Contacts of the strand formed by residues 357 - 363 (chain B) in PDB entry 2VZE
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 ILE 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315B TYR* 3.5 44.4 - - + -
334B CYS* 3.3 9.4 - - + +
336B THR* 3.7 33.7 - - + -
341B LEU* 3.9 24.4 - - + +
345B THR* 4.5 5.4 - - + +
346B LEU* 3.8 24.0 + - + +
349B TRP* 3.5 39.3 - - + +
355B LEU 4.2 0.2 + - - -
356B ASP* 1.3 71.7 - - - +
358B ARG* 1.3 66.0 + - - +
359B GLU 3.6 2.8 + - - -
378B ILE* 3.9 9.4 - - - +
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Residues in contact with ARG 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B TRP* 4.5 1.1 + - - -
249B THR 2.8 32.9 + - - -
332B GLN 4.9 3.0 + - - -
333B ASN* 3.6 25.9 + - - +
334B CYS 2.9 13.9 + - - +
335B VAL* 3.3 23.6 - - + +
336B THR 3.1 20.5 + - - -
356B ASP* 4.6 11.7 + - + +
357B ILE* 1.3 71.7 - - - +
359B GLU* 1.3 63.8 + - - +
372B VAL* 3.4 36.7 + - + +
373B SER 3.6 11.9 - - - -
374B LYS* 3.7 33.2 + - - +
376B MET 5.0 0.9 - - - -
378B ILE* 3.7 24.0 - - + -
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Residues in contact with GLU 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B TRP* 4.9 0.5 - - - -
336B THR* 3.6 19.9 - - + +
339B GLU 3.7 0.4 - - - +
340B SER* 3.8 2.1 + - - -
341B LEU* 3.1 45.9 + - + +
357B ILE 3.6 4.2 + - - -
358B ARG* 1.3 74.7 - - - +
360B SER* 1.3 64.7 + - - +
371B MET* 3.9 0.3 - - - +
372B VAL* 3.0 32.3 + - + +
381B GLY 4.8 1.9 + - - -
382B TYR 3.5 21.2 + - - +
383B MET* 3.7 24.2 - - + +
1570B AMP 2.8 34.0 + - - +
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Residues in contact with SER 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B TRP* 3.4 32.1 - - - -
309B MET* 3.8 1.7 - - - +
336B THR 2.6 26.1 + - - +
337B VAL* 3.2 22.7 - - - +
359B GLU* 1.3 75.8 - - - +
361B TYR* 1.3 62.2 + - - +
368B LEU* 4.0 7.9 - - - +
370B CYS 3.4 6.5 - - - -
371B MET* 3.6 10.5 - - - -
383B MET 4.0 3.4 - - - -
1570B AMP 2.9 20.6 + - - -
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Residues in contact with TYR 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B VAL* 3.9 4.5 - - - -
360B SER* 1.3 76.8 - - - +
362B GLY* 1.3 68.6 + - - +
368B LEU* 3.9 4.1 - - - +
369B THR* 2.9 28.7 + - + -
370B CYS* 2.8 32.9 + - + +
383B MET* 3.6 47.1 - - + -
410B ILE* 3.9 18.9 - - + +
444B LEU* 3.0 34.7 - - + +
446B ASP* 2.5 40.1 + - + +
458B PHE* 5.0 0.7 - + - -
1570B AMP 3.7 35.4 - + - +
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Residues in contact with GLY 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337B VAL* 4.2 5.3 - - - +
361B TYR* 1.3 83.6 - - - +
363B GLN* 1.3 61.2 + - - +
367B GLY 3.3 16.2 - - - -
368B LEU* 4.9 0.4 - - - -
369B THR* 3.6 8.5 - - - -
444B LEU* 4.7 2.2 - - - -
1570B AMP 3.4 35.1 + - - +
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Residues in contact with GLN 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B ILE* 4.8 3.8 - - - +
362B GLY* 1.3 74.2 - - - +
364B THR* 1.3 59.6 + - - +
365B GLU* 3.1 26.2 + - - +
366B THR* 3.1 20.9 + - + +
367B GLY* 2.8 31.5 + - - -
436B ASN* 5.5 0.5 + - - -
442B TRP* 3.2 27.4 + - - -
443B LEU 4.4 0.2 - - - +
444B LEU* 2.7 41.9 + - + +
461B ARG* 4.1 2.4 - - - +
472B ARG* 4.1 6.8 - - - +
1570B AMP 3.3 36.1 + - - +
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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