Contacts of the strand formed by residues 488 - 498 (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 VAL 488 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482A LEU* 3.3 34.8 - - + +
483A MET* 3.9 22.4 - - - +
485A HIS* 3.6 11.2 - - + +
486A PRO* 3.2 3.4 - - - +
487A ALA* 1.3 79.6 - - - +
489A VAL* 1.3 63.4 + - - +
490A GLU 3.8 18.2 - - - +
491A THR* 3.8 18.8 - - + -
509A VAL* 4.2 17.0 - - + -
510A VAL 3.8 2.7 - - - -
527A LEU* 3.9 26.0 - - + -
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Residues in contact with VAL 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A MET* 3.4 19.3 - - - +
486A PRO 5.1 1.8 - - - +
488A VAL* 1.3 75.7 - - - +
490A GLU* 1.3 67.8 + - + +
510A VAL* 3.0 37.4 + - + +
511A LEU 4.1 3.1 - - - +
512A ALA* 3.5 34.5 - - + +
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Residues in contact with GLU 490 (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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483A MET* 4.0 6.3 - - + -
488A VAL* 3.5 3.4 - - - +
489A VAL* 1.3 87.0 - - + +
491A THR* 1.3 67.7 + - - +
509A VAL* 3.6 0.9 - - - -
510A VAL* 2.8 47.4 + - + +
549A ASN* 5.7 1.0 - - - -
550A LEU* 4.2 15.0 + - + +
552A LYS* 2.8 41.5 + - - -
558A ILE* 4.1 14.2 - - + +
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Residues in contact with THR 491 (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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479A GLU* 3.8 44.0 - - + +
482A LEU* 3.6 21.7 - - + +
483A MET* 3.9 16.5 - - + -
488A VAL* 3.8 12.6 - - + -
490A GLU* 1.3 81.3 - - - +
492A ALA* 1.3 65.5 + - - +
493A VAL* 4.6 0.2 - - - +
507A ALA* 4.4 0.3 - - - +
508A PHE 2.9 16.7 + - - -
509A VAL* 3.6 5.1 - - - +
550A LEU* 3.7 5.4 - - - -
558A ILE* 3.9 14.6 - - - +
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Residues in contact with ALA 492 (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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479A GLU* 3.5 6.7 - - - +
491A THR* 1.3 76.0 + - - +
493A VAL* 1.3 63.6 + - - +
494A ILE* 4.5 0.7 - - - -
507A ALA* 3.6 0.3 - - - -
508A PHE* 2.8 39.3 + - - +
550A LEU* 3.8 7.2 - - + +
558A ILE* 3.7 27.8 - - + -
560A ARG* 4.6 7.9 - - + +
563A LEU* 3.9 20.4 - - + -
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Residues in contact with VAL 493 (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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464A ASP* 5.1 1.4 - - - +
466A ILE* 3.3 23.9 - - + +
475A PRO* 3.6 22.9 - - + +
478A VAL* 3.5 35.9 - - + -
479A GLU* 2.9 26.4 + - + +
482A LEU* 4.0 15.5 - - + -
492A ALA* 1.3 72.3 - - - +
494A ILE* 1.3 73.8 + - - +
505A VAL* 3.5 20.0 - - + -
506A LYS 3.3 3.4 - - - +
507A ALA* 4.2 7.2 - - + -
560A ARG* 3.7 6.1 - - - -
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Residues in contact with ILE 494 (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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464A ASP 5.6 1.1 - - - -
466A ILE* 3.6 16.1 - - - +
492A ALA 4.5 3.4 - - - +
493A VAL* 1.3 84.8 - - - +
495A SER* 1.3 74.2 + - - +
505A VAL 3.7 0.3 - - - -
506A LYS* 2.8 40.0 + - + +
508A PHE* 3.6 29.4 - - + -
560A ARG* 4.0 33.4 - - + +
563A LEU* 3.8 9.4 - - + -
564A ARG* 3.6 33.4 - - + +
567A GLU* 3.9 12.6 - - + -
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Residues in contact with SER 495 (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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465A ILE 5.1 2.7 - - - -
466A ILE* 3.8 15.9 - - - +
494A ILE* 1.3 92.7 - - - +
496A SER* 1.3 61.3 + - - +
503A GLU* 3.2 30.2 + - - -
504A VAL 3.5 4.7 - - - -
564A ARG* 3.9 19.8 - - - +
567A GLU* 3.7 1.4 - - - +
568A TRP* 3.2 25.2 + - - -
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Residues in contact with SER 496 (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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495A SER* 1.3 77.8 - - - +
497A PRO* 1.3 70.2 + - - +
503A GLU* 3.5 1.4 - - - -
504A VAL* 2.9 43.8 + - - +
506A LYS* 3.8 17.3 - - - -
543A LYS* 2.6 33.2 + - - -
567A GLU* 3.2 20.6 + - - -
568A TRP* 4.0 4.7 - - - -
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Residues in contact with PRO 497 (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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496A SER* 1.3 88.1 - - - +
498A ASP* 1.3 58.9 + - - +
499A PRO* 4.7 1.3 - - - +
502A GLY 3.5 9.6 - - - +
543A LYS* 2.9 23.8 + - - +
567A GLU* 3.4 27.4 - - + +
568A TRP* 3.5 40.8 - - + +
569A LYS* 5.8 3.6 - - + +
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Residues in contact with ASP 498 (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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316A ARG* 4.9 0.5 + - - -
497A PRO* 1.3 75.0 - - - +
499A PRO* 1.3 72.2 - - - +
500A VAL* 2.9 13.5 + - - +
501A ARG* 2.7 36.4 + - - +
502A GLY* 2.9 34.9 + - - +
504A VAL* 3.9 28.4 - - + +
543A LYS* 4.6 10.0 - - - +
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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