Contacts of the strand formed by residues 336 - 343 (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 CYS 336 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ILE* 4.1 14.1 - - + -
179A VAL 3.5 14.1 - - - +
180A SER* 3.8 17.7 - - - -
181A CYS* 3.4 14.6 - - - +
185A ARG* 5.9 0.9 - - - -
187A VAL* 4.6 11.7 - - - -
312A ILE* 3.7 0.2 - - - -
313A LYS* 2.9 30.9 + - - +
335A PHE* 1.3 86.2 - - - +
337A LEU* 1.3 60.7 + - - +
338A VAL* 4.4 3.2 + - + +
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Residues in contact with LEU 337 (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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177A PHE* 5.1 8.1 - - + +
178A ILE* 3.2 6.2 - - - +
179A VAL* 2.9 43.7 + - + +
181A CYS* 3.8 6.0 - - - -
224A GLN 4.5 1.1 - - - +
225A LEU* 3.9 27.1 - - + -
261A ARG* 4.3 15.0 - - + -
263A PHE* 5.6 7.6 - - + -
310A GLY* 5.0 0.9 - - - -
311A TYR 3.2 19.1 - - - +
312A ILE* 3.5 25.1 - - + -
336A CYS* 1.3 74.6 - - - +
338A VAL* 1.3 64.9 + - - +
339A ALA* 3.7 26.2 - - + +
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Residues in contact with VAL 338 (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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176A LEU* 3.6 23.8 - - + -
177A PHE 3.8 2.5 - - - -
178A ILE* 3.5 24.5 - - + -
310A GLY* 3.1 1.9 - - - -
311A TYR* 2.9 71.5 + - + +
313A LYS* 5.9 5.2 - - + +
336A CYS 5.3 2.9 - - - +
337A LEU* 1.3 76.3 - - - +
339A ALA* 1.3 63.8 + - - +
90B LEU* 4.2 17.9 - - + -
94B ALA* 4.4 3.4 - - + -
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Residues in contact with ALA 339 (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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176A LEU* 3.1 8.3 - - - +
177A PHE* 2.9 53.6 + - + -
308A CYS* 5.4 1.8 - - + -
309A THR 3.2 17.9 - - - +
310A GLY* 3.6 7.2 - - - -
337A LEU* 3.7 15.5 - - + -
338A VAL* 1.3 78.1 - - - +
340A ILE* 1.3 65.7 + - - +
94B ALA* 4.0 3.6 - - - -
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Residues in contact with ILE 340 (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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168A ILE* 5.0 4.7 - - + -
174A GLY* 5.0 1.8 - - - -
175A PHE 3.3 17.3 - - - +
176A LEU* 4.2 12.8 - - + -
177A PHE* 4.1 3.1 - - - -
307A HIS 3.8 0.5 - - - +
308A CYS* 3.5 1.6 - - - -
309A THR* 2.9 40.5 + - - +
339A ALA* 1.3 79.6 - - - +
341A GLY* 1.3 71.4 + - - +
342A ARG* 4.2 9.5 + - + +
91B TYR* 3.5 43.7 - - + +
94B ALA* 3.6 16.2 - - + -
95B LEU* 3.9 18.6 - - + +
225B MET* 6.4 0.7 - - + -
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Residues in contact with GLY 341 (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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174A GLY* 3.0 3.3 - - - -
175A PHE* 2.9 41.0 + - - -
177A PHE* 3.5 15.0 - - - -
196A VAL* 6.1 0.4 - - - -
306A VAL* 3.7 14.1 - - - -
307A HIS 3.1 9.9 - - - -
308A CYS* 4.2 1.6 - - - -
340A ILE* 1.3 75.6 - - - +
342A ARG* 1.3 60.6 + - - +
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Residues in contact with ARG 342 (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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172A ALA* 4.1 16.6 - - + -
173A ASP 3.3 13.0 - - - +
174A GLY* 4.0 1.8 - - - -
196A VAL* 5.8 1.3 - - - -
306A VAL* 3.7 5.0 - - - +
307A HIS* 2.9 59.9 + - + +
309A THR* 4.6 13.9 + - - +
340A ILE* 5.0 9.2 - - + +
341A GLY* 1.3 75.9 - - - +
343A LEU* 1.3 65.7 + - - +
344A GLN* 6.2 2.0 - - - +
95B LEU* 5.4 0.2 - - - +
194B HIS* 5.5 0.6 - - - -
196B THR* 3.6 26.9 + - - +
225B MET* 3.6 32.2 - - - +
227B GLU* 3.1 37.0 + - - -
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Residues in contact with LEU 343 (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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172A ALA* 5.8 1.4 - - - +
173A ASP* 3.1 43.3 + - + +
196A VAL* 3.7 38.7 - - + +
197A LEU* 5.6 1.1 - - + -
304A VAL* 5.8 11.0 - - + -
305A VAL 3.7 16.8 - - - +
306A VAL* 4.7 5.4 - - + +
307A HIS* 4.7 0.7 - - - -
342A ARG* 1.3 79.1 + - - +
344A GLN* 1.3 67.1 + - - +
345A VAL* 3.7 23.2 + - + +
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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