Contacts of the helix formed by residues 10 - 24 (chain B) in PDB entry 5WRV
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 SER 10 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9B VAL* 1.3 83.2 - - - +
11B VAL* 1.3 57.8 + - - +
12B PRO* 3.5 12.1 - - - +
13B ALA* 3.2 23.0 + - - +
14B LEU* 3.0 26.9 + - - +
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Residues in contact with VAL 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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9B VAL 4.0 0.2 + - - -
10B SER* 1.3 71.6 - - - +
12B PRO* 1.4 67.3 - - + +
14B LEU* 3.0 10.7 + - + +
15B TRP* 2.9 49.8 + - + +
37B ILE* 4.5 9.0 - - + -
40B ILE* 3.9 41.1 - - + -
41B ASN* 4.1 15.5 - - - +
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Residues in contact with PRO 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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606A LYS 4.1 13.0 - - - +
607A LEU* 4.0 22.5 - - - +
609A ALA* 3.7 26.9 - - + -
10B SER* 3.5 14.4 - - - +
11B VAL* 1.4 96.1 - - + +
13B ALA* 1.3 55.3 + - - +
15B TRP* 3.3 4.4 + - + +
16B SER* 3.0 25.3 + - - -
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Residues in contact with ALA 13 (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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9B VAL* 4.1 14.4 - - + +
10B SER* 3.2 22.5 + - - +
11B VAL 3.2 0.2 - - - -
12B PRO* 1.3 75.6 - - - +
14B LEU* 1.3 65.3 + - - +
16B SER* 3.3 10.9 + - - -
17B GLU* 3.2 24.7 + - - +
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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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9B VAL* 4.3 19.1 - - - +
10B SER 3.0 18.7 + - - +
11B VAL* 3.0 10.7 + - - +
13B ALA* 1.3 77.4 - - - +
15B TRP* 1.3 57.1 + - - +
17B GLU* 3.0 19.9 + - - +
18B VAL* 2.9 23.7 + - - +
33B THR* 3.3 21.8 - - + +
36B LYS* 4.3 28.9 - - + +
37B ILE* 3.7 27.6 - - + +
40B ILE* 4.2 24.5 - - + -
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Residues in contact with TRP 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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603A LEU* 3.8 27.3 - - + +
606A LYS* 3.6 47.9 - - + +
607A LEU* 3.5 15.2 - - + +
11B VAL* 2.9 43.0 + - + +
12B PRO* 3.5 8.5 - - + +
13B ALA 3.3 0.2 - - - -
14B LEU* 1.3 75.4 - - - +
16B SER* 1.3 58.1 + - - +
18B VAL* 3.2 20.8 + - + +
19B ASN* 2.9 26.7 + - - +
34B VAL* 5.1 1.6 - - + -
37B ILE* 3.6 19.8 - - + +
44B ASP* 3.7 21.1 + - - -
46B THR* 3.8 8.5 - - + -
47B ALA* 3.5 36.6 - - + -
50B CYS* 4.0 11.4 - - + -
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Residues in contact with SER 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607A LEU* 3.4 12.9 - - - +
12B PRO 3.0 12.9 + - - -
13B ALA* 3.3 14.8 - - - -
14B LEU 3.2 0.4 - - - -
15B TRP* 1.3 76.2 - - - +
17B GLU* 1.3 57.0 + - - +
19B ASN 3.5 0.2 + - - -
20B ARG* 3.0 14.6 + - - +
208B GOL 2.6 47.6 + - - -
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Residues in contact with GLU 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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13B ALA 3.2 9.4 + - - +
14B LEU* 3.0 29.8 + - - +
16B SER* 1.3 76.4 - - - +
18B VAL* 1.3 65.9 + - - +
20B ARG* 3.7 15.6 + - - +
21B TYR* 2.9 60.7 + - + -
33B THR* 3.9 10.2 + - + +
36B LYS* 5.8 1.9 + - - -
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Residues in contact with VAL 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
600A PHE* 3.6 25.0 - - + -
603A LEU* 4.1 4.5 - - + -
14B LEU 2.9 18.1 + - - +
15B TRP* 3.2 25.3 + - + +
17B GLU* 1.3 75.5 - - - +
19B ASN* 1.3 58.9 + - - +
21B TYR* 3.9 1.0 - - - +
22B GLY 2.9 25.8 + - - -
30B ALA* 4.2 7.5 - - + +
33B THR* 3.7 18.8 - - + +
34B VAL* 3.6 33.9 - - + -
37B ILE* 3.8 15.5 - - + -
50B CYS* 4.4 1.3 - - - -
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Residues in contact with ASN 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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600A PHE* 5.2 2.2 - - - -
603A LEU* 4.0 26.3 - - + +
607A LEU* 4.5 16.1 - - + +
15B TRP 2.9 16.0 + - - +
18B VAL* 1.3 78.1 - - - +
20B ARG* 1.3 56.3 + - - +
22B GLY* 3.8 0.2 - - - -
23B GLN* 2.9 58.7 + - - +
206B GOL 4.4 1.7 + - - -
208B GOL 3.0 37.7 + - - +
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Residues in contact with ARG 20 (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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16B SER 3.0 17.4 + - - +
17B GLU* 3.2 16.0 + - - +
19B ASN* 1.3 76.7 - - - +
21B TYR* 1.3 106.6 + - - +
23B GLN* 3.4 4.8 + - - +
24B ASN* 3.1 26.7 + - + +
208B GOL 3.5 24.8 + - - +
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Residues in contact with TYR 21 (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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17B GLU* 2.9 44.7 + - + +
20B ARG* 1.3 113.0 + - - +
22B GLY* 1.3 61.2 + - - +
24B ASN* 3.2 6.4 + - + -
25B GLY 3.0 4.3 + - - -
26B ASP* 2.8 53.2 + - + +
29B ARG* 3.6 50.5 - - + -
30B ALA* 3.7 9.2 - - + +
33B THR* 3.6 19.7 - - - -
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Residues in contact with GLY 22 (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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600A PHE* 3.6 23.5 - - - -
18B VAL 2.9 11.7 + - - -
21B TYR* 1.3 75.7 - - - +
23B GLN* 1.3 61.6 + - - +
25B GLY* 3.0 13.3 + - - -
27B PHE* 4.0 10.8 - - - -
30B ALA* 4.2 2.2 - - - +
206B GOL 3.0 28.1 + - - -
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Residues in contact with GLN 23 (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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19B ASN* 2.9 44.1 + - - +
20B ARG* 3.8 5.8 - - - +
22B GLY* 1.3 75.1 - - - +
24B ASN* 1.3 58.8 + - - +
25B GLY 3.3 0.8 + - - -
206B GOL 3.2 34.4 + - - +
208B GOL 6.1 0.2 - - - +
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Residues in contact with ASN 24 (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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20B ARG* 3.1 19.8 + - + +
21B TYR* 3.8 6.5 - - + +
22B GLY 3.1 0.2 - - - -
23B GLN* 1.3 76.0 - - - +
25B GLY* 1.3 60.2 + - - +
26B ASP* 3.3 15.5 + - - +
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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