Contacts of the helix formed by residues 3 - 15 (chain A) in PDB entry 6MOL
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 ASP 3 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A LEU* 1.3 77.1 + - + +
5A GLY* 3.4 5.5 - - - +
6A LYS* 3.8 12.4 + - - +
7A LYS* 3.4 21.8 + - - +
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Residues in contact with LEU 4 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ASP* 1.3 87.6 - - + +
5A GLY* 1.3 64.5 + - - +
7A LYS* 3.3 15.9 + - - +
8A LEU 3.4 8.3 + - - -
23A LEU* 4.7 9.9 - - + +
26A ASN* 5.3 9.4 - - + +
27A GLY* 4.2 24.5 - - - +
28A ALA* 3.6 24.6 - - + +
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Residues in contact with GLY 5 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ASP 3.4 3.6 - - - +
4A LEU* 1.3 79.4 - - - +
6A LYS* 1.3 59.6 + - - +
8A LEU* 3.1 14.0 + - - +
9A LEU* 3.4 15.1 + - - +
29A ASP* 4.5 18.1 - - - +
32A ALA* 3.8 25.3 - - - +
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Residues in contact with LYS 6 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ASP* 3.8 14.9 + - - +
4A LEU 3.4 0.6 - - - -
5A GLY* 1.3 74.6 - - - +
7A LYS* 1.3 60.7 + - - +
9A LEU* 3.5 20.4 - - + +
10A LYS* 3.3 24.6 + - - +
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Residues in contact with LYS 7 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3A ASP 3.4 13.5 + - - +
4A LEU* 3.3 13.2 + - - +
5A GLY 3.2 0.6 - - - -
6A LYS* 1.3 78.3 - - - +
8A LEU* 1.3 60.9 + - - +
10A LYS* 4.1 4.8 - - + +
11A ALA* 3.3 15.6 + - - +
19A GLU* 5.6 2.9 - - - +
23A LEU* 3.3 31.8 - - + +
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Residues in contact with LEU 8 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A LEU 3.4 9.1 + - - +
5A GLY 3.1 10.1 + - - +
7A LYS* 1.3 77.1 - - - +
9A LEU* 1.3 53.7 + - - +
10A LYS 3.2 0.2 - - - -
11A ALA* 3.1 2.6 + - - +
12A ALA* 2.7 35.2 + - + +
20A VAL* 3.8 31.0 - - + +
23A LEU* 3.8 24.0 - - + -
24A MET* 4.6 8.7 - - + +
28A ALA* 4.2 11.4 - - + +
29A ASP 3.3 25.8 - - - +
30A VAL* 4.0 14.4 - - + +
40A PRO* 4.1 18.4 - - + -
56A LEU* 5.0 8.7 - - + -
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Residues in contact with LEU 9 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A GLY 3.4 12.7 + - - +
6A LYS* 3.5 24.0 - - + +
8A LEU* 1.3 78.8 - - - +
10A LYS* 1.3 74.7 + - + +
12A ALA* 4.3 0.9 - - - -
13A ARG* 3.1 27.2 + - - +
32A ALA* 4.2 21.1 - - + +
33A THR 4.3 14.8 - - - +
34A ASP* 4.5 23.3 - - + +
35A ILE* 6.5 0.4 - - + -
38A ALA 4.8 1.3 - - - +
40A PRO* 3.8 22.6 - - + +
43A LEU* 3.3 24.8 - - + +
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Residues in contact with LYS 10 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LYS 3.3 17.3 + - - +
7A LYS* 4.2 6.5 - - + +
8A LEU 3.2 0.6 - - - -
9A LEU* 1.3 84.2 - - + +
11A ALA* 1.3 61.2 + - - +
13A ARG* 3.7 21.6 + - - +
14A ALA* 3.3 20.4 + - - +
60C GLU* 4.7 10.6 - - + +
61C ASP* 5.1 11.0 - - - +
95C PRO* 5.8 0.2 - - - +
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Residues in contact with ALA 11 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LYS 3.3 15.9 + - - +
8A LEU 3.1 4.8 + - - +
10A LYS* 1.3 78.1 - - - +
12A ALA* 1.3 58.8 - - - +
13A ARG 3.2 0.2 - - - -
14A ALA 3.2 0.3 + - - -
15A GLY 2.8 25.1 + - - -
16A GLN* 3.0 26.5 + - - +
19A GLU* 3.9 17.0 - - + -
20A VAL* 3.8 16.8 - - + +
23A LEU* 4.2 5.8 - - + -
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Residues in contact with ALA 12 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A LEU* 2.7 22.5 + - + +
9A LEU 4.0 4.3 - - - +
10A LYS 3.5 0.2 - - - -
11A ALA* 1.3 72.3 - - - +
13A ARG* 1.3 61.2 + - - +
15A GLY* 3.5 2.3 + - - +
20A VAL* 3.9 13.4 - - + +
40A PRO* 3.8 32.5 - - + +
43A LEU* 4.2 7.7 - - + +
44A ALA* 4.4 2.5 - - - +
47A ILE* 3.2 22.2 - - - +
52A ILE* 4.8 14.6 - - + +
56A LEU* 5.5 1.1 - - + -
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Residues in contact with ARG 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A LEU* 3.1 21.5 + - - +
10A LYS* 3.9 16.9 + - - +
11A ALA 3.2 0.4 - - - -
12A ALA* 1.3 78.7 - - - +
14A ALA* 1.3 58.4 + - - +
15A GLY 3.6 0.3 + - - -
43A LEU* 4.1 20.3 - - + +
47A ILE* 3.8 17.4 - - + +
58C GLN* 2.3 34.3 + - - +
59C LEU 3.6 13.7 + - - -
60C GLU* 4.0 19.4 - - - +
61C ASP 4.9 0.8 - - - +
64C TRP* 5.4 0.2 - - - +
95C PRO* 4.3 18.6 + - + +
97C GLU* 2.8 52.6 + - - +
112C VAL* 3.8 30.1 - - + +
114C HIS* 5.3 1.9 + - - -
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Residues in contact with ALA 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LYS 3.3 10.9 + - - +
11A ALA 3.2 1.6 + - - -
13A ARG* 1.3 78.1 - - - +
15A GLY* 1.3 61.3 + - - +
16A GLN* 3.3 32.8 + - + +
47A ILE* 4.9 0.7 - - - -
60C GLU* 4.6 7.0 - - - +
95C PRO* 3.8 26.0 - - + +
114C HIS* 5.2 6.9 + - - -
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Residues in contact with GLY 15 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A ALA 2.8 10.1 + - - -
12A ALA 3.5 0.8 + - - -
13A ARG 3.3 3.4 - - - -
14A ALA* 1.3 79.5 - - - +
16A GLN* 1.3 57.9 + - - -
17A ASP 3.2 6.9 + - - -
47A ILE* 3.9 21.3 - - - -
49A HIS* 3.4 16.5 + - - -
52A ILE* 3.9 12.6 - - - -
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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
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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