Contacts of the helix formed by residues 3 - 20 (chain G) in PDB entry 3G5G
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 SER 3 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G GLU* 1.3 76.9 - - - +
4G PHE* 1.3 62.8 + - - +
5G LEU* 4.2 0.3 - - - +
6G LEU* 3.1 30.6 + - - +
7G SER* 3.2 20.8 + - - -
44G ASN* 4.2 3.1 + - - +
50H ILE* 5.1 0.2 - - - +
51H LYS* 4.1 27.7 - - - +
54H GLU* 2.9 23.4 + - - -
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Residues in contact with PHE 4 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2G GLU 3.6 4.9 + - - -
3G SER* 1.3 71.2 + - - +
5G LEU* 1.3 67.3 + - - +
7G SER* 2.9 25.3 + - - -
8G LYS* 3.2 45.7 + - + +
75G ILE* 4.5 21.1 - - + -
54H GLU* 3.8 11.2 + - - +
64H ASP* 3.6 24.2 - - - -
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Residues in contact with LEU 5 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G PHE* 1.3 83.8 - - + +
6G LEU* 1.3 64.1 + - - +
8G LYS* 3.1 4.9 + - + +
9G VAL* 3.0 33.0 + - + +
71G LEU* 4.5 2.0 - - + -
75G ILE* 4.4 16.4 - - + -
50H ILE* 3.2 36.3 - - + +
53H LEU* 4.5 12.8 - - + -
54H GLU* 3.1 21.8 + - + +
57H MET* 4.0 26.2 - - + -
64H ASP* 4.4 6.1 - - - +
68H PHE* 4.0 24.2 - - + -
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Residues in contact with LEU 6 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G SER* 3.1 24.0 + - - +
5G LEU* 1.3 78.6 - - - +
7G SER* 1.3 62.1 + - - +
9G VAL* 3.4 2.7 + - + +
10G SER* 3.1 26.5 + - - -
41G ILE* 5.7 3.8 - - + +
44G ASN* 3.5 26.7 - - - +
46G ARG 3.6 25.8 - - - +
47G ASN* 4.1 11.0 - - - +
48G LEU* 4.3 25.1 - - + -
50H ILE* 4.0 16.9 - - + +
51H LYS* 3.9 26.7 - - + -
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Residues in contact with SER 7 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3G SER 3.2 7.3 + - - -
4G PHE* 2.9 21.3 + - - -
6G LEU* 1.3 76.3 - - - +
8G LYS* 1.3 65.6 + - - +
10G SER* 3.5 2.4 + - - -
11G PHE* 3.0 28.6 + - - +
44G ASN* 3.1 28.6 + - - +
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Residues in contact with LYS 8 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4G PHE* 3.2 43.7 + - + +
5G LEU* 3.1 9.3 + - + +
7G SER* 1.3 86.4 + - - +
9G VAL* 1.3 63.6 + - - +
11G PHE* 3.3 8.3 + - + +
12G VAL* 3.1 27.9 + - - +
71G LEU* 3.8 16.2 - - + -
74G GLU* 3.9 43.0 + - + +
75G ILE* 3.9 18.2 - - + +
77G LYS* 5.6 3.0 - - - +
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Residues in contact with VAL 9 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G LEU* 3.0 28.8 + - + +
6G LEU* 3.7 9.4 - - - +
8G LYS* 1.3 76.6 - - - +
10G SER* 1.3 58.4 + - - +
12G VAL* 3.2 5.5 + - - +
13G ILE* 3.0 33.7 + - + +
48G LEU* 3.8 30.1 - - + -
53G LEU* 4.2 15.9 - - + -
67G PHE* 4.1 6.8 - - + -
68G PHE* 6.4 0.2 - - + -
71G LEU* 4.0 24.0 - - + -
50H ILE* 4.5 17.7 - - + -
68H PHE* 5.8 0.7 - - + -
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Residues in contact with SER 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6G LEU* 3.1 15.3 + - - -
7G SER 3.5 2.1 + - - -
9G VAL* 1.3 74.9 - - - +
11G PHE* 1.3 68.7 + - - +
13G ILE* 3.5 11.7 - - - +
14G LYS* 3.0 24.6 + - - +
41G ILE* 3.1 35.1 + - - -
42G GLU* 4.1 10.4 + - - +
44G ASN* 3.0 25.9 + - - -
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Residues in contact with PHE 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7G SER 3.0 20.1 + - - +
8G LYS* 3.4 11.4 - - + +
9G VAL 3.2 0.2 - - - -
10G SER* 1.3 78.6 + - - +
12G VAL* 1.3 60.8 + - + +
14G LYS* 3.4 9.3 + - + +
15G LYS* 2.9 42.7 + - + +
74G GLU* 3.2 45.5 - - + -
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Residues in contact with VAL 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8G LYS 3.1 17.6 + - - +
9G VAL 3.2 7.1 + - - +
11G PHE* 1.3 74.4 - - + +
13G ILE* 1.3 66.2 + - - +
15G LYS* 3.3 6.5 + - + +
16G ILE* 3.0 36.9 + - + +
67G PHE* 3.6 29.4 - - + +
70G MET* 4.0 24.0 - - + +
71G LEU* 4.0 16.8 - - + -
74G GLU* 4.0 27.8 - - + +
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Residues in contact with ILE 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9G VAL* 3.0 33.7 + - + +
10G SER* 3.3 8.0 + - - +
12G VAL* 1.3 77.3 - - - +
14G LYS* 1.3 63.3 + - - +
16G ILE* 3.4 2.1 + - - +
17G ARG* 3.0 21.5 + - - +
27G LEU* 4.1 16.6 - - + -
38G ILE* 6.0 1.3 - - + -
41G ILE* 4.1 24.0 - - + -
42G GLU* 4.1 13.2 - - + +
48G LEU* 4.4 2.7 - - + -
53G LEU* 4.1 12.1 - - + -
56G ILE* 4.0 34.5 - - + -
60G LEU* 4.2 8.3 - - + +
67G PHE* 4.0 15.7 - - + -
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Residues in contact with LYS 14 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10G SER 3.0 15.9 + - - +
11G PHE* 3.6 8.5 - - + +
13G ILE* 1.3 77.7 - - - +
15G LYS* 1.3 63.0 + - - +
17G ARG* 3.3 17.3 + - - +
18G LEU* 3.0 39.5 + - + +
24G GLN* 5.7 0.2 - - - +
42G GLU* 3.6 41.5 + - + +
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Residues in contact with LYS 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11G PHE* 2.9 37.0 + - + +
12G VAL* 3.7 8.1 - - + +
13G ILE 3.3 0.2 - - - -
14G LYS* 1.3 76.9 - - - +
16G ILE* 1.3 58.1 + - - +
18G LEU* 3.4 7.7 + - - +
19G GLU* 3.0 49.8 + - + +
70G MET* 3.6 24.3 - - + +
74G GLU* 4.5 11.7 + - - +
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Residues in contact with ILE 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G VAL* 3.0 31.9 + - + +
13G ILE 4.1 1.8 - - - +
15G LYS* 1.3 72.4 - - - +
17G ARG* 1.3 60.1 + - - +
19G GLU* 3.2 12.5 + - - +
20G LYS* 2.8 49.5 + - + +
60G LEU* 4.0 27.6 - - + -
62G VAL* 4.3 20.0 - - + -
67G PHE* 3.8 20.9 - - + -
70G MET* 3.6 34.8 - - + -
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Residues in contact with ARG 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13G ILE 3.0 17.6 + - - +
14G LYS* 3.4 22.1 - - - +
16G ILE* 1.3 77.9 - - - +
18G LEU* 1.3 77.6 + - - +
20G LYS* 3.4 3.4 + - - -
21G GLY 3.2 4.2 + - - -
22G MET* 2.9 63.9 + - + +
23G THR* 3.8 22.8 - - - +
24G GLN* 3.8 17.9 - - - +
27G LEU* 3.9 19.3 - - + -
42G GLU* 2.8 41.2 + - - -
60G LEU* 3.8 15.4 - - + +
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Residues in contact with LEU 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LYS* 3.0 38.4 + - + +
15G LYS* 3.8 6.5 - - - +
17G ARG* 1.3 102.6 - - - +
19G GLU* 1.3 66.1 + - - +
21G GLY* 3.0 14.5 + - - +
22G MET 4.6 3.6 - - - +
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Residues in contact with GLU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15G LYS* 3.0 46.4 + - - +
16G ILE* 3.2 20.3 + - + +
18G LEU* 1.3 75.8 - - - +
20G LYS* 1.3 65.9 + - + +
21G GLY* 3.2 3.6 + - - -
70G MET* 4.8 7.6 - - - +
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Residues in contact with LYS 20 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16G ILE* 2.8 36.4 + - + +
17G ARG 3.9 1.8 - - - +
18G LEU 3.3 0.4 - - - -
19G GLU* 1.3 76.9 - - - +
21G GLY* 1.3 61.7 + - - +
22G MET* 3.4 26.1 + - - +
60G LEU* 3.0 33.5 + - - +
61G GLU* 3.2 20.4 + - + +
62G VAL* 4.5 5.8 - - - +
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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) + - + + + + + -
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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