Contacts of the helix formed by residues 9 - 20 (chain G) in PDB entry 6S1M
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 GLY 9 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6G LEU* 3.6 11.0 + - - -
7G VAL 3.0 10.7 + - - -
8G GLN* 1.3 73.4 - - - +
10G SER* 1.3 57.0 + - - +
11G ILE 2.9 0.9 - - - -
12G LEU 2.8 19.9 + - - -
13G LYS* 3.3 8.2 + - - +
83G GLY 5.6 0.9 - - - -
84G ASN 5.5 0.6 + - - -
85G GLU* 6.2 0.2 - - - +
86G ASP 3.8 6.9 + - - -
88G ILE* 3.3 39.6 - - - +
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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
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8G GLN* 2.8 12.0 + - - +
9G GLY* 1.3 72.8 - - - +
11G ILE* 1.3 62.7 + - - +
13G LYS* 3.3 16.5 + - - +
14G LYS* 2.8 49.4 + - - +
84G ASN* 3.6 36.9 + - - +
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Residues in contact with ILE 11 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G LEU* 4.5 14.6 - - + -
8G GLN* 2.8 42.0 + - + +
10G SER* 1.3 81.0 + - - +
12G LEU* 1.3 66.7 + - - +
14G LYS* 3.2 9.2 + - + +
15G VAL* 2.9 31.2 + - + +
52G LEU* 5.1 6.3 - - + -
221G LEU* 4.1 6.2 - - + +
241G ILE* 4.0 25.4 - - + -
242G ALA* 5.3 3.6 - - + +
244G MET* 4.1 24.2 - - + -
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Residues in contact with LEU 12 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6G LEU* 4.2 16.9 - - + +
9G GLY 2.8 10.0 + - - +
11G ILE* 1.3 80.9 - - + +
13G LYS* 1.3 63.5 + - - +
15G VAL* 3.1 6.8 + - + +
16G LEU* 3.1 39.6 + - + +
28G TRP* 4.4 16.2 - - + -
52G LEU* 4.6 17.0 - - + -
57G PHE* 6.3 1.1 - - + -
75G MET* 4.4 4.9 - - + -
79G LEU* 3.8 20.9 - - + -
88G ILE* 4.0 20.6 - - + -
90G LEU* 3.6 36.6 - - + -
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Residues in contact with LYS 13 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146E ARG* 4.9 2.6 - - - +
9G GLY 3.7 10.5 - - - +
10G SER* 3.4 17.0 - - - +
11G ILE 3.2 0.4 - - - -
12G LEU* 1.3 77.9 - - - +
14G LYS* 1.3 63.7 + - + +
16G LEU* 3.3 2.4 + - - +
17G GLU* 3.0 29.5 + - + +
79G LEU* 3.7 32.1 - - + +
80G LYS* 4.7 9.0 + - - +
82G ALA* 2.7 31.4 + - + +
83G GLY* 4.2 8.9 - - - +
84G ASN* 2.8 32.2 + - - +
88G ILE* 4.6 7.0 - - + -
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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
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10G SER* 2.8 35.2 + - - +
11G ILE* 3.7 3.6 - - + +
13G LYS* 1.3 76.9 - - + +
15G VAL* 1.3 62.9 + - - +
17G GLU* 3.4 8.4 + - - +
18G ALA* 3.2 22.3 + - - +
217G LYS 4.7 2.9 - - - +
220G PRO* 3.0 48.9 + - + +
221G LEU* 3.4 26.4 - - + +
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Residues in contact with VAL 15 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11G ILE* 2.9 27.0 + - + +
12G LEU* 3.1 14.1 + - + +
14G LYS* 1.3 75.9 - - - +
16G LEU* 1.3 66.3 + - + +
18G ALA* 2.9 18.3 + - - +
19G LEU* 3.1 26.2 + - + +
28G TRP* 4.6 2.9 - - + -
50G LEU* 3.6 32.8 - - + -
52G LEU* 4.9 4.5 - - + -
221G LEU* 4.3 13.5 - - + -
241G ILE* 4.2 24.7 - - + -
247G LEU* 5.1 2.5 - - + -
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Residues in contact with LEU 16 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12G LEU* 3.1 21.6 + - + +
13G LYS 3.3 3.8 + - - +
15G VAL* 1.3 76.4 - - + +
17G GLU* 1.3 59.5 + - + +
18G ALA 3.0 5.6 - - - -
19G LEU* 4.3 4.3 - - + +
20G LYS* 2.9 36.4 + - - +
28G TRP* 4.1 14.4 - - + -
72G LEU* 4.1 12.3 - - + +
75G MET* 3.2 62.4 - - + -
76G SER* 3.4 12.3 - - - +
79G LEU* 3.2 31.6 - - + -
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Residues in contact with GLU 17 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13G LYS* 3.0 22.6 + - + +
14G LYS* 3.8 8.5 - - - +
15G VAL 3.2 0.4 - - - -
16G LEU* 1.3 77.3 - - + +
18G ALA* 1.3 58.6 + - - +
20G LYS* 2.9 41.5 + - - +
21G ASP* 4.7 5.5 + - - +
76G SER* 3.6 5.9 + - - +
80G LYS* 3.6 23.9 + - + -
217G LYS* 3.6 22.6 - - - +
220G PRO* 6.3 1.8 - - + -
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Residues in contact with ALA 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14G LYS 3.2 11.1 + - - +
15G VAL 2.9 11.0 + - - +
17G GLU* 1.3 79.7 - - - +
19G LEU* 1.3 57.8 + - - +
21G ASP 5.3 1.1 - - - -
22G LEU* 4.8 4.7 - - - +
214G PHE 4.5 6.1 - - - +
217G LYS* 3.8 8.7 - - - +
218G ALA* 3.8 24.5 - - + -
221G LEU* 4.7 0.7 - - + -
247G LEU* 4.0 9.2 - - + -
249G TYR* 2.8 37.7 + - - +
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Residues in contact with LEU 19 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15G VAL* 3.1 35.5 + - + +
16G LEU* 4.3 4.5 - - - +
18G ALA* 1.3 85.1 - - - +
20G LYS* 1.3 53.4 + - - +
21G ASP 3.2 2.5 - - - -
22G LEU* 2.8 11.5 + - - +
23G ILE* 2.7 43.9 + - + +
28G TRP* 4.6 7.6 - - + -
37G LEU* 4.6 18.6 - - + -
48G VAL* 3.3 37.9 - - + -
50G LEU* 4.3 11.9 - - + -
72G LEU* 4.1 17.0 - - + -
247G LEU* 4.1 11.4 - - + -
249G TYR* 4.8 0.2 - - - +
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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
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16G LEU 2.9 14.8 + - - +
17G GLU* 2.9 35.6 + - - +
19G LEU* 1.3 76.6 - - - +
21G ASP* 1.3 88.5 + - - +
23G ILE 3.1 20.7 - - - +
24G ASN* 4.9 3.5 - - - +
72G LEU* 4.2 14.2 - - + +
73G THR* 4.6 11.9 + - + +
76G SER* 3.4 23.5 + - - +
80G LYS* 3.2 23.4 - - - +
15T T 4.6 12.9 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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