Contacts of the strand formed by residues 668 - 677 (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 GLU 668 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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540A VAL* 3.1 41.6 - - + +
592A GLU* 3.0 22.7 - - - +
607B GLU* 2.3 39.5 - - - +
622B ILE* 4.7 0.7 - - - +
640E ALA* 3.3 7.6 - - - +
641E LEU* 2.9 34.5 + - + +
667E ALA* 1.3 75.0 - - - +
669E TYR* 1.3 60.7 + - - +
689E PHE 3.4 4.5 - - - -
690E ARG* 3.7 35.5 + - - +
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Residues in contact with TYR 669 (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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638E TYR* 4.4 12.8 - + + -
639E ARG* 3.1 28.5 - - - -
640E ALA* 3.3 20.9 - - + +
641E LEU* 4.3 3.1 - - - +
646E LYS* 5.4 6.4 - - - -
663E LEU* 3.4 33.5 - - + +
664E ASP* 2.9 39.2 + - - -
667E ALA* 3.8 25.4 - - + -
668E GLU* 1.3 77.0 - - - +
670E GLU* 1.3 61.8 + - - +
688E VAL* 3.2 12.1 - - - +
689E PHE* 2.6 58.6 + + + -
691E THR* 4.1 10.1 - - + -
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Residues in contact with GLU 670 (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* 5.0 3.1 + - - -
638E TYR* 3.2 21.8 - - - +
639E ARG* 2.7 56.8 + - + +
641E LEU* 3.4 24.8 - - + +
645E TRP* 3.8 6.1 - - + -
669E TYR* 1.3 78.2 - - - +
671E VAL* 1.3 63.6 + - - +
672E TYR* 3.8 12.4 + - + -
686E HIS* 2.9 34.5 + - + +
687E PHE 3.1 7.6 - - - +
688E VAL* 4.1 3.8 - - + +
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Residues in contact with VAL 671 (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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606E LEU* 4.6 1.3 - - + +
619E VAL* 4.7 13.2 - - + -
636E VAL* 3.5 25.4 - - + -
637E ARG 3.4 11.2 - - - +
638E TYR* 3.9 4.7 - - + -
658E VAL* 5.5 2.2 - - + -
660E LEU* 3.6 28.3 - - + -
670E GLU* 1.3 79.3 - - - +
672E TYR* 1.3 67.5 + - - +
673E VAL* 4.2 10.5 - - + -
685E ALA 3.6 0.6 - - - +
686E HIS* 3.0 8.3 + - - -
687E PHE* 2.7 44.2 + - + +
689E PHE* 3.8 16.6 - - + -
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Residues in contact with TYR 672 (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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635E LEU 3.4 1.6 - - - +
636E VAL* 3.3 5.0 - - - +
637E ARG* 2.7 54.2 + - + +
645E TRP* 3.1 38.8 - + - -
670E GLU* 3.8 9.1 + - - -
671E VAL* 1.3 72.9 - - - +
673E VAL* 1.3 63.2 + - - +
674E VAL* 5.7 0.7 - - + -
684E ALA* 3.7 26.7 - - + -
685E ALA 3.2 7.9 - - - -
686E HIS* 3.2 50.2 + + + -
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Residues in contact with VAL 673 (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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604E PRO* 4.0 13.7 - - + +
606E LEU* 3.6 34.3 - - + -
619E VAL* 5.3 1.8 - - + -
621E LEU* 3.8 24.5 - - + -
634E TYR* 4.4 12.3 - - + -
635E LEU 3.2 6.3 - - - +
636E VAL* 4.2 20.6 - - + -
658E VAL* 5.2 5.2 - - + -
671E VAL* 4.2 10.5 - - + -
672E TYR* 1.3 79.1 - - - +
674E VAL* 1.3 64.2 + - - +
683E LYS 4.3 1.0 - - - +
684E ALA* 3.6 1.0 - - - -
685E ALA* 3.0 31.9 + - - +
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Residues in contact with VAL 674 (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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604E PRO* 4.8 0.2 - - - -
633E HIS 4.0 0.3 - - - +
634E TYR* 3.3 6.7 - - - -
635E LEU* 2.6 52.3 + - + +
637E ARG* 5.8 4.7 - - - +
672E TYR* 5.7 0.9 - - + -
673E VAL* 1.3 74.4 - - - +
675E ALA* 1.3 75.9 + - - +
676E GLU* 4.9 0.2 - - + -
681E LYS* 3.8 26.5 - - + +
682E SER* 3.5 24.9 - - - +
684E ALA* 3.6 28.5 - - + +
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Residues in contact with ALA 675 (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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601E PRO* 4.0 11.9 - - + +
602E SER 3.6 23.6 - - - +
604E PRO* 4.1 7.2 - - + +
631E ILE* 4.1 8.1 - - + -
633E HIS 3.9 3.6 - - - -
634E TYR* 3.9 23.8 - - + -
674E VAL* 1.3 76.8 - - - +
676E GLU* 1.3 58.9 + - - +
681E LYS* 3.3 0.3 - - - -
682E SER* 2.7 36.7 + - - +
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Residues in contact with GLU 676 (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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601E PRO* 3.9 3.6 - - - +
631E ILE* 3.5 5.2 - - - +
632E ARG* 2.8 36.1 + - + +
633E HIS* 3.0 39.6 + - - +
635E LEU* 4.3 12.5 - - + +
674E VAL* 4.9 2.0 - - + +
675E ALA* 1.3 77.9 - - - +
677E ASN* 1.3 68.7 + - - +
680E GLY* 3.3 13.9 - - - +
681E LYS* 3.1 32.4 - - + +
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Residues in contact with ASN 677 (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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599E ARG 3.0 24.4 + - - -
601E PRO* 3.2 17.2 - - + +
626E ASP 3.1 20.0 + - - -
629E SER* 3.8 13.5 + - - +
630E PRO 3.1 23.3 - - - +
631E ILE* 4.2 0.4 - - - -
632E ARG* 4.0 9.1 - - - +
676E GLU* 1.3 79.3 - - - +
678E GLN* 1.3 57.7 + - - +
679E GLN* 2.6 40.0 + - - +
680E GLY* 2.7 28.6 + - - +
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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