Contacts of the strand formed by residues 668 - 677 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607C GLU* 2.8 35.6 - - - +
622C ILE* 4.5 0.2 - - - +
540D VAL* 3.2 25.3 - - + +
541D GLY* 6.0 4.0 - - - -
592D GLU* 2.5 35.7 - - - +
640F ALA* 3.6 6.6 - - - +
641F LEU* 3.0 42.4 + - + +
667F ALA* 1.3 73.7 - - - +
669F TYR* 1.3 61.8 + - - +
689F PHE 3.4 3.6 - - - -
690F ARG* 3.8 26.5 + - - +
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Residues in contact with TYR 669 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638F TYR* 4.1 18.6 - + + -
639F ARG 3.2 20.2 - - - +
640F ALA* 3.5 22.6 - - + +
641F LEU* 4.1 4.0 - - - +
646F LYS* 5.3 1.6 - - - -
663F LEU* 3.8 28.2 - - + +
664F ASP* 2.8 39.5 + - - +
667F ALA* 3.7 25.8 - - + -
668F GLU* 1.3 75.9 - - - +
670F GLU* 1.3 63.1 + - - +
688F VAL* 3.2 11.3 - - - +
689F PHE* 2.7 65.0 + + + -
691F THR* 4.0 5.8 - - + -
1699F SO4 5.0 5.4 + - - -
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Residues in contact with GLU 670 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638F TYR* 3.2 3.6 - - - -
639F ARG* 2.7 74.8 + - - +
641F LEU* 4.1 12.8 - - + -
645F TRP* 3.3 12.0 - - + -
669F TYR* 1.3 77.1 - - - +
671F VAL* 1.3 74.0 + - - +
686F HIS* 3.0 35.1 - - - +
687F PHE 3.2 10.5 - - - +
688F VAL* 4.1 15.1 - - + +
689F PHE* 4.8 0.2 - - - -
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Residues in contact with VAL 671 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606F LEU* 4.7 3.6 - - + -
619F VAL* 4.3 22.0 - - + -
636F VAL* 4.4 9.6 - - + -
637F ARG 3.5 7.9 - - - +
638F TYR* 4.2 2.7 - - + +
658F VAL* 5.0 2.0 - - + -
660F LEU* 3.7 22.0 - - + -
670F GLU* 1.3 80.9 - - - +
672F TYR* 1.3 67.8 + - - +
673F VAL* 4.0 19.7 - - + -
685F ALA 4.5 0.7 - - - -
686F HIS* 3.4 6.8 - - - +
687F PHE* 2.7 40.9 + - + +
689F PHE* 3.5 28.5 - - + -
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Residues in contact with TYR 672 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635F LEU* 4.0 8.9 - - + +
636F VAL* 3.2 5.7 - - - +
637F ARG* 2.6 92.2 + - + +
645F TRP* 3.3 33.0 - + + -
648F GLU* 4.4 5.2 + - - -
671F VAL* 1.3 76.1 - - - +
673F VAL* 1.3 65.0 + - - +
674F VAL* 3.4 28.7 - - + +
681F LYS* 5.3 7.3 + - - +
684F ALA* 3.3 25.1 - - + +
685F ALA 3.5 4.9 - - - -
686F HIS* 4.2 7.4 - - + +
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Residues in contact with VAL 673 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604F PRO* 3.9 24.0 - - + +
606F LEU* 3.5 34.3 - - + -
619F VAL* 5.1 2.5 - - + -
621F LEU* 4.1 14.8 - - + -
634F TYR* 4.2 14.6 - - + -
635F LEU 3.3 6.5 - - - +
636F VAL* 4.4 17.0 - - + -
658F VAL* 5.2 2.0 - - + -
671F VAL* 4.0 11.4 - - + -
672F TYR* 1.3 82.6 - - - +
674F VAL* 1.3 64.7 + - - +
683F LYS 4.3 1.2 - - - +
684F ALA* 3.6 1.7 - - - -
685F ALA* 2.9 33.5 + - - +
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Residues in contact with VAL 674 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604F PRO* 4.8 0.4 - - - -
634F TYR* 3.2 6.9 - - - -
635F LEU* 2.7 59.9 + - + -
672F TYR* 3.4 35.7 - - + +
673F VAL* 1.3 80.7 - - - +
675F ALA* 1.3 67.3 + - - +
676F GLU 4.0 0.2 + - - -
681F LYS* 3.5 33.2 - - + -
682F SER* 3.9 10.1 - - - +
684F ALA* 3.7 19.5 - - + +
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Residues in contact with ALA 675 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601F PRO* 3.8 15.3 - - + +
602F SER 3.6 23.6 - - - +
604F PRO* 4.1 5.7 - - + +
631F ILE* 3.8 16.2 - - + -
633F HIS 3.8 3.1 - - - -
634F TYR* 4.0 13.9 - - + -
674F VAL* 1.3 75.5 - - - +
676F GLU* 1.3 59.0 + - - +
681F LYS* 3.4 2.8 - - - -
682F SER* 2.9 33.5 + - - +
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Residues in contact with GLU 676 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601F PRO* 4.1 1.8 - - - -
631F ILE* 3.6 4.2 - - - +
632F ARG* 2.7 32.6 + - + -
633F HIS* 2.8 50.6 + - - +
635F LEU* 4.3 22.8 - - + +
650F ARG* 5.8 0.5 - - - -
675F ALA* 1.3 75.1 - - - +
677F ASN* 1.3 65.0 - - - +
680F GLY* 3.4 12.1 - - - +
681F LYS* 4.1 21.6 - - + +
1700F SO4 4.1 8.6 + - - -
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Residues in contact with ASN 677 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599F ARG 3.0 19.2 + - - -
601F PRO* 3.2 13.4 - - + +
626F ASP 2.9 25.3 + - - -
629F SER* 3.6 17.6 - - - +
630F PRO 3.1 25.1 - - - +
631F ILE* 4.2 0.7 - - - -
632F ARG* 4.0 9.9 - - - +
676F GLU* 1.3 80.9 - - - +
678F GLN* 1.3 65.6 + - - +
679F GLN* 2.9 17.0 + - - +
680F GLY* 2.9 33.5 + - - +
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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