Contacts of the helix formed by residues 7 - 20 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6D LEU* 1.3 76.5 - - - +
8D LYS* 1.3 65.0 + - + +
9D THR* 4.0 4.4 + - - -
10D ASP* 2.8 44.0 + - - +
11D ILE* 3.1 15.0 + - - +
42D ARG* 3.0 27.3 + - - -
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Residues in contact with LYS 8 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ASP* 1.3 74.6 - - + +
9D THR* 1.3 73.6 + - + +
11D ILE* 3.8 10.7 + - - +
12D LYS* 3.3 40.1 + - - +
158D LEU* 5.4 12.7 - - + +
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Residues in contact with THR 9 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ASP* 3.2 3.5 + - - -
8D LYS* 1.3 91.9 + - + +
10D ASP* 1.3 60.0 + - - +
12D LYS* 3.2 13.2 + - + +
13D ILE* 2.9 30.7 + - - +
32D VAL* 3.7 24.4 - - + +
33D ALA* 5.3 0.9 - - + +
34D LEU* 4.5 19.6 - - + +
42D ARG* 3.3 30.7 + - - -
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Residues in contact with ASP 10 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.8 20.9 - - + +
7D ASP* 2.8 38.3 + - - +
9D THR* 1.3 68.8 - - - +
11D ILE* 1.3 65.4 + - - +
13D ILE* 3.4 6.6 + - - +
14D LEU* 3.1 28.7 + - - +
42D ARG* 3.1 38.7 + - - +
45D GLN* 4.2 8.3 + - - -
46D LEU* 3.9 19.8 - - + +
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Residues in contact with ILE 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D LEU* 3.9 20.0 - - + +
7D ASP 3.1 18.1 + - - +
8D LYS* 3.9 5.6 - - - +
10D ASP* 1.3 73.6 - - - +
12D LYS* 1.3 53.9 + - - +
14D LEU* 3.2 7.3 + - - +
15D GLN* 2.8 57.6 + - - +
154D LEU* 3.8 22.2 - - + +
155D ASN* 4.6 5.2 - - - +
157D LEU* 3.9 16.4 - - + -
158D LEU* 3.6 48.7 - - + +
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Residues in contact with LYS 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LYS* 3.3 28.2 + - - +
9D THR* 3.2 19.2 + - + +
11D ILE* 1.3 78.4 - - - +
13D ILE* 1.3 62.3 + - - +
15D GLN* 3.1 16.9 + - + +
16D VAL* 2.9 30.2 + - + +
31D ARG 4.7 6.7 - - - +
32D VAL* 3.8 35.2 - - + +
33D ALA* 5.9 1.8 - - - -
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Residues in contact with ILE 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D THR 2.9 17.2 + - - +
10D ASP* 3.5 18.2 - - - +
11D ILE 3.3 0.2 - - - -
12D LYS* 1.3 75.9 - - - +
14D LEU* 1.3 59.2 + - - +
16D VAL* 3.2 3.5 + - - +
17D LEU* 3.0 45.0 + - + +
28D LEU* 4.2 16.4 - - + +
32D VAL* 3.7 25.4 - - + -
34D LEU* 4.6 7.2 - - + -
39D CYS* 4.4 9.2 - - - +
42D ARG* 3.4 37.7 - - + +
43D LEU* 4.4 4.7 - - + +
46D LEU* 3.7 17.0 - - + -
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Residues in contact with LEU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C LEU* 4.1 19.1 - - + -
64C VAL* 4.8 4.0 - - + -
6D LEU* 3.5 31.4 - - + -
10D ASP 3.1 10.1 + - - +
11D ILE 3.2 3.1 + - - +
13D ILE* 1.3 79.4 - - - +
15D GLN* 1.3 56.6 + - - +
17D LEU* 3.5 9.2 + - + +
18D GLN* 3.1 34.7 + - - +
46D LEU* 4.2 20.9 - - + -
51D ILE* 3.7 32.5 - - + -
52D VAL* 4.3 10.8 - - + -
154D LEU* 3.4 27.1 - - + -
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Residues in contact with GLN 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D ILE* 2.8 33.6 + - + +
12D LYS* 3.5 23.4 - - + +
14D LEU* 1.3 72.6 - - - +
16D VAL* 1.3 63.9 + - + +
18D GLN* 4.1 9.8 - - - +
19D GLU* 3.3 27.5 + - - +
152D LEU 6.0 0.4 - - - +
154D LEU* 4.1 14.2 - - + +
155D ASN* 3.5 29.1 + - - +
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Residues in contact with VAL 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LYS* 2.9 21.2 + - + +
13D ILE 3.7 6.1 - - - +
15D GLN* 1.3 76.8 - - + +
17D LEU* 1.3 53.9 + - - +
19D GLU* 3.1 3.1 + - - -
20D ASN* 2.8 45.0 + - - +
23D LEU* 3.3 30.3 - - + -
28D LEU* 3.7 14.1 - - + -
31D ARG* 3.7 36.8 - - + +
32D VAL* 4.1 9.2 - - + -
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Residues in contact with LEU 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ARG* 4.3 21.5 - - - +
57C ALA* 3.0 35.3 + - + +
13D ILE* 3.0 27.4 + - + +
14D LEU* 3.9 16.6 - - + +
16D VAL* 1.3 78.1 - - - +
18D GLN* 1.3 62.5 + - - +
20D ASN 3.9 8.3 - - - +
21D GLY* 3.2 14.1 + - - +
23D LEU* 5.3 3.8 - - + -
28D LEU* 4.1 22.7 - - + -
43D LEU* 3.3 32.5 - - + -
52D VAL* 4.8 5.4 - - + -
55D TYR* 4.2 12.1 - - + +
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Residues in contact with GLN 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLN* 3.2 17.0 + - - -
56C ALA* 3.5 11.6 - - - +
57C ALA* 3.6 19.7 - - + +
59C LEU* 3.5 33.1 + - + +
14D LEU 3.1 18.2 + - - +
15D GLN* 4.1 10.1 - - - +
16D VAL 3.3 0.2 - - - -
17D LEU* 1.3 77.3 - - - +
19D GLU* 1.3 57.8 + - - +
150D THR* 4.1 5.4 + - - +
151D SER* 3.5 24.8 + - - +
152D LEU* 2.9 48.2 + - - +
154D LEU* 4.0 13.1 - - - +
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Residues in contact with GLU 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54C GLN* 3.1 31.2 + - - +
55C TYR 3.5 2.7 - - - +
15D GLN 3.3 17.0 + - - +
16D VAL* 3.1 4.3 + - - +
18D GLN* 1.3 78.5 - - - +
20D ASN* 1.3 75.4 + - - +
149D THR* 4.9 4.4 + - - -
151D SER* 4.2 15.2 + - - +
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Residues in contact with ASN 20 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C TYR* 3.7 2.5 - - - -
16D VAL* 2.8 23.9 + - - +
17D LEU* 3.3 10.8 - - - +
19D GLU* 1.3 90.7 + - - +
21D GLY* 1.3 61.0 + - - +
22D ARG 3.1 7.4 + - - +
23D LEU* 3.6 37.8 + - + +
31D ARG* 3.6 23.0 + - - +
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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