Contacts of the strand formed by residues 357 - 363 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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315A TYR* 3.7 35.2 - - + -
334A CYS* 3.3 9.2 - - + +
336A THR* 3.8 23.6 - - + -
341A LEU* 3.8 35.4 - - + +
345A THR* 4.4 6.7 - - + +
346A LEU* 3.5 28.3 - - + +
349A TRP* 3.4 41.3 - - + +
355A LEU 4.1 0.4 + - - -
356A ASP* 1.3 71.2 - - - +
358A ARG* 1.3 64.3 + - - +
359A GLU 3.6 2.3 + - - -
378A ILE* 3.6 9.4 - - - +
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Residues in contact with ARG 358 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248A TRP* 4.2 3.4 + - - -
249A THR* 2.8 36.6 + - - +
250A GLY 4.1 0.2 - - - +
332A GLN 4.7 3.2 + - - -
333A ASN* 4.0 24.2 + - - +
334A CYS 2.9 14.2 + - - +
335A VAL* 3.3 23.8 - - + +
336A THR 3.2 20.4 + - - -
356A ASP* 4.5 12.1 + - + +
357A ILE* 1.3 73.0 - - - +
359A GLU* 1.3 61.5 + - - +
372A VAL* 3.5 28.3 + - + +
373A SER 3.4 18.1 - - - -
374A LYS* 3.6 32.4 - - - +
376A MET 5.1 1.3 - - - -
378A ILE* 3.5 23.6 - - + -
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Residues in contact with GLU 359 (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 THR* 3.7 18.4 - - + +
339A GLU 5.0 0.2 - - - +
340A SER* 3.7 2.3 + - - -
341A LEU* 3.2 46.0 + - + +
357A ILE 3.6 4.2 + - - -
358A ARG* 1.3 75.5 - - - +
360A SER* 1.3 72.1 + - - +
371A MET* 3.7 0.9 - - - +
372A VAL* 3.0 33.7 + - + +
381A GLY* 4.7 2.4 + - - -
382A TYR 3.3 24.4 + - - +
383A MET* 3.4 24.3 - - + +
458A PHE* 6.0 0.5 - - - +
1570A AMP 2.9 24.0 + - - +
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Residues in contact with SER 360 (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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248A TRP* 3.3 32.9 - - - -
309A MET* 3.9 1.7 - - - +
336A THR 2.7 25.6 + - - +
337A VAL* 3.4 22.5 - - - +
359A GLU* 1.3 76.5 - - - +
361A TYR* 1.3 61.1 + - - +
368A LEU* 4.4 7.5 - - - +
370A CYS 3.4 6.5 - - - -
371A MET* 3.6 12.3 - - - +
383A MET 4.1 2.0 - - - -
1570A AMP 3.0 18.9 + - - -
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Residues in contact with TYR 361 (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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337A VAL* 4.1 4.2 - - - +
360A SER* 1.3 76.8 - - - +
362A GLY* 1.3 61.9 + - - +
368A LEU* 3.9 3.9 - - - +
369A THR* 2.8 33.3 + - + -
370A CYS* 2.8 27.3 + - + +
383A MET* 3.4 47.8 - - + -
410A ILE* 3.9 21.4 - - + +
444A LEU* 3.3 38.5 - - + +
446A ASP* 2.5 40.9 + - + +
458A PHE* 4.8 1.1 - + - -
1570A AMP 3.5 32.5 - + - +
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Residues in contact with GLY 362 (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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337A VAL* 4.3 6.6 - - - +
361A TYR* 1.3 83.1 - - - +
363A GLN* 1.3 65.0 + - - +
367A GLY 3.3 15.9 - - - -
368A LEU* 4.8 0.4 - - - -
369A THR* 3.7 8.7 - - - -
444A LEU* 4.8 2.2 - - - -
1570A AMP 3.3 31.8 + - - +
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Residues in contact with GLN 363 (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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266A ILE* 4.9 3.4 - - - +
362A GLY* 1.3 76.4 - - - +
364A THR* 1.3 61.8 + - - +
365A GLU* 3.2 25.1 + - - +
366A THR* 3.0 18.5 + - - +
367A GLY* 2.8 28.7 + - - -
442A TRP* 3.1 27.5 + - - -
443A LEU 4.4 0.3 - - - +
444A LEU* 2.8 43.3 + - + +
461A ARG* 4.1 1.6 - - - +
472A ARG* 4.0 6.4 - - - +
1570A AMP 3.2 36.4 + - - +
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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