Contacts of the helix formed by residues 190 - 196 (chain A) in PDB entry 3CVW
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 190 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ARG* 3.9 7.5 + - - -
99A SER* 4.6 5.6 + - - +
100A TRP* 3.2 31.3 + - + +
188A PRO 3.4 2.7 + - - +
189A LYS* 1.3 74.7 - - - +
191A GLU* 1.3 71.2 + - - +
192A VAL* 3.0 7.3 + - - +
193A GLU* 2.7 50.5 + - - +
194A GLN* 2.9 32.6 + - - +
200A TYR* 3.1 21.3 + - - -
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Residues in contact with GLU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ARG* 4.3 18.8 + - - +
99A SER* 3.3 34.6 + - - -
190A ASP* 1.3 79.7 - - - +
192A VAL* 1.3 61.7 + - + +
194A GLN* 4.3 9.8 + - - +
195A LYS* 3.5 33.2 + - - +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A ARG* 3.4 38.6 - - - +
190A ASP* 3.0 4.6 + - - +
191A GLU* 1.3 80.8 - - + +
193A GLU* 1.3 59.3 + - - +
194A GLN 3.2 1.6 - - - -
195A LYS* 3.2 6.7 + - + +
196A ASP* 2.9 28.4 + - + +
199A ALA* 3.9 19.1 - - + -
200A TYR* 3.4 15.7 - - + +
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Residues in contact with GLU 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A ARG* 3.0 38.2 + - - -
81A ARG* 5.5 2.4 + - - -
83A PHE* 4.2 6.8 - - - -
187A PRO 4.9 3.3 - - - +
189A LYS* 3.4 38.0 + - + +
190A ASP* 2.7 37.8 + - - +
192A VAL* 1.3 69.8 - - - +
194A GLN* 1.3 63.5 + - - +
196A ASP 3.1 24.7 - - - +
197A SER* 3.4 12.6 + - - +
199A ALA* 4.7 1.6 - - + -
200A TYR* 3.6 23.9 - - + +
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Residues in contact with GLN 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189A LYS* 2.8 39.1 + - + +
190A ASP* 2.9 21.5 + - - +
191A GLU* 4.2 9.8 + - - +
193A GLU* 1.3 79.6 - - - +
195A LYS* 1.3 62.3 + - + +
196A ASP* 3.6 0.5 + - - -
197A SER 5.2 0.3 + - - -
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Residues in contact with LYS 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191A GLU* 3.5 18.8 - - - +
192A VAL* 3.2 10.9 + - + +
194A GLN* 1.3 79.7 - - + +
196A ASP* 1.3 61.8 + - + +
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Residues in contact with ASP 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192A VAL* 2.9 7.9 + - + +
193A GLU* 3.1 20.5 - - - +
194A GLN 3.3 0.6 - - - -
195A LYS* 1.3 81.2 - - + +
197A SER* 1.3 66.7 + - - +
198A ALA* 3.5 14.8 + - - +
199A ALA* 3.2 32.6 + - + +
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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