Contacts of the helix formed by residues 7 - 20 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B THR 3.9 1.7 + - - +
6B LEU* 1.3 72.0 - - - +
8B LYS* 1.3 70.6 + - - +
9B THR* 3.1 17.7 + - - -
10B ASP* 2.7 45.2 + - - +
11B ILE* 3.0 22.7 + - - +
158B LEU* 3.8 8.1 - - - -
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Residues in contact with LYS 8 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ASP* 1.3 76.0 - - - +
9B THR* 1.3 55.6 + - - +
11B ILE* 3.3 3.3 + - - +
12B LYS* 2.8 36.1 + - - +
15B GLN* 5.2 0.2 - - - +
158B LEU* 3.6 31.0 - - + +
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Residues in contact with THR 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B ASP* 3.2 17.2 + - - -
8B LYS* 1.3 79.4 - - - +
10B ASP* 1.3 55.4 + - - +
12B LYS* 3.3 7.7 + - - +
13B ILE* 2.8 33.8 + - + +
32B VAL* 3.7 26.4 + - + +
33B ALA 5.3 0.7 - - - +
34B LEU* 3.7 33.9 - - + -
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Residues in contact with ASP 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B THR 3.6 0.9 - - - +
6B LEU* 3.3 18.5 - - + -
7B ASP* 2.7 37.5 + - - +
9B THR* 1.3 74.5 - - - +
11B ILE* 1.3 66.2 + - - +
13B ILE* 3.3 10.2 + - - +
14B LEU* 3.0 29.3 + - - +
34B LEU* 5.9 0.2 - - - +
42B ARG* 2.8 54.4 + - - +
46B LEU* 4.6 5.7 - - + +
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Residues in contact with ILE 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6B LEU* 4.3 17.7 - - + -
7B ASP 3.0 18.1 + - - +
8B LYS 3.5 7.2 - - - +
10B ASP* 1.3 74.3 - - - +
12B LYS* 1.3 53.5 + - - +
14B LEU* 3.0 11.9 + - + +
15B GLN* 2.7 63.8 + - + +
154B LEU* 3.9 17.9 - - + +
155B ASN* 4.1 1.6 - - - +
157B LEU* 3.6 37.7 - - + -
158B LEU* 3.9 34.1 - - + -
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Residues in contact with LYS 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS 2.8 20.5 + - - +
9B THR* 3.5 8.5 - - - +
11B ILE* 1.3 73.7 - - - +
13B ILE* 1.3 56.0 + - - +
15B GLN* 3.5 21.2 + - + +
16B VAL* 2.9 46.6 + - + +
31B ARG* 3.5 21.1 - - - +
32B VAL* 4.1 20.6 - - + +
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Residues in contact with ILE 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B THR 2.8 21.8 + - - +
10B ASP* 3.4 11.4 - - - +
12B LYS* 1.3 71.9 - - - +
14B LEU* 1.3 58.1 + - + +
16B VAL* 3.8 1.2 - - - +
17B LEU* 3.0 48.4 + - + +
28B LEU* 4.1 13.0 - - + +
32B VAL* 3.8 26.0 - - + +
34B LEU* 4.1 20.4 - - + -
39B CYS* 5.0 6.7 - - - +
42B ARG* 3.9 31.6 - - + -
43B LEU* 4.3 6.1 - - + +
46B LEU* 3.8 19.5 - - + -
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Residues in contact with LEU 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A LEU* 4.2 10.7 - - + +
64A VAL* 5.0 3.1 - - + -
6B LEU* 4.3 20.6 - - + -
10B ASP 3.0 20.1 + - - +
11B ILE* 3.0 12.1 + - + +
13B ILE* 1.3 75.9 - - + +
15B GLN* 1.3 64.6 + - - +
17B LEU* 4.2 4.2 - - + +
18B GLN* 3.0 29.5 + - - +
43B LEU* 5.8 0.2 - - + -
46B LEU* 4.1 20.4 - - + -
51B ILE* 3.8 33.2 - - + -
52B VAL* 4.0 22.0 - - + -
154B LEU* 3.5 22.4 - - + -
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Residues in contact with GLN 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS 5.2 0.2 - - - +
11B ILE* 2.7 38.8 + - + +
12B LYS* 3.5 30.2 + - + +
14B LEU* 1.3 72.6 - - - +
16B VAL* 1.3 65.2 + - + +
18B GLN* 3.5 18.2 + - - +
19B GLU* 3.5 18.1 + - - +
154B LEU* 4.1 10.5 - - + +
155B ASN* 3.0 33.1 + - - +
158B LEU* 5.6 0.2 - - - +
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Residues in contact with VAL 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS* 2.9 37.3 + - + +
13B ILE 3.8 3.1 - - - +
15B GLN* 1.3 77.3 - - + +
17B LEU* 1.3 57.8 + - - +
19B GLU* 3.4 0.9 + - - -
20B ASN* 2.7 40.7 + - - +
23B LEU* 3.4 30.5 - - + -
28B LEU* 3.6 16.6 - - + -
31B ARG* 4.2 23.3 - - + +
32B VAL* 4.5 6.3 - - + -
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Residues in contact with LEU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ARG* 3.2 26.5 - - - +
57A ALA* 2.8 33.4 + - + -
13B ILE* 3.0 26.3 + - + +
14B LEU* 4.2 4.0 - - - +
16B VAL* 1.3 73.3 - - - +
18B GLN* 1.3 63.4 + - - +
20B ASN 3.5 12.8 - - - +
21B GLY* 3.2 14.3 + - - +
23B LEU* 4.6 3.1 - - + -
28B LEU* 3.5 24.0 - - + -
43B LEU* 3.4 41.3 - - + -
52B VAL* 5.3 3.4 - - + -
55B TYR* 3.9 10.5 - - + +
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Residues in contact with GLN 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 3.1 14.4 + - - -
56A ALA* 3.2 15.1 - - - +
57A ALA* 3.5 20.6 - - - +
59A LEU* 3.4 33.4 + - + +
14B LEU 3.0 18.6 + - - +
15B GLN* 3.7 9.4 - - - +
16B VAL 3.3 0.2 - - - -
17B LEU* 1.3 76.2 - - - +
19B GLU* 1.3 58.9 + - - +
150B THR* 3.9 5.7 + - - +
151B SER* 3.4 23.1 + - - +
152B LEU* 2.8 47.4 + - - +
154B LEU* 3.8 15.4 - - - +
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Residues in contact with GLU 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54A GLN* 3.2 25.7 + - - +
55A TYR 3.2 9.3 + - - +
15B GLN 3.5 10.8 + - - +
16B VAL 3.4 3.3 + - - +
18B GLN* 1.3 75.7 - - - +
20B ASN* 1.3 77.7 + - - +
149B THR* 5.5 2.0 + - - +
151B SER* 3.7 18.2 + - - +
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Residues in contact with ASN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A TYR* 3.7 1.1 - - - -
16B VAL* 2.7 28.9 + - - +
17B LEU* 3.5 17.4 - - - +
19B GLU* 1.3 91.7 + - - +
21B GLY* 1.3 57.4 + - - +
22B ARG 3.0 11.6 + - - -
23B LEU* 3.4 30.2 + - + +
31B ARG* 3.4 30.9 + - - +
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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