Contacts of the helix formed by residues 3 - 20 (chain N) 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 N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51M LYS* 3.7 33.6 - - - +
54M GLU* 2.8 22.9 + - - -
4N PHE* 1.3 62.1 + - - +
5N LEU* 4.4 0.2 - - - +
6N LEU* 3.1 31.0 + - - +
7N SER* 3.2 20.4 + - - -
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Residues in contact with PHE 4 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36K THR* 4.7 19.1 - - + +
46K ARG* 3.2 43.7 - - - -
54M GLU* 3.6 14.2 + - - +
64M ASP* 3.9 21.3 - - - -
3N SER* 1.3 70.0 + - - +
5N LEU* 1.3 65.8 + - - +
7N SER* 2.9 21.9 + - - -
8N LYS* 3.0 52.3 + - + +
75N ILE* 4.3 12.6 - - + -
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Residues in contact with LEU 5 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M ILE* 3.5 33.4 - - + +
53M LEU* 4.5 12.3 - - + -
54M GLU* 3.0 29.2 + - + +
57M MET* 3.7 22.9 - - + -
64M ASP* 4.3 9.4 - - - +
68M PHE* 4.0 26.7 - - + -
3N SER 3.5 0.2 - - - -
4N PHE* 1.3 77.5 - - + +
6N LEU* 1.3 67.5 + - - +
8N LYS* 3.3 2.5 + - - +
9N VAL* 2.8 30.5 + - + +
71N LEU* 4.3 8.1 - - + -
75N ILE* 4.1 18.4 - - + -
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Residues in contact with LEU 6 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M ILE* 3.8 12.8 - - + +
51M LYS* 3.5 26.2 - - + -
3N SER* 3.1 24.2 + - - +
5N LEU* 1.3 77.0 - - - +
7N SER* 1.3 57.4 + - - +
9N VAL* 2.9 6.8 + - + +
10N SER* 2.9 34.3 + - - -
41N ILE* 5.8 0.2 - - + -
45N SER* 3.4 33.9 - - - +
46N ARG 3.6 17.3 - - - +
47N ASN* 3.8 18.6 - - - +
48N LEU* 3.9 24.5 - - + -
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Residues in contact with SER 7 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3N SER 3.2 10.4 + - - -
4N PHE* 2.9 21.6 + - - -
6N LEU* 1.3 75.3 - - - +
8N LYS* 1.3 72.8 + - - +
10N SER* 3.8 8.3 + - - -
11N PHE* 3.2 25.3 + - - +
45N SER* 6.0 7.2 - - - -
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Residues in contact with LYS 8 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4N PHE* 3.0 56.6 + - + +
5N LEU* 3.6 8.1 - - + +
7N SER* 1.3 82.5 - - - +
9N VAL* 1.3 62.7 + - - +
11N PHE* 3.4 5.8 + - + +
12N VAL* 3.2 26.7 + - - +
71N LEU* 3.6 19.7 - - + -
74N GLU* 3.8 37.4 + - + +
75N ILE* 3.8 9.8 + - + +
77N LYS 5.4 5.9 + - - -
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Residues in contact with VAL 9 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50M ILE* 3.8 26.7 - - + -
68M PHE* 5.8 1.8 - - + -
5N LEU* 2.8 28.1 + - + +
6N LEU* 2.9 10.3 + - - +
8N LYS* 1.3 76.3 - - - +
10N SER* 1.3 62.2 + - - +
12N VAL* 3.2 6.6 + - - +
13N ILE* 3.1 30.5 + - + +
48N LEU* 3.7 28.7 - - + -
53N LEU* 4.5 13.9 - - + -
67N PHE* 4.1 8.0 - - + -
68N PHE* 6.5 0.4 - - + -
71N LEU* 4.0 16.8 - - + +
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Residues in contact with SER 10 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6N LEU* 2.9 21.9 + - - -
7N SER* 3.8 10.2 + - - -
9N VAL* 1.3 71.4 - - - +
11N PHE* 1.3 62.1 + - - +
13N ILE* 3.5 12.1 + - - +
14N LYS* 3.1 27.7 + - - +
41N ILE* 3.2 38.5 + - - -
42N GLU* 4.4 12.4 + - - +
45N SER* 5.4 3.8 - - - -
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Residues in contact with PHE 11 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7N SER 3.2 19.7 + - - +
8N LYS* 3.5 7.9 - - + +
10N SER* 1.3 77.5 + - - +
12N VAL* 1.3 59.5 + - - +
14N LYS* 3.4 9.2 + - + +
15N LYS* 2.8 45.5 + - + +
74N GLU* 2.8 43.1 - - + -
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Residues in contact with VAL 12 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8N LYS 3.2 13.0 + - - +
9N VAL 3.7 7.4 - - - +
11N PHE* 1.3 77.9 - - + +
13N ILE* 1.3 65.2 + - - +
15N LYS* 3.7 6.1 - - - +
16N ILE* 3.0 37.6 + - + +
67N PHE* 3.4 40.2 - - + +
70N MET* 4.0 15.0 - - + +
71N LEU* 3.9 24.5 - - + -
74N GLU* 4.0 20.6 - - + +
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Residues in contact with ILE 13 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9N VAL* 3.1 33.1 + - + +
10N SER* 3.6 14.1 - - - +
12N VAL* 1.3 78.0 - - - +
14N LYS* 1.3 63.1 + - - +
16N ILE* 3.9 1.4 - - - +
17N ARG* 2.9 25.3 + - - +
27N LEU* 4.1 12.1 - - + -
38N ILE* 5.9 1.3 - - + -
41N ILE* 4.0 18.4 - - + -
42N GLU* 4.1 17.9 - - + +
48N LEU* 4.6 4.3 - - + -
53N LEU* 4.4 9.0 - - + -
56N ILE* 4.1 32.8 - - + -
60N LEU* 4.3 8.7 - - + +
67N PHE* 4.1 15.3 - - + -
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Residues in contact with LYS 14 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J GLU* 3.8 33.1 + - - +
10N SER 3.1 17.5 + - - +
11N PHE* 3.7 9.4 - - + +
13N ILE* 1.3 75.9 - - - +
15N LYS* 1.3 64.6 + - - +
17N ARG* 3.2 15.1 + - - +
18N LEU* 3.0 43.7 + - + +
42N GLU* 3.3 41.3 - - + +
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Residues in contact with LYS 15 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11N PHE* 2.8 29.6 + - + +
12N VAL* 3.7 6.7 - - + +
13N ILE 3.3 0.2 - - - -
14N LYS* 1.3 77.7 - - - +
16N ILE* 1.3 57.3 + - - +
18N LEU* 3.3 8.2 + - - +
19N GLU* 3.1 47.8 + - + +
70N MET* 3.6 22.0 - - + +
74N GLU* 4.3 21.0 + - - +
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Residues in contact with ILE 16 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N VAL* 3.0 29.0 + - + +
13N ILE 4.1 1.8 - - - +
15N LYS* 1.3 73.0 - - - +
17N ARG* 1.3 66.0 + - - +
19N GLU* 3.6 11.1 - - - +
20N LYS* 2.9 48.2 + - + +
60N LEU* 4.0 23.3 - - + -
62N VAL* 4.4 17.5 - - + -
67N PHE* 3.6 30.7 - - + -
70N MET* 3.7 29.6 - - + -
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Residues in contact with ARG 17 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61J GLU* 5.4 3.0 + - - -
13N ILE 2.9 19.0 + - - +
14N LYS* 3.3 15.5 - - - +
16N ILE* 1.3 78.5 - - - +
18N LEU* 1.3 83.6 + - - +
20N LYS* 3.4 2.7 + - - -
21N GLY 3.2 3.3 + - - -
22N MET* 2.7 77.3 + - + +
23N THR* 3.6 23.8 - - - +
24N GLN* 3.6 19.9 - - - +
27N LEU* 3.8 20.2 - - + -
42N GLU* 2.7 41.0 + - - -
60N LEU* 3.7 15.0 - - + +
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Residues in contact with LEU 18 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14N LYS* 3.0 38.2 + - + +
15N LYS* 3.8 7.0 - - - +
16N ILE 3.2 0.2 - - - -
17N ARG* 1.3 102.8 - - - +
19N GLU* 1.3 61.8 + - - +
21N GLY* 3.0 20.7 + - - +
22N MET 4.7 1.8 - - - +
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Residues in contact with GLU 19 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15N LYS* 3.1 42.6 + - + +
16N ILE* 3.6 21.5 - - + +
18N LEU* 1.3 76.3 - - - +
20N LYS* 1.3 67.4 + - + +
21N GLY* 3.2 0.7 + - - -
70N MET* 4.5 8.7 - - - +
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Residues in contact with LYS 20 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N ILE* 2.9 34.7 + - + +
17N ARG 3.8 4.3 - - - +
18N LEU 3.2 0.4 - - - -
19N GLU* 1.3 82.8 - - - +
21N GLY* 1.3 62.6 + - - +
22N MET* 3.5 22.5 + - - +
60N LEU* 3.1 32.1 + - - +
61N GLU* 3.4 17.0 + - + +
62N VAL* 4.3 7.5 - - - +
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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