Contacts of the strand formed by residues 502 - 511 (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 GLY 502 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A ARG* 3.5 16.0 - - - +
339A GLU* 4.4 4.5 - - - -
342A LEU* 5.3 5.4 - - - -
497A PRO* 3.5 7.4 - - - +
498A ASP* 2.9 33.0 + - - +
501A ARG* 1.3 75.2 - - - +
503A GLU* 1.3 60.4 + - - +
568A TRP* 4.4 4.4 - - - -
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Residues in contact with GLU 503 (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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339A GLU* 3.8 10.4 + - + +
458A PHE* 5.7 5.2 - - - -
461A ARG* 6.0 1.0 - - - +
465A ILE 4.7 1.6 - - - +
466A ILE* 3.9 1.3 - - + -
467A ASN* 2.9 50.0 + - - +
468A SER* 3.3 19.6 + - - -
469A SER* 3.9 4.0 + - - -
495A SER* 3.2 30.6 - - - -
496A SER 3.5 3.8 - - - +
501A ARG* 3.5 6.3 + - - +
502A GLY* 1.3 78.1 - - - +
504A VAL* 1.3 69.0 + - - +
568A TRP* 4.1 21.2 - - + -
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Residues in contact with VAL 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ILE* 4.4 4.7 - - - -
468A SER* 4.0 7.0 - - - +
495A SER* 3.5 5.0 - - - -
496A SER* 2.9 51.2 + - - +
498A ASP* 3.9 23.3 - - + +
501A ARG* 3.8 19.1 - - + -
503A GLU* 1.3 80.5 - - - +
505A VAL* 1.3 68.7 + - - +
542A ARG* 3.8 30.5 - - + +
543A LYS* 4.3 17.7 - - + -
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Residues in contact with VAL 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466A ILE* 3.8 12.6 - - + -
468A SER* 4.2 6.1 + - - +
473A ILE* 3.6 34.3 - - + -
478A VAL* 4.4 2.9 - - + -
493A VAL* 3.5 26.7 - - + -
494A ILE 3.7 3.6 - - - -
504A VAL* 1.3 74.8 - - - +
506A LYS* 1.3 62.3 + - - +
538A TYR 4.9 0.9 - - - +
539A LYS* 3.8 16.8 - - - +
540A TYR 3.5 11.9 + - - +
541A PRO* 3.6 18.6 - - + +
542A ARG* 3.0 28.0 + - - +
543A LYS* 3.4 6.2 + - - +
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Residues in contact with LYS 506 (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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492A ALA 3.9 0.7 - - - +
493A VAL* 3.3 3.9 - - - +
494A ILE* 2.8 42.6 + - + +
496A SER* 3.8 16.8 - - - -
504A VAL 3.6 0.4 + - - -
505A VAL* 1.3 77.7 - - - +
507A ALA* 1.3 65.5 + - - +
508A PHE* 3.6 25.5 - - + -
543A LYS* 3.3 25.3 - - + +
544A ILE 4.8 1.6 - - - -
545A GLU* 3.0 42.7 + - - +
567A GLU* 3.2 38.8 + - - +
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Residues in contact with ALA 507 (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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482A LEU* 3.5 32.5 - - + -
491A THR* 4.4 0.4 - - - +
492A ALA 3.6 4.0 - - - -
493A VAL* 4.2 5.4 - - + -
506A LYS* 1.3 76.4 - - - +
508A PHE* 1.3 61.5 + - - +
509A VAL* 4.3 5.6 - - + -
541A PRO* 3.7 16.3 - - + +
543A LYS 2.9 7.3 + - - +
544A ILE* 3.2 11.8 - - + +
545A GLU 2.9 24.4 + - - -
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Residues in contact with PHE 508 (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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491A THR* 2.9 18.9 + - - -
492A ALA 2.8 26.8 + - - +
494A ILE* 3.6 31.4 - - + -
506A LYS* 3.6 9.4 - - - -
507A ALA* 1.3 74.8 - - - +
509A VAL* 1.3 58.1 + - - +
545A GLU* 3.3 38.8 - - + +
547A VAL* 4.2 18.2 - - + -
550A LEU* 3.7 20.4 - - + +
563A LEU* 3.8 38.6 - - + -
566A LYS* 6.4 1.6 - - + -
567A GLU* 3.5 19.7 - - - -
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Residues in contact with VAL 509 (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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482A LEU* 4.4 7.4 - - + -
488A VAL* 4.2 24.0 - - + -
490A GLU 3.6 2.5 - - - -
491A THR* 3.6 17.3 - - - +
507A ALA* 4.3 8.5 - - + -
508A PHE* 1.3 77.2 - - - +
510A VAL* 1.3 75.4 + - - +
511A LEU* 3.9 11.8 + - + -
527A LEU* 4.7 6.7 - - + -
544A ILE* 4.1 15.3 - - + -
545A GLU 2.9 10.0 + - - +
546A PHE* 3.3 27.5 - - + +
547A VAL* 2.9 24.8 + - - +
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Residues in contact with VAL 510 (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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488A VAL* 3.8 3.5 - - - -
489A VAL* 3.0 46.3 + - + +
490A GLU* 2.8 35.6 + - + +
509A VAL* 1.3 73.0 - - - +
511A LEU* 1.3 66.1 + - - +
547A VAL* 3.4 15.9 - - + +
548A LEU* 3.6 18.8 - - - +
549A ASN* 4.0 18.8 - - - -
550A LEU* 4.1 16.6 - - + -
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Residues in contact with LEU 511 (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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487A ALA* 3.2 23.1 - - + +
489A VAL* 4.1 4.8 - - - +
509A VAL* 3.9 7.3 + - + -
510A VAL* 1.3 83.9 - - - +
512A ALA* 1.3 70.2 + - - +
513A SER* 3.6 2.1 + - - -
515A PHE* 3.8 26.7 - - + +
516A LEU* 4.4 24.8 - - + +
523A LEU* 3.6 25.6 - - + -
527A LEU* 5.0 1.3 - - + -
546A PHE* 3.6 45.1 - - + -
547A VAL 4.3 2.4 + - - -
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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