Contacts of the strand formed by residues 512 - 516 (chain B) in PDB entry 2VGB
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 512 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B SER 5.6 0.7 - - - +
481B ALA* 4.1 13.5 - - + +
485B SER* 4.0 14.1 - - - -
493B VAL* 3.3 15.9 - - + +
495B ALA* 3.7 22.4 - - + -
506B VAL* 2.7 38.9 - - + +
507B HIS* 4.6 8.8 + - - -
509B CYS* 3.3 31.2 + - + +
511B GLY* 1.3 80.5 - - - +
513B PHE* 1.3 69.1 - - - +
514B PRO* 3.8 6.8 - - - +
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Residues in contact with PHE 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B ALA* 3.5 25.4 - - + -
86B ARG 3.5 26.9 - - - -
87B SER* 4.1 12.8 - - - -
492B ALA* 3.4 29.2 - - + -
493B VAL 2.8 12.4 + - - +
494B ILE* 3.4 11.4 - - + +
495B ALA 2.9 22.1 + - - -
507B HIS* 6.6 0.2 - + - -
511B GLY* 3.3 26.5 - - - -
512B VAL* 1.3 74.7 - - - +
514B PRO* 1.3 68.6 - - + +
515B LEU* 3.7 4.0 + - + +
543B ARG* 5.8 2.0 - - - +
545B PHE* 4.2 27.8 - + + -
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Residues in contact with PRO 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150B PRO* 4.0 20.1 - - + +
495B ALA* 3.4 11.9 - - + +
497B THR* 5.7 0.9 - - + -
503B ALA* 3.2 42.4 - - + +
506B VAL* 4.3 11.9 - - + -
507B HIS* 3.7 31.9 - - + +
512B VAL 3.8 6.5 - - - +
513B PHE* 1.3 83.3 - - + +
515B LEU* 1.3 71.6 + - - +
543B ARG* 4.8 2.3 + - - -
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Residues in contact with LEU 515 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PRO 6.1 0.2 - - - +
148B TYR 6.1 0.2 - - - -
150B PRO* 5.6 0.2 - - - -
494B ILE* 3.7 30.3 - - + -
495B ALA 2.7 12.4 + - - +
496B VAL* 3.6 4.8 - - + +
497B THR* 3.1 27.6 + - - +
513B PHE* 4.2 6.7 - - + +
514B PRO* 1.3 95.1 - - - +
516B LEU* 1.3 62.7 + - - +
517B TYR 3.7 0.2 + - - -
535B PHE* 3.9 15.7 - - + -
536B GLY* 4.1 9.6 - - - -
539B SER* 3.1 35.9 - - - +
540B GLY 4.9 0.4 - - - +
543B ARG* 3.4 39.3 - - - +
545B PHE* 5.6 2.9 - - + -
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Residues in contact with LEU 516 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145B PRO* 5.2 3.8 - - - +
148B TYR* 4.8 23.2 - - + +
150B PRO* 5.3 5.0 - - + +
497B THR* 3.2 17.9 - - + +
498B ARG* 3.5 24.2 - - - +
499B SER 4.0 2.2 - - - +
500B ALA* 3.7 33.7 - - + +
503B ALA* 4.6 9.5 - - + +
514B PRO 4.2 0.4 - - - -
515B LEU* 1.3 71.6 - - - +
517B TYR* 1.3 66.1 + - - +
518B ARG* 4.1 37.9 + - + +
535B PHE* 3.6 16.4 - - - -
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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