Contacts of the helix formed by residues 42 - 48 (chain V) in PDB entry 3EXG
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 GLY 42 (chain V).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31V ALA 5.9 0.2 + - - -
34V ASP* 3.1 15.2 + - - -
40V SER 3.2 1.6 + - - -
41V ARG* 1.3 75.1 - - - +
43V LEU* 1.3 57.9 + - - +
44V TRP 3.2 3.8 + - - +
45V LYS* 3.3 12.3 + - - +
46V LYS* 2.8 28.9 + - - +
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Residues in contact with LEU 43 (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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10V ASN* 3.2 23.6 - - - +
13V MET* 3.9 37.7 - - + -
14V ASP* 4.7 10.5 - - + +
17V LEU* 4.1 21.3 - - + -
25V LEU* 4.7 2.7 - - + -
40V SER* 3.1 17.1 + - - +
41V ARG 3.1 17.9 - - - +
42V GLY* 1.3 74.9 - - - +
44V TRP* 1.3 62.3 + - - +
46V LYS* 3.6 3.6 - - + +
47V TYR* 2.9 33.0 + - + -
52V ILE* 3.5 24.9 - - + +
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Residues in contact with TRP 44 (chain V).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30V VAL 5.4 0.2 + - - -
31V ALA* 3.5 34.6 + - + +
32V GLN* 3.6 42.6 - - + -
34V ASP* 6.1 0.9 - - - -
40V SER 4.6 2.0 + - - -
42V GLY 3.3 1.4 - - - +
43V LEU* 1.3 77.1 - - - +
45V LYS* 1.3 87.6 + - + +
48V GLY* 2.7 47.1 + - - -
49V ASP* 2.6 32.6 + - - +
52V ILE* 3.9 23.3 - - + +
206W ARG* 4.4 3.0 - - - +
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Residues in contact with LYS 45 (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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32B GLN* 3.9 19.5 + - - -
44B TRP* 5.3 9.0 - - - -
206C ARG* 6.3 0.6 - - - +
42V GLY* 3.3 13.1 + - - +
44V TRP* 1.3 99.9 - - + +
46V LYS* 1.3 58.7 + - - +
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Residues in contact with LYS 46 (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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14V ASP* 2.9 34.2 + - - +
18V GLU* 4.0 14.3 + - - -
42V GLY 2.8 19.5 + - - +
43V LEU* 4.4 2.0 - - + -
44V TRP 3.1 0.4 - - - -
45V LYS* 1.3 76.0 - - - +
47V TYR* 1.3 94.9 + - + +
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Residues in contact with TYR 47 (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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14V ASP* 2.4 41.4 + - - -
17V LEU* 3.7 33.4 - - + -
18V GLU* 3.3 22.8 + - + +
43V LEU* 2.9 26.0 + - + +
46V LYS* 1.3 104.3 - - + +
48V GLY* 1.3 64.0 + - - +
50V LYS* 4.6 2.3 + - - +
51V ARG* 3.5 43.0 + - + +
52V ILE* 4.7 2.0 - - + -
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Residues in contact with GLY 48 (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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43V LEU 3.8 0.8 + - - -
44V TRP* 2.7 36.8 + - - -
45V LYS 5.0 0.2 + - - -
46V LYS 3.7 0.2 - - - -
47V TYR* 1.3 73.1 - - - +
49V ASP* 1.3 66.4 + - - -
50V LYS 3.0 5.0 + - - -
51V ARG 3.1 3.5 + - - -
52V ILE* 3.0 18.7 + - - -
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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