Contacts of the helix formed by residues 195 - 206 (chain A) in PDB entry 2WV4
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 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72A PHE* 5.7 1.0 - - - -
103A PHE* 4.7 0.2 - - - -
104A ARG 3.5 5.8 - - - -
105A ASP* 3.0 22.1 + - - +
193A CYS 4.3 0.4 + - - -
194A VAL* 1.3 73.4 - - - +
196A ARG* 1.3 63.2 + - - +
197A SER* 3.1 3.6 + - - -
198A MET* 3.1 28.9 + - - +
199A LEU* 3.1 24.1 + - - +
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Residues in contact with ARG 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
100A THR* 3.3 24.4 - - - +
101A LYS* 4.2 13.1 + - - +
103A PHE* 3.4 36.7 + - + +
104A ARG* 2.9 38.0 + - - +
105A ASP* 2.7 31.2 + - - +
194A VAL 3.7 1.4 + - - -
195A SER* 1.3 71.7 + - - +
197A SER* 1.3 60.4 + - - +
199A LEU* 3.2 7.0 + - - +
200A GLN* 2.9 29.8 + - + +
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Residues in contact with SER 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105A ASP* 2.8 33.7 + - - -
195A SER* 3.6 2.9 - - - -
196A ARG* 1.3 78.8 + - - +
198A MET* 1.3 58.9 + - - +
200A GLN* 3.8 7.5 - - - +
201A LYS* 3.0 30.1 + - - +
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Residues in contact with MET 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.4 32.8 - - + -
195A SER* 3.1 26.4 + - - +
197A SER* 1.3 76.9 - - - +
199A LEU* 1.3 58.4 + - - +
201A LYS* 3.5 4.5 + - - +
202A MET* 3.0 30.5 + - - +
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Residues in contact with LEU 199 (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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36A VAL* 4.4 9.2 - - + -
37A PHE* 4.0 5.7 - - + -
42A LEU* 4.0 25.6 - - + -
72A PHE* 4.1 13.9 - - + -
87A LEU* 4.3 13.2 - - + -
100A THR* 3.6 28.3 - - + -
103A PHE* 3.7 48.5 - - + -
194A VAL* 3.9 4.9 - - + -
195A SER 3.1 14.1 + - - +
196A ARG* 3.6 6.5 - - - +
197A SER 3.2 0.2 - - - -
198A MET* 1.3 77.3 - - - +
200A GLN* 1.3 56.8 + - - +
202A MET* 3.3 4.8 + - - +
203A LYS* 2.9 29.3 + - - +
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Residues in contact with GLN 200 (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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100A THR* 5.0 6.2 - - - +
196A ARG* 2.9 19.2 + - + +
197A SER* 3.8 8.5 - - - +
198A MET 3.4 0.2 - - - -
199A LEU* 1.3 76.5 - - - +
201A LYS* 1.3 60.4 + - - +
203A LYS* 3.4 17.8 + - - +
204A ALA* 3.4 13.0 + - - +
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Residues in contact with LYS 201 (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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197A SER 3.0 17.8 + - - +
198A MET* 3.9 5.8 - - - +
200A GLN* 1.3 72.5 - - - +
202A MET* 1.3 66.9 + - - +
203A LYS 3.0 2.0 - - - -
204A ALA* 3.1 17.3 + - - +
205A HIS* 3.1 15.3 + - - +
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Residues in contact with MET 202 (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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37A PHE* 4.0 2.5 - - - -
70A PHE* 3.4 45.1 - - + -
71A GLU 4.4 11.4 - - - +
72A PHE* 4.8 15.9 - - + -
87A LEU* 3.2 31.0 - - + -
198A MET 3.0 20.9 + - - +
199A LEU* 3.6 6.7 - - - +
201A LYS* 1.3 76.4 - - - +
203A LYS* 1.3 59.5 + - - +
205A HIS* 4.0 12.3 - - - -
206A VAL* 3.2 36.6 + - + +
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Residues in contact with LYS 203 (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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37A PHE* 3.4 42.6 - - + -
38A GLY 5.6 0.4 - - - +
98A ASP* 3.1 27.8 - - - +
100A THR* 5.0 5.8 - - + +
199A LEU 2.9 13.1 + - - +
200A GLN* 3.4 14.8 - - - +
201A LYS 3.0 0.4 - - - -
202A MET* 1.3 77.1 - - - +
204A ALA* 1.3 63.5 + - - +
207A ASP* 3.4 31.4 + - + +
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Residues in contact with ALA 204 (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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200A GLN 3.4 8.5 + - - +
201A LYS* 3.1 10.6 + - - +
203A LYS* 1.3 81.8 - - - +
205A HIS* 1.3 62.2 + - - +
206A VAL 3.3 6.4 + - - +
207A ASP 4.2 3.9 - - - +
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Residues in contact with HIS 205 (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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70A PHE* 4.0 25.5 - + - -
201A LYS 3.1 12.9 + - - +
202A MET* 4.2 15.3 - - - +
204A ALA* 1.3 78.1 - - - +
206A VAL* 1.3 67.7 + - + +
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Residues in contact with VAL 206 (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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37A PHE* 5.1 4.9 - - + -
70A PHE* 4.0 24.7 - - + -
89A VAL* 3.6 34.1 - - + -
202A MET* 3.2 28.6 + - + +
203A LYS* 3.7 0.9 - - - -
204A ALA 3.2 3.2 - - - +
205A HIS* 1.3 92.4 - - - +
207A ASP* 1.3 82.8 + - - +
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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