Contacts of the strand formed by residues 288 - 292 (chain A) in PDB entry 2VZ9
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 GLU 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A SER 3.1 3.8 + - - +
287A LEU* 1.3 74.3 - - - +
289A TYR* 1.3 59.4 - - - +
319A PRO 3.8 2.9 - - - +
320A LEU* 3.3 4.4 - - - -
321A LEU* 3.0 49.2 + - + +
353A TRP* 3.2 34.3 + - + -
383A ILE* 3.2 17.4 - - - +
384A ARG* 3.5 15.2 + - - -
385A GLY 2.9 46.1 + - - +
386A GLY* 4.2 1.3 - - - -
387A ASN 3.2 12.2 + - - +
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Residues in contact with TYR 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A LEU* 4.3 2.5 - - - +
288A GLU* 1.3 79.4 - - + +
290A ILE* 1.3 66.3 + - - +
291A GLU* 3.1 34.7 - - + +
320A LEU* 4.6 1.3 - - - -
321A LEU* 3.3 14.1 - - + -
323A GLY* 2.8 37.7 - - - -
343A LYS* 2.9 26.3 + - - -
344A VAL* 5.4 2.2 - - + -
353A TRP* 3.4 58.6 - + + -
354A ALA 5.2 1.5 + - - -
377A VAL* 3.9 18.4 - - + -
387A ASN 4.1 0.9 - - - +
388A VAL* 3.1 18.2 - - + +
389A GLY 3.1 21.1 + - - -
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273A ILE* 4.5 2.2 - - + -
287A LEU* 5.4 3.8 - - + -
289A TYR* 1.3 82.8 - - - +
291A GLU* 1.3 65.7 + - - +
292A ALA 5.0 0.2 - - - +
308A ILE* 3.5 38.1 - - + -
312A LEU* 4.0 16.2 - - + -
320A LEU* 3.1 31.4 - - + +
321A LEU 3.3 3.2 + - - +
322A ILE* 3.3 35.4 - - + +
323A GLY 3.7 0.2 + - - -
389A GLY* 3.7 7.9 - - - +
391A ASN* 4.2 9.4 - - - +
401A HIS* 4.2 21.1 - - + -
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Residues in contact with GLU 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A TYR* 3.1 27.8 - - + +
290A ILE* 1.3 71.6 - - - +
292A ALA* 1.3 87.2 + - - +
323A GLY 3.9 0.9 - - - +
324A SER* 3.1 4.5 + - - -
325A THR* 2.5 46.6 + - - -
326A LYS* 4.6 2.3 + - - -
340A ALA* 3.6 21.4 - - - +
343A LYS* 3.6 6.6 + - - +
344A VAL* 4.1 19.7 - - + -
389A GLY 3.1 15.5 + - - +
390A ILE* 3.6 5.0 - - + +
391A ASN* 3.1 25.8 + - - +
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Residues in contact with ALA 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A PHE* 4.1 18.8 - - + -
290A ILE* 3.5 4.0 + - - -
291A GLU* 1.3 93.0 - - - +
293A HIS* 1.3 65.8 + - - +
294A GLY 3.7 9.0 - - - +
304A GLU* 3.4 16.2 - - - +
305A LEU* 4.3 10.5 - - + -
308A ILE* 4.7 2.5 - - + -
322A ILE* 4.4 4.5 - - + -
323A GLY 3.1 18.0 + - - +
324A SER* 4.2 1.0 + - - -
326A LYS* 4.4 1.9 + - - -
391A ASN* 4.2 11.5 - - - +
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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
------------------------------------------------------------
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