Contacts of the helix formed by residues 3 - 20 (chain I) 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 I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I GLU* 1.3 74.3 - - - +
4I PHE* 1.3 62.7 + - - +
5I LEU* 4.2 0.7 - - - +
6I LEU* 3.0 29.3 + - - +
7I SER* 3.2 20.3 + - - -
44I ASN* 4.4 1.9 - - - +
50J ILE* 4.8 0.2 - - - +
51J LYS* 3.7 34.3 - - - +
54J GLU* 2.8 23.0 + - - -
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Residues in contact with PHE 4 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2I GLU 3.1 7.0 + - - +
3I SER* 1.3 71.8 + - - +
5I LEU* 1.3 67.7 + - - +
7I SER* 3.1 23.9 + - - -
8I LYS* 3.3 46.9 + - + +
75I ILE* 4.6 18.6 - - + -
78I HIS 4.8 11.0 - - - -
54J GLU* 3.6 13.0 + - - +
64J ASP* 3.5 25.1 - - - -
43N ARG* 6.3 0.4 - - - -
44N ASN* 4.2 13.7 - - - -
46N ARG* 6.5 1.1 - - - -
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Residues in contact with LEU 5 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I SER 3.4 0.2 - - - -
4I PHE* 1.3 78.7 - - + +
6I LEU* 1.3 67.5 + - - +
8I LYS* 3.1 4.4 + - + +
9I VAL* 3.0 30.9 + - + +
71I LEU* 4.5 2.5 - - + -
75I ILE* 4.4 15.3 - - + -
50J ILE* 3.3 36.8 - - + +
53J LEU* 4.2 16.4 - - + -
54J GLU* 3.0 24.7 + - + +
57J MET* 4.1 25.1 - - + -
64J ASP* 4.5 5.4 - - - +
68J PHE* 3.9 27.1 - - + -
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Residues in contact with LEU 6 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I SER* 3.0 24.4 + - - +
5I LEU* 1.3 75.9 - - - +
7I SER* 1.3 58.0 + - - +
9I VAL* 3.2 4.3 + - + +
10I SER* 3.0 33.1 + - - -
41I ILE* 5.5 3.6 - - + +
44I ASN* 4.0 17.9 - - - +
45I SER 5.7 0.9 - - - -
46I ARG 3.5 26.7 - - - +
47I ASN* 4.4 5.6 - - - +
48I LEU* 4.4 24.9 - - + -
50J ILE* 3.8 25.9 - - + +
51J LYS* 3.8 27.4 - - + +
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Residues in contact with SER 7 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3I SER 3.2 9.6 + - - -
4I PHE* 3.1 17.9 + - - -
5I LEU 3.2 1.0 - - - -
6I LEU* 1.3 76.1 - - - +
8I LYS* 1.3 66.1 + - - +
10I SER* 3.4 2.3 + - - -
11I PHE* 3.0 28.4 + - - +
44I ASN* 3.0 31.0 + - - +
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Residues in contact with LYS 8 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4I PHE* 3.3 42.3 + - + +
5I LEU* 3.1 9.9 + - + +
7I SER* 1.3 84.3 + - - +
9I VAL* 1.3 64.6 + - - +
11I PHE* 3.4 8.5 + - + +
12I VAL* 3.1 27.7 + - - +
71I LEU* 3.8 16.6 - - + -
74I GLU* 4.0 41.4 + - + +
75I ILE* 4.0 17.0 - - + +
77I LYS* 5.8 2.0 - - - +
78I HIS 4.6 9.3 + - - -
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Residues in contact with VAL 9 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I LEU* 3.0 32.9 + - + +
6I LEU* 3.6 9.6 - - + +
8I LYS* 1.3 76.0 - - - +
10I SER* 1.3 58.9 + - - +
12I VAL* 3.1 5.8 + - - +
13I ILE* 3.0 34.5 + - + +
48I LEU* 3.8 28.7 - - + -
53I LEU* 4.3 15.5 - - + -
67I PHE* 4.1 6.8 - - + -
68I PHE* 6.4 0.4 - - + -
71I LEU* 4.1 19.1 - - + -
50J ILE* 4.4 19.3 - - + -
68J PHE* 5.7 0.7 - - + -
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Residues in contact with SER 10 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6I LEU* 3.0 15.6 + - - -
7I SER 3.4 1.9 + - - -
9I VAL* 1.3 74.8 - - - +
11I PHE* 1.3 66.7 + - - +
13I ILE* 3.4 11.3 + - - +
14I LYS* 3.0 24.6 + - - +
41I ILE* 3.0 35.5 + - - -
42I GLU* 4.1 9.5 + - - +
44I ASN* 2.8 28.3 + - - -
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Residues in contact with PHE 11 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I SER 3.0 19.5 + - - +
8I LYS* 3.4 11.2 - - + +
10I SER* 1.3 78.7 + - - +
12I VAL* 1.3 60.5 + - + +
14I LYS* 3.5 9.7 + - + +
15I LYS* 3.0 41.4 + - + +
74I GLU* 3.1 46.0 - - + -
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Residues in contact with VAL 12 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8I LYS 3.1 16.5 + - - +
9I VAL* 3.1 4.7 + - - +
11I PHE* 1.3 75.9 - - + +
13I ILE* 1.3 66.4 + - - +
15I LYS* 3.6 6.6 - - + +
16I ILE* 3.0 37.0 + - + +
67I PHE* 3.6 29.2 - - + +
70I MET* 3.9 41.1 - - + +
71I LEU* 4.0 12.1 - - + -
74I GLU* 4.0 15.5 - - + +
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Residues in contact with ILE 13 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9I VAL* 3.0 34.2 + - + +
10I SER* 3.6 8.3 - - - +
12I VAL* 1.3 78.0 - - - +
14I LYS* 1.3 63.4 + - - +
16I ILE* 3.9 1.7 - - - +
17I ARG* 2.9 22.2 + - - +
27I LEU* 4.0 17.0 - - + -
38I ILE* 5.9 1.1 - - + -
41I ILE* 4.1 22.4 - - + -
42I GLU* 4.1 12.8 - - + +
48I LEU* 4.4 3.1 - - + -
53I LEU* 4.2 7.0 - - + -
56I ILE* 4.0 40.4 - - + -
60I LEU* 4.2 8.7 - - + +
67I PHE* 4.0 15.7 - - + -
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Residues in contact with LYS 14 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61G GLU* 3.4 24.5 + - - -
10I SER 3.0 17.2 + - - +
11I PHE* 3.7 9.9 - - + +
13I ILE* 1.3 78.3 - - - +
15I LYS* 1.3 55.4 + - - +
17I ARG* 3.4 16.8 + - - +
18I LEU* 2.9 49.5 + - + +
24I GLN* 5.7 0.4 - - - +
42I GLU* 3.5 42.0 - - + +
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Residues in contact with LYS 15 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I PHE* 3.0 38.3 + - + +
12I VAL* 3.6 7.4 - - + +
13I ILE 3.3 0.2 - - - -
14I LYS* 1.3 76.1 - - - +
16I ILE* 1.3 59.3 + - - +
18I LEU* 3.4 9.0 + - - +
19I GLU* 3.0 49.9 + - + +
70I MET* 3.6 23.5 - - + +
74I GLU* 4.6 10.5 + - - +
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Residues in contact with ILE 16 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12I VAL* 3.0 19.8 + - + +
13I ILE 4.0 1.8 - - - +
15I LYS* 1.3 71.7 - - - +
17I ARG* 1.3 56.0 + - - +
19I GLU* 3.0 13.2 + - - +
20I LYS* 2.7 55.3 + - + +
60I LEU* 3.9 27.8 - - + -
62I VAL* 4.1 20.9 - - + -
67I PHE* 3.8 30.7 - - + -
70I MET* 3.7 34.3 - - + -
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Residues in contact with ARG 17 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13I ILE 2.9 17.8 + - - +
14I LYS* 3.4 22.7 - - - +
16I ILE* 1.3 76.5 - - - +
18I LEU* 1.3 78.2 + - - +
20I LYS* 3.3 3.5 + - - -
21I GLY 3.2 3.8 + - - -
22I MET* 2.9 61.0 + - + +
23I THR* 3.7 25.4 - - - +
24I GLN* 3.7 17.3 - - - +
27I LEU* 3.9 18.6 - - + -
38I ILE* 5.2 0.2 - - - -
42I GLU* 2.8 42.1 + - - -
60I LEU* 3.7 17.1 - - + +
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Residues in contact with LEU 18 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14I LYS* 2.9 39.7 + - + +
15I LYS* 3.8 5.6 - - - +
17I ARG* 1.3 99.3 - - - +
19I GLU* 1.3 62.4 + - - +
21I GLY* 2.9 20.8 + - - +
22I MET 4.6 4.0 - - - +
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Residues in contact with GLU 19 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15I LYS* 3.0 45.4 + - + +
16I ILE* 3.0 20.6 + - + +
18I LEU* 1.3 76.0 - - - +
20I LYS* 1.3 68.3 + - + +
21I GLY* 3.3 0.9 + - - -
70I MET* 4.7 7.3 - - - +
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Residues in contact with LYS 20 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I ILE* 2.7 36.8 + - + +
17I ARG* 3.3 4.7 + - - +
19I GLU* 1.3 78.8 - - - +
21I GLY* 1.3 61.7 + - - +
22I MET* 3.5 22.7 + - - +
60I LEU* 3.1 32.6 + - - +
61I GLU* 3.3 20.2 + - + +
62I VAL* 4.5 5.6 - - - +
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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) + - + + + + + -
------------------------------------------------------------
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