Contacts of the strand formed by residues 376 - 381 (chain A) in PDB entry 2V5Y
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 376 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A VAL* 5.4 0.9 - - + -
370A GLU* 3.5 12.6 - - - +
371A VAL* 3.8 21.5 - - + -
372A LYS* 4.0 4.5 - - - +
375A GLN* 1.3 88.3 - - - +
377A THR* 1.3 68.7 - - - +
378A ILE* 4.5 9.0 - - + -
424A HIS 4.1 0.2 - - - +
425A THR* 3.3 3.6 - - - -
426A ILE* 2.8 44.7 + - + +
429A LEU* 4.1 8.9 - - + +
435A VAL* 4.8 10.3 - - + -
437A VAL* 4.5 15.7 - - + -
455A VAL* 4.0 32.8 - - + -
457A THR* 4.6 11.0 - - + -
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Residues in contact with THR 377 (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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368A VAL* 3.8 2.9 - - - +
369A VAL* 3.0 39.1 + - + -
370A GLU* 3.0 29.3 + - - +
375A GLN* 4.7 2.6 + - - -
376A ILE* 1.3 74.5 - - - +
378A ILE* 1.3 76.8 + - - +
423A GLN* 4.3 17.5 - - + +
424A HIS 3.5 9.4 - - - +
425A THR* 3.0 29.2 + - - +
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Residues in contact with ILE 378 (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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366A LEU* 4.1 17.7 - - + -
367A GLU 3.4 14.4 - - - +
368A VAL* 4.6 9.2 - - + -
369A VAL* 3.8 3.1 - - - -
376A ILE* 4.5 19.5 - - + +
377A THR* 1.3 80.2 - - - +
379A ARG* 1.3 63.1 + - - +
380A TRP* 4.5 3.4 - - + -
397A VAL* 3.7 20.6 - - + -
423A GLN* 3.3 6.8 - - - +
424A HIS* 2.9 46.4 + - + +
426A ILE* 4.6 5.8 - - + -
437A VAL* 3.5 32.3 - - + -
439A LEU* 4.5 8.1 - - + -
453A LEU* 4.8 4.7 - - + -
455A VAL* 5.3 0.2 - - + -
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Residues in contact with ARG 379 (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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365A LYS* 4.1 9.0 - - - +
366A LEU* 3.2 5.9 - - - +
367A GLU* 3.0 65.8 + - + +
368A VAL 4.7 3.6 + - - -
369A VAL* 3.6 31.8 - - + +
378A ILE* 1.3 77.7 - - - +
380A TRP* 1.3 77.2 + - - +
421A HIS* 5.2 17.1 - - - +
422A PRO 3.2 17.9 - - - +
423A GLN* 4.3 7.2 - - + +
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Residues in contact with TRP 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A PRO* 3.9 15.0 - - + -
364A ARG 3.4 13.9 - - - +
365A LYS* 3.5 8.1 - - - +
366A LEU* 4.4 2.7 - - - -
378A ILE* 4.2 6.1 - - + -
379A ARG* 1.3 93.7 + - - +
381A GLU* 1.3 79.7 + - - +
382A PRO* 3.7 0.3 - - - +
383A PHE* 3.8 7.5 - + - -
395A LEU* 3.4 32.8 - - + +
414A SER* 3.9 18.4 - - - -
416A ASP* 4.9 5.1 + - + -
421A HIS* 4.6 2.4 - - - -
422A PRO* 3.2 51.1 + - + +
423A GLN 3.8 32.1 - - - -
424A HIS* 3.9 13.9 - - + -
439A LEU* 3.6 34.8 - - + -
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Residues in contact with GLU 381 (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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361A ARG* 3.3 23.6 + - - +
363A PRO* 4.4 3.1 - - - +
364A ARG* 2.7 51.2 + - + +
365A LYS* 4.2 18.6 - - + +
380A TRP* 1.3 85.3 - - - +
382A PRO* 1.4 80.5 - - + +
383A PHE* 3.5 5.7 - - - -
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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