Contacts of the strand formed by residues 251 - 261 (chain A) in PDB entry 4ZCH
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 ASN 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89A ILE 3.9 3.8 - - - +
90A ARG* 3.7 11.6 - - - -
91A SER* 3.3 22.5 + - - +
208A LEU* 3.4 5.8 - - - +
209A TYR* 2.9 36.6 + - - +
242A GLN* 3.7 25.7 - - + +
243A ASN 3.3 23.0 + - - -
244A MET* 3.6 20.7 - - - -
245A PRO* 3.7 18.2 - - - +
250A ASN* 1.3 75.4 + - - +
252A SER* 1.3 60.2 + - - +
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Residues in contact with SER 252 (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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88A CYS* 3.6 14.4 - - - -
89A ILE 2.9 37.1 + - - -
90A ARG* 2.9 26.3 + - - -
206A GLN* 4.1 22.3 + - - -
207A VAL 3.4 7.4 - - - -
208A LEU* 3.5 12.1 - - - +
242A GLN* 3.9 5.4 - - - +
251A ASN* 1.3 73.3 - - - +
253A CYS* 1.3 59.8 + - - +
254A TYR 4.2 0.4 + - - -
284A VAL* 4.2 6.5 - - - -
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Residues in contact with CYS 253 (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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90A ARG* 5.6 0.2 - - - +
206A GLN* 3.2 3.8 - - - -
207A VAL 2.8 28.9 + - - -
209A TYR* 3.5 27.6 - - + -
218A HIS* 3.2 8.2 - - + -
240A CYS* 2.1 47.8 - - + -
241A ILE* 3.4 17.7 - - - -
242A GLN* 3.5 25.8 - - + +
252A SER* 1.3 73.8 - - - +
254A TYR* 1.3 58.0 + - - +
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Residues in contact with TYR 254 (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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90A ARG* 5.6 3.7 - - - +
104A TYR* 3.6 27.6 + + - +
105A SER* 4.0 5.6 - - - -
106A ALA* 3.6 41.0 - - + +
202A PHE* 4.2 6.4 - - - -
204A TYR* 3.3 27.4 - - + +
205A GLY 3.5 11.9 - - - -
206A GLN* 3.7 24.0 - - + +
240A CYS* 3.3 13.0 - - - -
242A GLN* 5.6 0.4 - - - +
252A SER 4.2 0.8 + - - -
253A CYS* 1.3 72.9 - - - +
255A SER* 1.3 60.8 + - - +
256A ALA* 3.4 20.2 - - + +
286A PHE* 4.4 3.6 - + - -
357A GLN* 4.1 1.4 - - - +
403A SER* 5.1 0.9 + - - -
405A TYR* 3.5 50.8 + + + +
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Residues in contact with SER 255 (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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204A TYR* 3.6 0.7 - - - -
205A GLY 3.1 31.8 + - - +
218A HIS* 5.2 0.2 - - - -
220A ILE* 3.8 10.6 - - - +
238A PHE* 3.8 12.7 - - - +
239A ARG 3.9 5.7 + - - -
240A CYS* 3.9 18.5 - - - +
254A TYR* 1.3 79.6 - - - +
256A ALA* 1.4 63.1 + - - +
357A GLN* 2.7 29.2 + - - -
405A TYR* 4.4 1.1 - - - -
437A PHE* 3.6 9.5 - - - -
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Residues in contact with ALA 256 (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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202A PHE* 3.7 10.3 - - + -
203A ILE 3.2 13.7 - - - +
204A TYR* 3.6 6.7 - - + -
238A PHE* 4.4 4.9 - - - -
254A TYR* 3.4 23.3 - - + +
255A SER* 1.4 78.4 + - - +
257A GLY* 1.3 59.6 + - - +
355A TYR* 4.3 1.6 - - - -
405A TYR* 3.3 28.4 + - - +
437A PHE* 3.1 25.0 - - - -
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Residues in contact with GLY 257 (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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202A PHE* 3.4 7.7 - - - -
203A ILE* 2.8 38.3 + - - +
238A PHE* 3.4 25.6 - - - -
256A ALA* 1.3 75.7 - - - +
258A ILE* 1.3 61.5 + - - -
307A GLN* 3.9 3.8 - - - -
355A TYR* 4.3 9.2 - - - -
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Residues in contact with ILE 258 (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 TYR* 4.5 4.3 - - + -
201A PHE 3.3 10.5 - - - +
202A PHE* 4.1 19.1 - - + -
238A PHE* 3.4 6.9 - - - -
257A GLY* 1.3 77.5 - - - +
259A ALA* 1.3 67.2 + - - +
292A LEU* 4.0 24.7 - - + -
305A CYS* 4.3 10.8 - - + -
306A LEU 6.0 0.2 - - - +
307A GLN* 2.9 32.5 + - - +
331A PHE* 3.4 29.7 - - + -
355A TYR* 3.5 25.8 - - + +
440A ALA 5.1 0.7 - - - +
441A LEU* 4.2 24.9 - - + -
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Residues in contact with ALA 259 (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 TYR* 4.5 1.6 - - - -
201A PHE* 2.9 31.2 + - - +
203A ILE* 3.8 18.1 - - + +
237A LEU* 3.9 29.8 - - + -
238A PHE* 4.7 2.5 - - + -
258A ILE* 1.3 79.6 - - - +
260A LYS* 1.4 63.1 + - - +
261A LEU* 3.7 10.4 + - + +
331A PHE* 5.4 3.1 - - - -
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Residues in contact with LYS 260 (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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198A THR* 3.5 20.0 - - - +
199A GLY* 3.4 14.4 - - - +
200A TYR* 3.8 47.3 - - + +
222A ARG* 3.9 17.2 + - - -
259A ALA* 1.4 69.8 - - - +
261A LEU* 1.3 69.5 + - - +
262A GLU* 3.4 24.4 + - - +
331A PHE* 5.9 1.4 - - - -
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Residues in contact with LEU 261 (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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186A LEU* 5.9 0.2 - - + -
195A VAL* 3.8 25.1 - - + -
198A THR* 3.4 6.6 - - - +
199A GLY 2.8 31.7 + - - +
201A PHE* 3.8 28.3 - - + -
203A ILE* 4.1 8.5 - - + -
222A ARG* 3.7 30.3 - - + +
237A LEU* 4.3 1.3 - - + -
259A ALA* 4.0 16.8 - - + +
260A LYS* 1.3 84.8 - - - +
262A GLU* 1.3 61.8 + - - +
265A ASP* 4.0 4.7 - - + +
267A LEU* 3.6 36.8 - - + -
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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