Contacts of the helix formed by residues 192 - 198 (chain A) in PDB entry 4ZPK
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 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165A LYS* 5.4 1.6 + - - -
169A LEU* 4.1 22.1 - - - +
174A GLY 3.3 22.0 - - - -
175A PHE* 3.6 11.2 - - - -
190A SER* 3.1 9.7 + - - -
191A ASP* 1.3 82.2 + - - +
193A VAL* 1.3 61.0 + - - +
194A THR 3.1 0.9 - - - -
195A PRO* 3.2 19.4 - - - +
196A VAL* 3.1 22.7 - - - +
91B TYR* 4.4 3.8 + - - -
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Residues in contact with VAL 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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175A PHE* 3.6 34.1 - - + +
189A VAL* 3.6 14.8 - - + -
190A SER 3.2 19.9 + - - +
191A ASP 2.7 6.0 + - - +
192A SER* 1.3 78.1 - - - +
194A THR* 1.3 59.3 + - - +
196A VAL 3.8 0.2 - - - -
197A LEU* 2.9 30.0 + - + +
198A ASN 3.9 0.2 + - - -
199A GLN* 4.0 14.4 + - + +
201A GLN* 3.8 21.1 - - + -
204A TRP* 3.9 29.6 - - + -
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Residues in contact with THR 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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191A ASP 2.9 10.7 + - - -
193A VAL* 1.3 77.7 - - - +
195A PRO* 1.4 66.9 - - + +
196A VAL 3.0 4.5 - - - -
198A ASN* 3.0 31.6 + - - +
199A GLN 3.0 29.7 + - - +
200A PRO* 4.5 3.8 - - + +
201A GLN* 4.7 5.4 + - - +
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Residues in contact with PRO 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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169A LEU* 5.8 6.1 - - + -
173A ASP* 4.5 8.7 - - - +
191A ASP 3.4 4.9 - - - +
192A SER* 3.2 26.5 - - - +
194A THR* 1.4 95.4 - - + +
196A VAL* 1.3 62.6 + - + +
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Residues in contact with VAL 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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169A LEU* 5.4 2.7 - - + -
173A ASP* 3.9 11.0 - - + +
174A GLY* 3.3 34.5 - - - +
175A PHE* 4.1 12.3 - - + -
192A SER* 3.1 20.5 + - - +
193A VAL 4.1 2.5 - - - +
194A THR 3.0 0.6 - - - -
195A PRO* 1.3 86.2 - - + +
197A LEU* 1.3 77.6 + - + +
198A ASN 3.9 0.4 - - - -
304A VAL* 5.2 5.2 - - - +
306A VAL* 5.9 1.3 - - + -
341A GLY 5.6 0.4 - - - +
342A ARG* 5.8 0.4 - - - -
343A LEU* 3.7 32.8 - - + +
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Residues in contact with LEU 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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175A PHE* 3.9 15.0 - - + -
193A VAL* 2.9 14.0 + - + +
196A VAL* 1.3 106.8 - - + +
198A ASN* 1.3 57.7 + - - +
199A GLN* 3.8 8.3 - - + +
204A TRP* 3.5 37.9 - - + -
267A MET* 3.8 12.6 - - + -
268A ARG 3.4 23.8 - - - +
269A CYS* 2.8 35.4 - - - +
304A VAL* 4.2 14.4 - - + -
306A VAL* 4.4 11.7 - - + -
343A LEU* 5.6 0.4 - - + -
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Residues in contact with ASN 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 THR* 3.0 25.6 + - - +
197A LEU* 1.3 82.5 - - - +
199A GLN* 1.3 63.0 + - - +
200A PRO* 4.1 8.6 - - - +
269A CYS 3.0 12.6 - - - +
270A GLY* 3.6 2.1 - - - +
271A THR* 3.3 38.6 + - - -
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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