Contacts of the strand formed by residues 507 - 515 (chain B) in PDB entry 5VXZ
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 507 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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492B TYR* 3.7 28.7 - - + -
505B TRP* 4.2 6.5 - - + -
506B GLU* 1.3 81.2 - - - +
508B GLU* 1.3 61.9 + - - +
509B VAL* 4.0 19.7 - - + -
523B PHE* 4.2 3.6 - - + -
525B LEU* 4.9 3.6 - - + -
535B LEU* 3.9 29.8 - - + -
579B VAL 3.8 1.0 - - - +
580B SER* 3.5 2.6 - - - -
581B LEU* 2.8 44.9 + - + +
611B LEU* 4.9 1.1 - - + -
615B LEU* 4.1 20.9 - - + -
649B ASN* 3.5 3.1 - - - +
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Residues in contact with GLU 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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506B GLU* 4.2 10.5 - - - +
507B VAL* 1.3 72.7 - - - +
509B VAL* 1.3 63.6 + - - +
510B VAL* 5.5 5.0 - - + +
578B THR* 5.9 1.6 - - - -
579B VAL 3.3 4.1 - - - +
580B SER* 2.4 33.1 + - - -
582B ARG* 2.1 39.7 + - - +
647B GLU 3.7 0.3 - - - +
648B VAL* 3.3 4.9 - - - +
649B ASN* 2.7 50.9 + - - +
650B ARG* 4.7 11.4 + - + +
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Residues in contact with VAL 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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507B VAL* 4.0 10.3 - - + -
508B GLU* 1.3 81.5 + - - +
510B VAL* 1.3 68.8 + - - +
511B ALA* 4.2 4.9 - - + +
523B PHE* 3.7 47.3 - - + -
537B VAL* 5.6 3.1 - - + -
577B VAL 5.3 0.9 - - - +
578B THR* 3.3 5.2 - - - -
579B VAL* 3.0 45.4 + - + +
646B LEU* 4.0 26.2 - - + -
647B GLU 3.3 6.1 - - - +
648B VAL* 4.5 4.0 - - + -
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Residues in contact with VAL 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B GLU* 5.5 5.2 - - + +
509B VAL* 1.3 80.6 - - - +
511B ALA* 1.3 60.3 + - - +
512B HIS* 3.9 27.5 + - + +
576B VAL* 4.1 15.7 - - + -
577B VAL 3.5 2.2 - - - -
578B THR* 4.2 13.2 - - + +
645B THR* 3.5 3.1 - - - +
646B LEU* 3.6 0.5 - - - -
647B GLU* 2.8 65.5 + - + +
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Residues in contact with ALA 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B VAL* 4.7 5.2 - - + -
510B VAL* 1.3 74.3 - - - +
512B HIS* 1.3 61.9 + - - +
513B ILE* 3.8 13.6 + - + +
522B LEU* 5.1 6.3 - - + -
523B PHE* 6.4 0.2 - - + -
575B HIS 3.5 2.3 - - - +
576B VAL* 3.5 2.7 - - - -
577B VAL* 2.7 53.2 + - + +
644B MET* 4.7 3.6 - - - -
645B THR 3.2 5.2 - - - +
646B LEU* 3.9 18.8 - - + -
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Residues in contact with HIS 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B VAL* 3.9 26.0 + - + +
511B ALA* 1.3 72.1 - - - +
513B ILE* 1.3 58.8 + - - +
574B GLU* 3.9 29.8 - - - +
575B HIS 3.5 5.2 - - - -
576B VAL* 3.7 27.6 - - + +
643B CYS* 4.4 0.9 - - - -
644B MET* 3.2 4.5 - - - -
645B THR* 2.9 50.9 + - + +
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Residues in contact with ILE 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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511B ALA* 4.3 11.2 - - + +
512B HIS* 1.3 78.1 - - - +
514B ARG* 1.3 61.0 + - - +
515B PRO* 3.9 15.8 - - + +
522B LEU* 4.2 19.7 - - + -
539B LEU* 4.3 7.2 - - + -
567B ILE* 4.0 18.6 - - + -
573B GLN 3.9 0.9 - - - +
574B GLU* 3.2 7.5 - - - +
575B HIS* 2.8 48.4 + - + +
577B VAL* 3.9 21.3 - - + -
640B TYR* 3.5 13.0 - - - +
643B CYS 3.3 3.8 - - - -
644B MET* 4.0 25.6 - - + -
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Residues in contact with ARG 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286B PHE* 3.3 21.9 - - + -
475B GLU* 3.2 27.8 + - - +
513B ILE* 1.3 74.4 - - - +
515B PRO* 1.3 67.2 - - - +
572B GLY* 3.2 27.4 + - - +
573B GLN* 3.9 11.5 - - - +
574B GLU* 3.8 42.3 + - + +
640B TYR* 3.4 1.8 - - - -
643B CYS* 2.9 40.7 + - + -
671B PRO 5.7 0.4 - - - -
673B VAL* 4.1 15.6 - - + +
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Residues in contact with PRO 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284B VAL* 3.8 17.7 - - - +
286B PHE* 4.1 1.9 - - - -
513B ILE* 3.7 17.5 - - + +
514B ARG* 1.3 93.0 - - - +
516B ALA* 1.3 60.5 + - - +
517B ALA 3.8 16.8 - - - +
539B LEU* 4.0 10.1 - - + -
569B VAL* 3.9 37.5 - - + +
572B GLY* 5.2 3.4 - - - -
573B GLN 4.1 8.5 - - - +
575B HIS* 4.7 6.1 - - + -
640B TYR* 3.3 21.1 - - + +
641B ARG 3.7 1.6 - - - +
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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