Contacts of the strand formed by residues 304 - 312 (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 VAL 304 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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196A VAL 5.2 5.8 - - - +
197A LEU* 4.2 20.4 - - + -
266A ARG* 3.4 5.5 - - - -
267A MET 2.9 39.1 + - - +
268A ARG 3.6 7.2 - - - +
269A CYS* 3.5 23.1 - - - -
302A HIS* 4.6 2.7 - - + +
303A PHE* 1.3 75.9 - - - +
305A VAL* 1.3 65.4 + - - +
306A VAL* 3.5 7.6 + - + +
343A LEU* 5.8 10.8 - - + -
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Residues in contact with VAL 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A ILE* 3.6 25.8 - - + -
265A CYS 3.8 4.9 - - - +
266A ARG* 4.6 14.4 - - + +
303A PHE 5.6 1.1 - - - +
304A VAL* 1.3 71.7 - - - +
306A VAL* 1.3 61.8 + - - +
307A HIS* 4.2 3.0 + - - +
343A LEU* 3.7 23.6 - - - +
344A GLN 4.1 4.5 + - - -
306B GLN* 4.1 34.8 - - + +
344B LEU* 4.8 9.0 - - + -
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
175A PHE* 5.4 3.6 - - + -
196A VAL* 5.9 1.6 - - + -
197A LEU* 4.4 10.1 - - + -
264A ILE* 3.5 3.8 - - - -
265A CYS* 2.8 42.7 + - - +
267A MET* 4.0 33.0 - - + -
304A VAL* 3.8 20.2 - - + +
305A VAL* 1.3 77.8 - - - +
307A HIS* 1.3 74.8 + - - +
308A CYS* 3.9 9.1 + - - -
341A GLY* 3.7 10.5 - - - -
342A ARG 3.7 16.8 - - - +
343A LEU* 5.2 5.8 - - + -
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Residues in contact with HIS 307 (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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263A PHE 3.9 3.3 + - - +
264A ILE* 3.8 24.7 - - + +
305A VAL* 4.8 3.6 - - + +
306A VAL* 1.3 71.9 - - - +
308A CYS* 1.3 59.8 + - - +
309A THR* 5.1 1.6 - - - +
340A ILE 3.8 0.3 - - - +
341A GLY* 3.1 5.2 - - - -
342A ARG* 2.9 71.1 + - + +
343A LEU 4.7 0.2 - - - -
344A GLN* 3.3 40.3 + - + +
303B VAL* 6.2 0.4 - - + -
306B GLN* 4.4 6.5 + - + -
320B GLU* 3.7 31.4 + - - -
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Residues in contact with CYS 308 (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* 3.9 28.0 - - + -
262A SER* 2.8 24.2 + - - -
263A PHE* 2.8 53.5 + - + +
265A CYS* 4.2 15.7 - - - -
267A MET* 4.3 2.9 - - - -
306A VAL* 4.0 20.2 - - - -
307A HIS* 1.3 80.8 - - - +
309A THR* 1.3 57.9 + - - +
310A GLY 4.4 0.2 - - - -
339A ALA* 5.5 1.8 - - + -
340A ILE 3.5 3.8 - - - +
341A GLY* 4.2 1.8 - - - -
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Residues in contact with THR 309 (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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260A ARG* 4.9 0.7 - - - +
261A ARG 4.1 0.2 - - - -
262A SER* 3.6 14.5 + - - +
307A HIS* 5.1 0.9 - - - +
308A CYS* 1.3 78.7 + - - +
310A GLY* 1.3 60.5 + - - +
339A ALA* 3.2 4.0 - - - +
340A ILE* 2.9 37.6 + - - +
342A ARG* 4.6 17.0 + - - -
94B ALA 2.9 22.6 - - - +
95B LEU* 4.7 6.5 - - + +
96B GLU* 3.4 40.6 - - + +
227B GLU* 5.6 1.2 + - - -
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Residues in contact with GLY 310 (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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260A ARG* 3.2 14.9 + - - -
261A ARG* 2.9 39.0 + - - +
309A THR* 1.3 77.0 - - - +
311A TYR* 1.3 63.6 + - - -
337A LEU* 5.0 2.9 - - - -
338A VAL 3.1 12.8 - - - -
339A ALA* 3.6 7.3 - - - +
94B ALA 3.8 6.7 - - - -
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Residues in contact with TYR 311 (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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259A SER 4.6 0.7 - - - +
260A ARG* 3.5 31.4 - - + +
261A ARG 4.2 0.9 - - - +
310A GLY* 1.3 76.9 - - - +
312A ILE* 1.3 75.7 + - - +
313A LYS* 3.6 35.1 + - + +
337A LEU* 3.2 10.6 - - - +
338A VAL* 2.9 64.0 + - + +
90B LEU* 3.4 30.3 - - - +
93B LYS* 4.0 15.3 - - + +
94B ALA* 3.6 32.1 - - - -
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Residues in contact with ILE 312 (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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181A CYS* 3.7 24.2 - - - -
225A LEU* 6.1 0.9 - - + -
227A THR* 5.9 2.2 - - + -
259A SER 3.2 29.3 + - - +
260A ARG* 4.5 0.2 - - - -
261A ARG* 3.4 33.4 - - - +
311A TYR* 1.3 90.3 - - - +
313A LYS* 1.3 74.6 + - - +
335A PHE* 3.8 15.5 - - + -
336A CYS 3.7 1.3 - - - -
337A LEU* 3.5 23.6 - - + -
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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