Contacts of the strand formed by residues 351 - 356 (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 TYR 351 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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312A GLN* 4.2 29.4 - - + +
314A PHE* 3.7 38.6 - + + -
348A GLU* 5.7 0.7 - - - -
349A LYS* 3.5 36.4 - - + +
350A TYR* 1.3 77.7 - - - +
352A SER* 1.3 65.9 + - - +
353A SER* 3.0 11.4 + - - +
370A CYS 3.6 1.0 - - - +
371A ASP* 3.7 4.3 - - - -
372A LEU 2.9 23.5 + - - +
374A GLU* 4.0 35.6 + - + -
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Residues in contact with SER 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A GLU* 5.8 1.3 - - - -
312A GLN 4.6 3.4 + - - -
313A THR* 3.3 26.9 - - - +
314A PHE 2.9 22.9 + - - -
351A TYR* 1.3 71.7 - - - +
353A SER* 1.3 62.4 + - - +
369A ARG* 3.6 27.2 - - - +
370A CYS 3.8 5.4 - - - -
371A ASP* 5.0 4.7 - - - +
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Residues in contact with SER 353 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE* 3.1 15.5 - - - +
316A TYR* 3.8 23.0 + - - -
351A TYR* 3.0 15.6 + - - +
352A SER* 1.3 77.6 + - - +
354A SER* 1.3 61.2 + - - +
368A GLU 4.6 0.2 - - - -
369A ARG* 3.3 6.3 - - - -
370A CYS* 2.9 40.9 + - - -
372A LEU* 3.8 24.5 + - - +
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Residues in contact with SER 354 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A PHE 2.9 6.2 + - - -
315A MET* 3.2 15.8 - - - +
316A TYR* 2.9 27.9 + - - -
353A SER* 1.3 72.8 - - - +
355A ILE* 1.3 68.6 + - - +
356A TRP* 3.1 25.6 + - - -
365A ARG* 5.4 0.4 - - - -
367A VAL 3.4 7.9 - - - -
368A GLU* 3.3 23.1 - - - -
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Residues in contact with ILE 355 (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* 3.5 7.6 - - + +
318A VAL* 3.9 34.5 - - + -
338A PRO* 3.7 26.2 - - + -
354A SER* 1.3 79.1 - - - +
356A TRP* 1.3 66.9 + - - +
365A ARG* 3.8 1.2 - - - +
366A ILE* 2.9 30.9 + - + -
367A VAL* 3.0 33.2 + - + +
370A CYS* 4.4 1.8 - - - -
372A LEU* 4.2 13.7 - - + -
381A MET* 3.6 32.1 - - + -
383A PHE* 4.3 6.5 - - + -
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Residues in contact with TRP 356 (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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315A MET* 3.3 29.3 - - + +
316A TYR 2.9 11.5 + - - +
317A TYR* 3.5 28.8 - + + -
318A VAL* 2.9 30.8 + - - +
354A SER* 3.1 27.9 + - - -
355A ILE* 1.3 81.7 - - - +
357A GLY* 1.3 61.3 + - - +
360A CYS* 6.2 2.5 - - - -
361A ASP 4.4 8.3 - - - -
362A GLY* 4.2 19.3 - - - -
364A ASP 3.3 24.9 - - - +
365A ARG* 3.6 39.9 - - + -
366A ILE* 3.9 5.8 - - - +
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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