Contacts of the strand formed by residues 365 - 372 (chain A) in PDB entry 4ZGY
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 ARG 365 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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322A VAL* 3.9 1.9 - - - +
329A ILE* 3.5 23.6 - - - +
354A SER* 5.5 0.7 - - - -
355A ILE 4.0 5.2 - - - +
356A TRP* 3.6 44.7 - - + -
362A GLY 5.1 1.8 - - - +
363A LEU 2.8 13.0 + - - +
364A ASP* 1.3 72.5 - - - +
366A ILE* 1.3 63.1 + - - +
367A VAL 4.1 8.5 - - - +
368A GLU* 3.6 56.7 + - - +
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Residues in contact with ILE 366 (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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318A VAL* 3.6 18.8 - - + -
320A ASP 3.2 26.7 - - - +
321A GLY* 4.0 12.3 - - - -
322A VAL* 4.9 2.5 - - + -
326A PHE* 3.8 33.4 - - + -
329A ILE* 3.3 22.4 - - + +
334A ALA 5.1 0.2 - - - +
335A HIS* 5.8 0.2 - - - -
336A VAL* 3.4 28.9 + - + +
355A ILE* 2.9 16.4 + - + +
356A TRP 3.9 7.0 - - - -
357A GLY 3.9 7.9 - - - +
364A ASP* 4.5 1.6 - - - +
365A ARG* 1.3 75.9 - - - +
367A VAL* 1.3 64.6 + - + +
383A PHE* 4.5 6.1 - - + -
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Residues in contact with VAL 367 (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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336A VAL* 3.6 30.3 - - + +
338A PRO* 4.1 8.7 - - + -
354A SER* 3.4 4.5 - - - -
355A ILE* 3.0 50.4 + - + +
365A ARG* 4.1 3.7 - - - +
366A ILE* 1.3 84.1 - - + +
368A GLU* 1.3 65.5 + - - +
369A ARG 3.9 9.6 - - - +
370A CYS* 3.7 34.8 - - + -
383A PHE* 4.3 4.5 - - + -
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Residues in contact with GLU 368 (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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335A HIS* 5.9 0.7 + - - -
353A SER 4.6 0.2 - - - -
354A SER* 3.3 17.9 - - - -
365A ARG* 3.6 52.4 + - - +
366A ILE 4.3 0.2 - - - -
367A VAL* 1.3 72.9 - - - +
369A ARG* 1.3 67.3 + - + +
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Residues in contact with ARG 369 (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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352A SER* 3.6 24.9 - - - +
353A SER 3.3 5.2 - - - -
367A VAL* 3.5 5.6 - - - +
368A GLU* 1.3 88.9 - - + +
370A CYS* 1.3 67.3 + - - +
371A ASP* 5.3 2.9 - - - +
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Residues in contact with CYS 370 (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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338A PRO* 3.9 19.3 - - + -
351A TYR 3.6 0.2 - - - +
352A SER* 3.8 0.7 - - - -
353A SER* 2.9 39.7 + - - -
355A ILE* 4.4 3.6 - - - -
367A VAL* 3.7 20.6 - - + -
369A ARG* 1.3 78.3 - - - +
371A ASP* 1.3 68.1 + - - +
372A LEU* 3.6 31.9 - - + -
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Residues in contact with ASP 371 (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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340A LEU* 5.5 0.9 - - - +
350A TYR* 4.3 32.8 - - + +
351A TYR 3.7 8.5 - - - -
352A SER* 5.1 4.0 - - - -
369A ARG* 5.3 4.0 - - - +
370A CYS* 1.3 78.9 - - - +
372A LEU* 1.3 69.6 + - - +
373A PRO* 4.7 0.5 - - - +
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Residues in contact with LEU 372 (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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316A TYR* 4.1 5.4 - - + -
338A PRO* 4.2 15.7 - - + +
340A LEU* 4.0 24.5 - - + -
350A TYR* 3.9 5.4 - - - -
351A TYR* 2.9 33.6 + - - +
353A SER* 3.8 18.6 + - - +
355A ILE* 4.2 15.0 - - + -
370A CYS* 3.6 29.4 + - + -
371A ASP* 1.3 82.2 - - - +
373A PRO* 1.3 78.5 - - + +
375A MET* 3.6 24.2 - - + -
381A MET* 4.4 2.2 - - - -
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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