Contacts of the strand formed by residues 605 - 610 (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 LYS 605 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641B LEU* 5.6 2.8 - - - +
670B GLU* 3.6 23.0 + - - -
672B TYR* 4.6 5.9 + - - -
686B HIS* 5.7 9.7 + - - +
688B VAL* 4.1 20.9 - - + +
604E PRO* 1.3 74.5 - - - +
606E LEU* 1.3 64.1 + - - +
620E ASN 3.5 2.4 - - - +
621E LEU* 3.7 2.3 - - - -
622E ILE* 2.8 59.6 + - + +
624E GLN* 3.6 17.0 - - - +
571F THR* 5.7 2.1 + - - +
594F LYS* 3.7 35.4 - - + +
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Residues in contact with LEU 606 (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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688B VAL* 3.6 22.1 + - - +
604E PRO* 4.1 6.5 + - + -
605E LYS* 1.3 78.6 - - - +
607E GLU* 1.3 60.9 + - - +
619E VAL* 4.1 15.5 - - + -
620E ASN 3.6 0.9 - - - -
621E LEU* 3.6 23.1 - - + -
622E ILE* 5.3 0.4 - - - -
671E VAL* 4.6 2.0 - - + +
673E VAL* 3.6 33.9 - - + +
685E ALA* 3.7 36.5 - - + +
686E HIS 4.1 3.8 - - - +
687E PHE* 3.8 36.2 - - + +
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Residues in contact with GLU 607 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B LEU* 4.3 0.7 - - - +
668B GLU* 2.7 37.3 - - - +
688B VAL* 3.5 22.7 - - + +
689B PHE* 3.7 18.4 - - - -
690B ARG* 3.5 21.6 + - + +
606E LEU* 1.3 74.9 - - - +
608E GLY* 1.3 63.1 + - - +
618E LYS 3.7 0.3 - - - +
619E VAL* 3.5 4.5 - - - -
620E ASN* 2.7 67.8 + - + +
622E ILE* 4.0 14.2 - - + +
687E PHE* 4.4 1.1 - - - -
592F GLU* 4.5 1.8 - - - +
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Residues in contact with GLY 608 (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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688B VAL 3.1 12.1 + - - -
689B PHE* 3.1 10.1 - - - +
690B ARG 2.9 24.3 + - - +
607E GLU* 1.3 72.8 - - - +
609E GLN* 1.3 58.8 + - - -
617E ILE* 4.4 4.7 - - - -
618E LYS 4.1 1.6 - - - -
619E VAL* 4.8 0.9 - - - -
687E PHE* 3.2 31.6 - - - -
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Residues in contact with GLN 609 (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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666B ASN* 5.8 0.6 + - - -
690B ARG* 3.5 39.9 + - + +
691B THR 4.6 6.5 + - - +
692B ALA* 5.4 4.4 - - - +
608E GLY* 1.3 74.1 - - - +
610E ARG* 1.3 76.4 + - + +
617E ILE* 3.1 24.9 - - - +
618E LYS* 3.0 54.0 + - + +
620E ASN* 3.0 24.4 - - - +
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Residues in contact with ARG 610 (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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610B ARG* 2.8 68.6 - - + +
611B GLY 4.0 15.0 + - - +
612B GLU 4.9 1.0 + - - -
613B ASP* 3.4 9.7 + - - +
614B GLY* 3.3 39.0 + - - +
616B SER 4.9 2.2 + - - -
690B ARG 4.4 3.4 + - - +
692B ALA* 4.8 20.6 - - + +
609E GLN* 1.3 91.1 + - + +
611E GLY* 1.3 66.8 + - - +
616E SER 5.4 0.4 - - - -
618E LYS* 4.3 5.9 - - - +
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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