Contacts of the strand formed by residues 339 - 347 (chain A) in PDB entry 3GVJ
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 VAL 339 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335A VAL* 3.4 5.2 - - - -
336A TYR 3.0 31.4 + - - +
337A GLU* 3.1 11.0 - - + +
338A ASN* 1.3 80.6 - - - +
340A ILE* 1.3 67.6 + - - +
341A TYR* 3.4 34.0 - - + +
361A LYS* 4.0 17.0 - - + -
362A SER 3.7 13.7 - - - +
363A GLY* 4.9 8.1 - - - -
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Residues in contact with ILE 340 (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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334A PHE 3.9 3.4 - - - +
335A VAL* 4.4 9.0 - - + -
338A ASN 4.9 0.9 - - - +
339A VAL* 1.3 74.9 - - - +
341A TYR* 1.3 64.0 - - - +
361A LYS* 3.2 6.1 - - - +
362A SER* 2.9 34.0 + - - +
365A ASP* 4.0 6.3 - - - -
366A GLY* 4.0 18.2 - - - +
369A TRP* 3.9 21.4 - - + -
708A VAL* 4.0 21.1 - - + -
710A LYS* 4.4 16.2 - - + -
715A TYR* 3.6 43.7 - - + +
717A MET* 4.2 10.8 - - + -
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Residues in contact with TYR 341 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A ALA* 3.3 18.7 - - - +
334A PHE* 3.0 57.9 + + + +
336A TYR* 4.1 14.7 + - + +
339A VAL* 3.4 40.3 - - + +
340A ILE* 1.3 75.0 - - - +
342A ALA* 1.3 59.4 + - - +
343A PRO* 3.3 12.8 - - + +
359A TRP* 3.7 31.2 - + + -
360A VAL 3.9 3.1 - - - -
361A LYS* 3.5 30.8 + - + +
423A MET* 4.0 14.1 - - + +
717A MET* 4.2 2.1 - - - +
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Residues in contact with ALA 342 (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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319A ILE* 4.0 14.8 - - + -
329A PRO* 6.0 0.9 - - + -
333A ALA* 4.5 1.6 - - - -
340A ILE 4.1 0.6 + - - -
341A TYR* 1.3 72.8 - - - +
343A PRO* 1.3 66.3 - - - +
344A TYR* 3.5 6.8 - - - -
359A TRP* 3.5 2.6 - - - +
360A VAL* 2.9 35.5 + - + +
369A TRP* 3.9 12.1 - - + -
717A MET* 3.7 28.0 - - + -
747A LEU* 4.5 4.4 - - + +
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Residues in contact with PRO 343 (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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329A PRO* 3.2 25.5 - - - +
332A LYS* 3.5 32.1 - - + +
333A ALA* 3.6 16.4 - - + -
334A PHE* 4.2 5.4 - - + -
341A TYR* 3.3 12.3 - - + +
342A ALA* 1.3 87.5 - - - +
344A TYR* 1.3 61.5 + - - +
357A VAL* 5.6 0.7 - - + -
358A SER 3.2 13.2 - - - +
359A TRP* 3.6 17.0 - - + -
392A MET* 3.7 24.9 - - + -
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Residues in contact with TYR 344 (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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320A THR* 4.2 17.4 - - + +
322A THR* 5.0 1.7 + - - +
326A ASN* 3.4 37.6 + - + -
327A ALA 3.5 11.0 - - - +
328A TRP 3.5 10.3 - - - +
329A PRO 4.2 1.8 - - - -
332A LYS* 3.7 3.6 - - - +
342A ALA 3.5 13.2 - - - -
343A PRO* 1.3 76.5 - - - +
345A MET* 1.3 86.7 + - - +
346A GLY* 4.1 4.5 - - - -
357A VAL* 3.7 4.7 - - - +
358A SER* 2.9 51.8 + - - +
359A TRP* 3.8 15.7 - - - -
360A VAL* 4.0 2.5 - - + -
372A PRO* 3.5 29.5 - - - +
747A LEU* 3.7 22.0 - - + -
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Residues in contact with MET 345 (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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325A TYR 3.4 3.5 - - - +
327A ALA 3.1 28.3 + - - +
328A TRP* 3.5 43.2 + - + -
332A LYS* 4.4 0.4 - - - +
344A TYR* 1.3 85.4 - - - +
346A GLY* 1.3 59.3 + - - +
347A SER 3.9 0.2 - - - -
355A LEU* 3.3 29.4 - - + -
356A HIS 3.8 1.3 - - - -
357A VAL* 4.2 13.5 - - + -
388A HIS* 3.5 32.3 - - + +
389A CYS 3.4 40.6 - - - +
390A MET* 3.9 7.6 - - + -
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Residues in contact with GLY 346 (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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324A TYR* 4.3 10.7 - - - -
325A TYR 3.4 6.7 - - - -
326A ASN* 3.7 16.6 - - - -
344A TYR* 3.9 6.3 - - - -
345A MET* 1.3 69.7 - - - +
347A SER* 1.3 59.9 + - - -
354A ARG 3.5 3.6 - - - +
355A LEU* 3.0 14.6 - - - +
356A HIS* 3.1 26.5 + - - +
358A SER* 4.2 2.4 + - - -
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Residues in contact with SER 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A TYR* 3.6 14.0 - - - -
325A TYR* 2.7 30.0 + - - -
328A TRP* 3.6 13.5 - - - -
345A MET 3.9 0.2 - - - -
346A GLY* 1.3 74.9 - - - -
348A ASP* 1.3 57.9 + - - +
349A ARG 2.8 24.1 + - - -
351A GLY 3.8 12.6 - - - -
353A SER 3.5 16.2 - - - -
354A ARG* 4.0 3.4 - - - -
355A LEU* 3.6 18.4 - - - +
743A HIS* 4.4 0.2 + - - -
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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