Contacts of the helix formed by residues 31 - 39 (chain V) in PDB entry 3HOU
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 31 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1038N SER 5.1 1.6 - - - +
1040N ASN* 5.3 8.8 + - - +
25V LEU* 4.2 2.7 - - - -
30V LEU* 1.3 77.9 - - - +
32V GLU* 1.3 74.5 + - - +
33V GLY* 4.0 7.2 + - - +
34V THR* 2.4 41.3 + - - -
35V ALA* 2.9 10.1 + - - +
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Residues in contact with GLU 32 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039N GLY* 3.2 26.7 - - - +
1040N ASN* 4.6 5.5 - - - +
21V TYR* 3.3 26.0 - - + +
25V LEU* 3.8 21.3 - - + +
31V ASP* 1.3 78.1 - - - +
33V GLY* 1.3 67.1 + - - +
34V THR 2.8 1.6 + - - -
35V ALA* 4.3 2.5 - - - -
36V LEU* 2.9 28.7 + - + +
51V LEU* 4.3 10.5 - - + -
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Residues in contact with GLY 33 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1037N LEU 4.6 0.8 - - - +
1038N SER 3.2 31.0 + - - -
1039N GLY* 3.8 3.3 + - - -
1040N ASN* 5.5 0.8 + - - +
31V ASP* 3.1 9.4 + - - +
32V GLU* 1.3 78.6 + - - +
34V THR* 1.3 59.5 + - - +
37V SER* 3.4 4.0 + - - -
47V ARG* 3.0 30.3 + - - -
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Residues in contact with THR 34 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30V LEU* 3.6 21.1 - - + +
31V ASP* 2.4 37.9 + - - -
33V GLY* 1.3 69.8 - - - -
35V ALA* 1.3 65.2 + - - -
36V LEU 2.9 2.2 - - - -
37V SER* 2.7 11.4 + - - +
38V ARG* 2.7 37.5 + - - +
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Residues in contact with ALA 35 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21V TYR* 3.9 17.5 - - + -
24V LEU* 3.6 29.1 - - + +
25V LEU* 4.0 13.9 - - + -
30V LEU* 4.6 4.8 - - + +
31V ASP 2.9 14.6 + - - +
32V GLU 3.7 2.7 - - - +
34V THR* 1.3 76.4 - - - +
36V LEU* 1.3 61.9 + - - +
38V ARG* 3.2 10.0 - - - +
39V LEU* 3.2 30.6 + - - +
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Residues in contact with LEU 36 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1039N GLY* 5.0 0.4 - - - -
21V TYR* 3.3 33.4 - - + -
32V GLU* 2.9 19.6 + - + +
34V THR 2.9 0.6 - - - -
35V ALA* 1.3 75.1 - - - +
37V SER* 1.3 65.7 + - - +
39V LEU* 3.1 13.3 + - + -
41V LEU* 3.2 34.0 + - + +
47V ARG* 3.1 51.4 - - + +
50V ILE* 3.5 19.1 - - + -
51V LEU* 3.9 31.2 - - + +
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Residues in contact with SER 37 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33V GLY 3.4 4.9 + - - -
34V THR* 2.7 19.0 + - - -
36V LEU* 1.3 74.4 - - - +
38V ARG* 1.3 63.3 + - - +
40V GLY* 3.1 13.5 + - - -
41V LEU 4.5 7.1 + - - +
47V ARG* 2.6 27.2 + - - +
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Residues in contact with ARG 38 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24V LEU* 3.4 33.9 - - + -
28V ASP* 5.9 0.7 - - - -
30V LEU* 2.9 39.4 - - - +
34V THR* 2.7 26.5 + - - +
35V ALA* 3.2 12.1 - - - +
37V SER* 1.3 77.6 - - - +
39V LEU* 1.3 57.7 + - + +
40V GLY 3.1 4.7 + - - -
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Residues in contact with LEU 39 (chain V).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12V LYS* 5.4 0.7 + - - -
17V LYS* 3.7 46.2 - - + +
20V SER* 3.4 32.1 - - - -
21V TYR* 3.2 38.6 - - + -
24V LEU* 3.8 14.1 - - + -
35V ALA 3.2 16.2 - - - +
36V LEU* 3.1 9.4 + - - +
38V ARG* 1.3 74.3 - - + +
40V GLY* 1.3 59.8 + - - +
41V LEU* 3.3 12.3 + - + +
50V ILE* 5.3 0.4 - - + -
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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