLU* 1.3 60.3 + - - +
121G ASP* 3.4 7.2 + - - +
122G ASN* 2.7 38.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 119 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115G LYS* 2.9 42.7 + - + +
116G GLU* 2.8 21.0 + - - +
118G ASP* 1.3 76.0 - - - +
120G LEU* 1.3 58.2 + - + +
121G ASP 3.1 0.4 - - - -
122G ASN* 3.1 7.1 + - - +
123G ILE* 3.1 32.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116G GLU* 2.7 38.5 + - + +
117G LYS* 3.8 4.5 - - - +
119G GLU* 1.3 74.4 - - + +
121G ASP* 1.3 61.4 + - - +
122G ASN 3.3 0.2 - - - -
123G ILE* 3.3 41.0 - - + +
65M LEU* 4.1 9.0 - - + -
66M LYS* 3.8 36.1 - - + +
69M ARG* 3.5 51.3 + - + +
70M GLU* 5.8 2.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 121 (chain G).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117G LYS* 3.1 50.4 + - - +
118G ASP* 3.6 8.9 - - - +
119G GLU 3.1 0.6 - - - -
120G LEU* 1.3 77.5 - - - +
122G ASN* 1.3 66.7 + - - +
123G ILE* 3.6 0.7 - - - -
300L LYS* 3.5 27.5 + - - +
303L ASP* 4.2 9.1 - - - +
360L THR* 5.4 3.6 + - - -
69M ARG* 2.6 35.2 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
118G ASP* 2.7 36.8 + - - +
119G GLU* 3.1 7.9 + - - +
121G ASP* 1.3 88.7 - - - +
123G ILE* 1.3 64.3 + - - +
124G GLU* 3.2 12.0 + - - +
300L LYS* 5.1 3.3 + - - -
360L THR* 5.3 1.5 - - - +
----------------------------------------------------------
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 GLU* 3.1 20.6 + - + +
120G LEU* 3.3 43.3 - - + +
121G ASP 3.6 0.4 - - - -
122G ASN* 1.3 75.7 - - - +
124G GLU* 1.3 66.3 + - - +
125G VAL* 4.9 1.5 - - + +
360L THR* 2.9 29.4 + - - +
69M ARG* 5.4 3.8 - - + -
73M LEU* 4.4 29.2 - - + -
----------------------------------------------------------
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