Contacts of the helix formed by residues 7 - 20 (chain G) in PDB entry 2P5V
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 7 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5G THR 3.9 2.2 + - - +
6G LEU* 1.3 74.1 - - - +
8G LYS* 1.3 64.8 + - - +
9G THR* 3.0 17.6 + - - -
10G ASP* 3.0 20.8 + - - +
11G ILE* 3.0 23.7 + - - +
42G ARG* 2.8 24.0 + - - -
157G LEU 6.1 0.2 - - - -
158G LEU* 5.4 0.4 - - - -
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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
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7G ASP* 1.3 76.3 - - - +
9G THR* 1.3 63.3 + - + +
11G ILE* 3.5 3.5 - - - +
12G LYS* 3.2 23.4 + - - +
158G LEU* 4.1 27.8 - - + +
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Residues in contact with THR 9 (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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7G ASP* 3.0 6.1 + - - +
8G LYS* 1.3 83.4 - - + +
10G ASP* 1.3 59.8 + - - +
11G ILE 3.3 0.4 - - - -
12G LYS* 3.4 7.9 + - - +
13G ILE* 3.1 32.6 + - - +
32G VAL* 3.8 15.1 - - - +
34G LEU* 4.4 5.9 - - + +
42G ARG* 2.9 34.8 + - - +
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Residues in contact with ASP 10 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5G THR 4.1 4.7 - - - +
6G LEU* 3.8 30.0 - - + -
7G ASP* 3.0 40.7 + - - +
9G THR* 1.3 74.3 - - - +
11G ILE* 1.3 64.6 + - - +
13G ILE* 3.5 8.5 + - - +
14G LEU* 3.2 28.6 + - - +
42G ARG* 3.5 34.9 + - - +
45G GLN* 5.1 3.1 - - - +
46G LEU* 4.3 11.1 - - + +
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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 13.2 - - + +
7G ASP 3.0 20.0 + - - +
8G LYS 3.5 8.3 - - - +
9G THR 3.3 0.2 - - - -
10G ASP* 1.3 75.7 - - - +
12G LYS* 1.3 63.4 - - - +
14G LEU* 3.0 10.0 + - + +
15G GLN* 2.9 48.9 + - - +
154G LEU* 4.1 17.9 - - + +
157G LEU* 3.5 44.4 - - + +
158G LEU* 3.8 29.2 - - + -
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Residues in contact with LYS 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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8G LYS 3.2 12.4 + - - +
9G THR* 3.5 12.3 - - - +
11G ILE* 1.3 79.3 - - - +
13G ILE* 1.3 56.9 + - - +
15G GLN* 3.3 19.2 + - + +
16G VAL* 2.9 43.4 + - + +
31G ARG 3.6 19.1 - - - -
32G VAL* 4.0 22.2 - - + +
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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
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9G THR 3.1 18.5 + - - +
10G ASP* 3.7 11.0 - - - +
11G ILE 3.2 0.4 - - - -
12G LYS* 1.3 74.8 - - - +
14G LEU* 1.3 58.8 + - - +
16G VAL* 3.4 1.6 + - - +
17G LEU* 3.0 47.7 + - + +
28G LEU* 4.2 13.9 - - + +
32G VAL* 3.7 28.9 - - + -
34G LEU* 4.5 1.1 - - + -
39G CYS* 4.4 17.3 - - - +
42G ARG* 4.1 35.2 - - + +
43G LEU* 4.3 5.4 - - + +
46G LEU* 4.0 16.6 - - + -
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Residues in contact with LEU 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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6G LEU* 3.9 27.8 - - + -
10G ASP 3.2 16.8 + - - +
11G ILE* 3.0 9.2 + - + +
13G ILE* 1.3 74.4 - - + +
15G GLN* 1.3 66.5 + - - +
17G LEU* 4.1 3.7 - - + +
18G GLN* 3.0 31.6 + - - +
46G LEU* 3.8 18.6 - - + -
51G ILE* 3.6 28.0 - - + -
52G VAL* 3.8 23.3 - - + -
154G LEU* 3.6 22.9 - - + -
157G LEU* 5.6 0.2 - - + -
59H LEU* 3.8 10.9 - - + +
64H VAL* 5.0 2.2 - - + -
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Residues in contact with GLN 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 40.6 + - + +
12G LYS* 3.6 22.8 + - + +
14G LEU* 1.3 79.7 - - - +
16G VAL* 1.3 63.3 + - + +
18G GLN* 3.5 11.1 + - - +
19G GLU* 3.4 22.5 + - - +
154G LEU* 4.2 15.5 - - + +
155G ASN* 4.3 16.6 + - - -
158G LEU* 5.5 2.0 - - - +
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Residues in contact with VAL 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 LYS* 2.9 34.7 + - + +
13G ILE 3.7 4.5 - - - +
14G LEU 3.3 0.2 - - - -
15G GLN* 1.3 77.2 - - + +
17G LEU* 1.3 58.7 + - - +
19G GLU* 3.3 2.0 + - - -
20G ASN* 2.8 40.7 + - - +
23G LEU* 3.3 30.3 - - + -
28G LEU* 3.7 17.0 - - + -
31G ARG* 4.3 24.9 - - + -
32G VAL* 4.4 7.6 - - + -
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Residues in contact with LEU 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 ILE* 3.0 28.6 + - + +
14G LEU* 4.1 4.3 - - + +
16G VAL* 1.3 74.0 - - + +
18G GLN* 1.3 64.4 + - - +
20G ASN 3.7 13.9 - - - +
21G GLY* 3.2 14.0 + - - +
23G LEU* 4.8 4.5 - - + -
28G LEU* 3.9 22.7 - - + -
43G LEU* 3.3 34.5 - - + -
52G VAL* 5.0 6.7 - - + -
55G TYR* 3.9 13.5 - - + +
22H ARG* 3.6 26.9 - - - +
57H ALA* 2.9 32.0 + - + -
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Residues in contact with GLN 18 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14G LEU 3.0 22.5 + - - +
15G GLN* 3.8 10.5 - - - +
16G VAL 3.3 0.2 - - - -
17G LEU* 1.3 76.1 - - - +
19G GLU* 1.3 57.3 + - + +
150G THR* 4.0 5.0 + - - +
151G SER* 3.5 26.6 + - - +
152G LEU* 2.8 46.8 + - - +
154G LEU* 4.1 10.7 - - - +
54H GLN* 3.3 4.3 + - - -
56H ALA* 3.2 25.3 - - - +
57H ALA* 3.5 19.2 - - - +
59H LEU* 3.3 36.8 + - + +
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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
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15G GLN 3.4 11.1 + - - +
16G VAL* 3.3 4.2 + - - +
18G GLN* 1.3 78.9 - - + +
20G ASN* 1.3 77.3 + - - +
149G THR* 4.1 5.7 + - - -
151G SER* 2.7 29.3 + - - +
54H GLN* 3.2 31.6 + - - +
55H TYR 3.2 6.2 - - - +
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Residues in contact with ASN 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 VAL* 2.8 26.3 + - - +
17G LEU* 3.4 12.6 - - - +
19G GLU* 1.3 92.9 - - - +
21G GLY* 1.3 63.5 + - - +
22G ARG 3.2 4.6 + - - -
23G LEU* 3.5 38.0 + - + +
31G ARG* 5.7 3.5 - - - +
55H TYR* 3.7 2.2 - - - -
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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