Contacts of the strand formed by residues 668 - 677 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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607A GLU* 2.5 40.6 - - - +
622A ILE* 4.8 0.2 - - - +
540B VAL* 3.6 22.3 - - + +
592B GLU* 2.5 33.3 - - - +
640D ALA* 3.4 6.1 - - - +
641D LEU* 2.8 41.0 + - + +
667D ALA* 1.3 73.2 - - - +
669D TYR* 1.3 62.3 + - - +
689D PHE 3.4 2.7 - - - -
690D ARG* 2.8 35.1 + - + +
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Residues in contact with TYR 669 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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638D TYR* 4.2 14.8 - + + -
639D ARG 3.1 26.5 - - - +
640D ALA* 3.5 17.7 - - + -
641D LEU* 4.3 3.6 - - - +
646D LYS* 5.1 8.1 - - - -
663D LEU* 3.2 31.0 - - + +
664D ASP* 2.6 44.5 + - + +
667D ALA* 3.8 25.4 - - + -
668D GLU* 1.3 77.0 - - - +
670D GLU* 1.3 63.5 + - - +
688D VAL* 3.3 10.5 - - - +
689D PHE* 2.9 62.0 + + + -
691D THR* 4.0 5.8 - - + -
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Residues in contact with GLU 670 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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605A LYS* 4.3 8.3 + - - -
637D ARG 4.2 0.3 - - - +
638D TYR* 3.4 3.7 - - - +
639D ARG* 2.7 65.7 + - + +
641D LEU* 3.4 26.9 - - + +
669D TYR* 1.3 77.5 - - - +
671D VAL* 1.3 63.5 + - - +
672D TYR* 3.6 14.6 + - + -
686D HIS* 2.9 34.7 + - + -
687D PHE 3.2 7.4 - - - +
688D VAL* 4.0 5.4 - - + -
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Residues in contact with VAL 671 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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606D LEU* 5.3 0.7 - - + -
619D VAL* 4.7 9.4 - - + -
636D VAL* 4.0 21.8 - - + -
637D ARG 3.7 1.8 - - - +
638D TYR* 3.9 15.0 - - + -
658D VAL* 5.4 1.8 - - + -
660D LEU* 3.9 15.5 - - + -
670D GLU* 1.3 78.7 - - - +
672D TYR* 1.3 66.2 + - - +
673D VAL* 4.3 12.3 - - + -
685D ALA 3.4 0.8 - - - +
686D HIS* 3.4 9.9 + - - -
687D PHE* 2.7 50.4 + - + +
689D PHE* 3.6 28.3 - - + -
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Residues in contact with TYR 672 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635D LEU 3.5 3.7 - - - +
636D VAL* 3.6 2.1 - - - -
637D ARG* 2.9 42.8 + - + +
639D ARG* 4.6 4.4 + - - -
645D TRP* 3.6 33.4 - + + -
670D GLU* 3.6 18.5 + - + -
671D VAL* 1.3 78.1 - - - +
673D VAL* 1.3 63.1 + - - +
674D VAL* 4.2 2.5 - - + -
684D ALA* 3.8 26.0 - - + -
685D ALA 3.1 6.3 - - - +
686D HIS* 3.0 42.3 + + + -
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Residues in contact with VAL 673 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604D PRO* 3.9 21.9 - - + +
606D LEU* 3.7 33.4 - - + -
619D VAL* 5.1 4.7 - - + -
621D LEU* 4.2 13.7 - - + -
634D TYR* 4.4 14.4 - - + -
635D LEU 3.7 2.5 - - - +
636D VAL* 4.3 19.7 - - + -
658D VAL* 5.2 2.5 - - + -
671D VAL* 4.3 10.3 - - + -
672D TYR* 1.3 79.2 - - - +
674D VAL* 1.3 69.0 + - - +
683D LYS 4.2 1.4 - - - +
684D ALA* 3.6 0.5 - - - -
685D ALA* 2.8 38.3 + - + +
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Residues in contact with VAL 674 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604D PRO* 4.8 0.4 - - - -
634D TYR* 3.2 10.8 - - - -
635D LEU* 2.9 44.9 + - + +
637D ARG* 6.3 1.6 - - - +
672D TYR* 5.1 2.7 - - + -
673D VAL* 1.3 79.6 - - - +
675D ALA* 1.3 73.3 + - - +
681D LYS* 3.7 20.6 - - + -
682D SER* 3.4 27.1 - - - +
684D ALA* 3.7 25.6 - - + +
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Residues in contact with ALA 675 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601D PRO* 3.5 9.6 - - + +
602D SER 3.9 21.5 - - - +
604D PRO* 4.2 5.3 - - + +
631D ILE* 4.0 13.9 - - + -
633D HIS 4.1 0.2 - - - -
634D TYR* 3.7 26.9 - - + -
674D VAL* 1.3 75.9 - - - +
676D GLU* 1.3 60.7 + - - +
681D LYS* 3.5 1.4 - - - -
682D SER* 2.9 33.6 + - - +
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Residues in contact with GLU 676 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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601D PRO* 4.6 0.7 - - - -
631D ILE* 3.2 8.2 - - - +
632D ARG* 2.7 52.0 + - - +
633D HIS* 2.8 49.9 + - + +
635D LEU* 3.9 11.5 - - + +
674D VAL* 4.1 0.4 + - + -
675D ALA* 1.3 77.5 - - - +
677D ASN* 1.3 65.0 + - - +
680D GLY* 3.5 11.7 - - - +
681D LYS* 3.4 31.1 - - + +
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Residues in contact with ASN 677 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599D ARG 2.9 26.3 + - - -
601D PRO* 3.1 14.6 - - + +
626D ASP 2.9 19.9 + - - +
629D SER* 3.6 16.7 + - - +
630D PRO 3.3 21.5 - - - +
631D ILE* 4.4 1.8 - - - -
632D ARG* 3.6 18.0 + - - +
676D GLU* 1.3 80.5 - - - +
678D GLN* 1.3 64.0 + - - +
679D GLN* 2.5 29.1 + - - +
680D GLY* 2.8 21.6 + - - +
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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