Contacts of the strand formed by residues 685 - 690 (chain E) in PDB entry 2VKX
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 ALA 685 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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603E ALA* 4.2 7.8 - - + +
604E PRO* 3.6 25.6 - - + +
605E LYS* 5.3 0.2 - - - -
606E LEU* 3.7 24.8 - - + +
671E VAL 3.6 0.5 - - - +
672E TYR* 3.2 7.5 - - - -
673E VAL 3.0 35.2 + - - +
683E LYS 3.8 1.6 + - - -
684E ALA* 1.3 73.3 - - - +
686E HIS* 1.3 60.1 + - - +
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Residues in contact with HIS 686 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605B LYS* 4.8 11.9 + - - -
606E LEU* 4.1 4.9 - - - +
670E GLU* 2.9 44.5 + - + -
671E VAL 3.0 12.0 + - - -
672E TYR* 3.2 40.2 + + + -
684E ALA 3.8 3.7 + - - +
685E ALA* 1.3 75.6 - - - +
687E PHE* 1.3 64.7 + - - +
688E VAL* 3.6 21.9 - - + +
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Residues in contact with PHE 687 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687B PHE* 3.5 38.8 - + - -
688B VAL 3.6 16.4 - - - -
606E LEU* 3.8 33.4 - - + -
608E GLY* 3.2 27.4 - - - -
617E ILE* 3.6 27.4 - - + -
619E VAL* 4.6 12.6 - - + -
670E GLU* 3.1 2.6 - - - -
671E VAL* 2.7 44.0 + - + +
686E HIS* 1.3 79.7 - - - +
688E VAL* 1.3 63.9 + - - +
689E PHE* 4.2 20.3 + + + -
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Residues in contact with VAL 688 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B LYS* 4.4 13.7 - - - +
606B LEU 3.6 17.4 + - - +
607B GLU* 3.2 28.6 - - + +
608B GLY 3.0 20.8 + - - -
622B ILE* 4.8 5.8 - - + -
687B PHE* 3.8 8.4 - - - -
641E LEU* 4.4 14.1 - - + -
669E TYR 3.2 15.7 - - - +
670E GLU* 4.1 4.0 - - + -
686E HIS* 3.6 30.3 - - + +
687E PHE* 1.3 80.9 - - - +
689E PHE* 1.3 62.1 + - - +
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Residues in contact with PHE 689 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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607B GLU* 3.8 4.7 - - - -
608B GLY* 3.3 14.1 - - - +
687B PHE* 5.8 0.2 - - + -
616E SER 5.1 1.3 - - - -
617E ILE* 3.6 54.3 - - + -
660E LEU* 4.3 4.9 - - + -
663E LEU* 3.8 23.8 - - + -
668E GLU* 3.4 1.7 - - - +
669E TYR* 2.6 68.6 + + + +
671E VAL* 3.8 23.6 - - + -
687E PHE* 4.2 14.6 - + + -
688E VAL* 1.3 77.2 - - - +
690E ARG* 1.3 67.5 + - - +
691E THR* 4.0 12.6 - - + -
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Residues in contact with ARG 690 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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592A GLU* 5.3 2.8 + - - -
607B GLU* 3.2 25.9 + - - +
608B GLY 2.9 12.5 + - - +
609B GLN* 3.9 42.2 + - + +
610B ARG* 4.7 3.1 + - - +
620B ASN* 4.4 2.4 + - - -
666E ASN* 3.0 34.6 + - - -
667E ALA 3.1 17.0 - - - +
668E GLU* 3.7 24.8 + - + -
689E PHE* 1.3 79.5 - - - +
691E THR* 1.3 71.2 + - - +
692E ALA 4.0 0.3 + - - -
1695E SO4 3.1 32.9 + - - -
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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