Contacts of the helix formed by residues 32 - 40 (chain Z) in PDB entry 2W4V
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 LYS 32 (chain Z).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18Z PHE* 2.4 57.7 - - + -
22Z ASP* 6.0 2.2 - - - -
29Z ASP* 2.6 20.4 + - + +
31Z PHE* 1.3 102.3 - - - +
33Z LEU* 1.3 52.3 + - - +
34Z GLY 2.7 17.9 + - - -
35Z ASP* 2.9 22.6 + - + +
36Z VAL* 3.0 12.4 + - - +
58Z MET* 4.0 32.0 - - - +
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Residues in contact with LEU 33 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28Z VAL* 4.6 11.7 - - + -
29Z ASP 3.7 2.3 + - - +
30Z ALA* 3.5 23.5 + - - +
32Z LYS* 1.3 76.2 - - - +
34Z GLY* 1.3 59.3 + - - +
36Z VAL* 2.3 31.4 - - + +
37Z CYS* 3.5 7.1 + - - +
49Z VAL* 5.5 2.0 - - + -
52Z VAL* 5.2 4.7 - - + -
53Z GLY* 4.7 4.9 - - - -
54Z GLY* 4.6 17.5 - - - +
63Z LEU* 4.1 26.2 - - + -
68Z PHE* 3.0 43.5 - - + -
71Z ALA* 4.2 21.3 - - + -
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Residues in contact with GLY 34 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Z ALA 5.0 0.2 + - - -
31Z PHE 4.8 2.8 + - - -
32Z LYS 2.7 6.7 + - - -
33Z LEU* 1.3 74.8 - - - +
35Z ASP* 1.3 53.6 + - - -
36Z VAL 2.7 11.8 + - - -
37Z CYS* 2.7 33.0 + - - -
38Z ARG* 3.0 12.6 + - - -
49Z VAL* 4.1 22.2 - - - +
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Residues in contact with ASP 35 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794C ILE* 3.3 29.4 - - - +
18Z PHE* 5.6 5.8 - - + -
31Z PHE 5.6 0.2 + - - -
32Z LYS* 2.9 19.9 + - + +
34Z GLY* 1.3 69.1 - - - +
36Z VAL* 1.3 66.1 + - - +
38Z ARG* 3.5 15.8 - - - +
39Z CYS* 2.9 29.3 + - - -
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Residues in contact with VAL 36 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Z LEU* 6.1 0.2 - - - -
14Z VAL* 5.0 12.4 - - + +
15Z PHE* 6.0 6.1 - - + -
18Z PHE* 4.4 30.1 - - + -
28Z VAL* 5.6 2.9 - - + -
32Z LYS* 3.0 18.7 + - + +
33Z LEU* 2.3 44.9 - - + +
34Z GLY 2.7 4.9 + - - -
35Z ASP* 1.3 73.2 - - - +
37Z CYS* 1.3 66.0 + - + +
39Z CYS* 2.9 31.0 + - - +
40Z LEU* 3.6 5.6 + - - +
68Z PHE* 3.4 30.3 - - + -
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Residues in contact with CYS 37 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11Z LEU* 5.8 0.2 - - - -
33Z LEU 3.5 11.0 - - - +
34Z GLY* 2.7 31.5 + - - -
36Z VAL* 1.3 77.6 - - + +
38Z ARG* 1.3 59.1 + - - +
39Z CYS 2.9 6.2 + - - -
40Z LEU* 3.1 20.3 + - - +
42Z ILE* 2.6 33.4 + - + +
44Z PRO* 3.3 6.1 - - - -
49Z VAL* 5.1 1.6 - - - -
68Z PHE* 5.4 1.8 - - + -
72Z TYR* 4.3 17.7 - - + -
75Z LEU* 2.7 40.2 - - + -
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Residues in contact with ARG 38 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787C ALA* 2.8 18.6 + - - +
790C ARG* 2.7 48.9 - - - +
791C GLY* 2.9 6.7 - - - +
794C ILE* 3.3 35.7 - - + -
795C ARG* 2.5 36.5 + - - +
34Z GLY* 3.0 20.0 + - - +
35Z ASP* 3.5 16.8 - - - +
36Z VAL 3.1 0.2 - - - -
37Z CYS* 1.3 76.2 - - - +
39Z CYS* 1.3 56.7 + - - +
40Z LEU 3.5 0.2 - - - -
42Z ILE 3.1 13.9 - - - +
43Z ASN* 4.0 2.4 + - - +
44Z PRO* 2.9 35.2 + - + +
45Z ARG 4.7 0.2 - - - -
46Z ASN* 4.6 9.7 - - - +
49Z VAL* 5.2 4.8 - - - +
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Residues in contact with CYS 39 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794C ILE* 3.2 20.0 - - - -
795C ARG* 3.8 11.1 - - - +
798C TYR* 4.0 33.5 - - + -
14Z VAL* 4.5 11.2 - - + +
17Z LEU* 6.3 0.2 - - - -
35Z ASP* 2.9 34.1 + - - -
36Z VAL* 2.9 13.3 + - - +
38Z ARG* 1.3 76.1 - - - +
40Z LEU* 1.3 57.4 + - - +
41Z GLY 3.0 9.8 + - - -
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Residues in contact with LEU 40 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Z GLU 5.0 0.7 - - - +
10Z ASP* 3.8 28.5 - - + +
11Z LEU* 2.9 51.6 - - + +
14Z VAL* 4.4 18.4 - - + -
36Z VAL 3.6 2.1 + - - +
37Z CYS* 3.1 11.9 + - - +
39Z CYS* 1.3 76.8 - - - +
41Z GLY* 1.3 55.9 + - - +
42Z ILE* 3.5 9.8 + - - +
72Z TYR* 3.8 27.4 + - + +
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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