Contacts of the helix formed by residues 192 - 200 (chain A) in PDB entry 3KSS
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 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190A VAL 3.9 1.1 + - - +
191A ILE* 1.3 74.7 - - - +
193A PRO* 1.3 65.7 - - - +
194A GLN* 3.6 18.4 + - - +
195A ARG* 2.7 62.3 + - + +
196A LEU* 3.0 9.7 + - - +
262A VAL 2.9 17.5 + - - +
263A ALA* 5.5 0.9 - - - -
773A PRO* 4.7 4.9 - - + +
776A TRP* 4.9 5.5 + - - -
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Residues in contact with PRO 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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191A ILE* 3.7 9.8 - - - +
192A ASP* 1.3 90.1 - - - +
194A GLN* 1.3 59.5 + - + +
196A LEU* 3.2 11.2 + - + +
197A ALA* 3.0 27.9 + - - +
772A TYR* 3.7 36.3 - - + +
773A PRO* 4.1 9.0 - - + -
776A TRP* 4.1 19.5 - - + +
787A PRO* 3.6 27.1 - - + +
795A GLN* 5.3 2.8 + - - +
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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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192A ASP* 3.0 17.8 + - - +
193A PRO* 1.3 78.0 - - + +
195A ARG* 1.3 66.2 + - - +
197A ALA* 3.5 7.1 + - - +
198A GLN* 2.9 41.2 + - - +
776A TRP* 4.1 24.4 - - + -
795A GLN* 5.5 5.4 - - - +
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Residues in contact with ARG 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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192A ASP* 2.7 39.2 + - + +
194A GLN* 1.3 80.0 + - - +
196A LEU* 1.3 63.8 + - - +
198A GLN* 3.5 33.3 + - - +
199A TYR* 3.0 38.7 + - - -
261A ASP 3.5 18.3 + - - +
262A VAL* 3.6 24.5 - - - +
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Residues in contact with LEU 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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191A ILE* 3.3 38.4 - - + -
192A ASP 3.0 6.5 + - - +
193A PRO* 3.3 11.2 - - + +
195A ARG* 1.3 75.8 - - - +
197A ALA* 1.3 54.6 + - - +
199A TYR 3.6 0.2 - - - -
200A GLY* 2.6 37.1 + - - -
201A ILE* 3.1 30.7 + - + +
202A SER* 4.8 1.3 - - - -
203A LEU* 4.5 24.5 - - + +
206A VAL* 4.9 3.8 - - + -
262A VAL* 3.5 28.9 - - + -
746A PHE* 6.4 0.4 - - + -
772A TYR* 4.7 11.4 - - + +
789A LEU* 4.5 6.7 - - + +
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Residues in contact with ALA 197 (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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193A PRO 3.0 12.9 + - - +
194A GLN* 3.7 9.2 - - - +
196A LEU* 1.3 75.9 - - - +
198A GLN* 1.3 65.8 + - + +
200A GLY* 3.0 13.2 + - - -
789A LEU* 3.9 19.5 - - + +
793A LYS* 5.7 1.0 - - - +
795A GLN* 3.9 31.9 - - + +
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Residues in contact with GLN 198 (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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194A GLN* 2.9 28.0 + - + +
195A ARG* 3.6 40.0 + - - +
196A LEU 3.3 0.2 - - - -
197A ALA* 1.3 80.3 - - + +
199A TYR* 1.3 72.5 + - + +
200A GLY* 4.7 0.2 - - - -
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Residues in contact with TYR 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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195A ARG* 3.0 40.2 + - - +
198A GLN* 1.3 89.2 + - + +
200A GLY* 1.3 63.6 + - - +
201A ILE* 3.4 24.4 + - + +
249A LYS* 5.0 7.3 - - - +
257A VAL* 3.5 37.2 - - + +
261A ASP* 3.9 30.6 + - + +
262A VAL* 3.9 7.0 - - + -
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Residues in contact with GLY 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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196A LEU 2.6 17.8 + - - -
197A ALA 3.0 11.5 + - - -
198A GLN 4.7 0.2 - - - -
199A TYR* 1.3 75.5 - - - +
201A ILE* 1.3 59.6 + - - +
202A SER 4.1 1.2 + - - -
205A GLU* 5.5 1.0 - - - +
249A LYS* 5.6 1.7 - - - +
789A LEU* 4.6 11.6 - - - +
793A LYS* 4.3 22.8 - - - +
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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