Contacts of the strand formed by residues 605 - 610 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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571A THR* 4.7 5.3 + - - -
594A LYS* 4.2 35.0 - - + +
604B PRO* 1.3 74.9 - - - +
606B LEU* 1.3 62.3 + - - +
621B LEU* 3.7 4.5 - - - -
622B ILE* 2.9 65.5 + - + +
624B GLN* 3.0 28.0 - - - +
685B ALA* 5.2 0.2 - - - -
641E LEU* 4.9 8.3 - - - +
670E GLU* 5.0 4.6 + - - -
686E HIS* 4.8 12.2 + - - -
688E VAL* 4.4 22.2 - - - +
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Residues in contact with LEU 606 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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604B PRO* 4.4 3.8 - - + +
605B LYS* 1.3 83.1 - - - +
607B GLU* 1.3 61.7 + - - +
619B VAL* 4.3 13.2 - - + -
620B ASN 3.6 2.2 - - - -
621B LEU* 3.8 19.3 - - + -
622B ILE* 5.4 1.2 - - - +
671B VAL* 4.4 2.7 - - + +
673B VAL* 3.8 34.3 - - + -
685B ALA* 3.7 37.0 - - + +
686B HIS 3.7 22.0 - - - +
687B PHE* 3.8 20.7 - - + +
688E VAL* 3.6 19.6 + - - +
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Residues in contact with GLU 607 (chain B).
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* 4.7 2.0 - - - +
606B LEU* 1.3 76.2 - - - +
608B GLY* 1.3 70.3 + - - +
619B VAL* 3.6 3.1 - - - +
620B ASN* 2.7 67.6 + - + +
622B ILE* 4.3 11.6 - - + +
687B PHE* 4.2 1.8 - - - -
641E LEU* 4.6 0.2 - - - +
668E GLU* 2.3 38.0 - - - +
688E VAL* 3.2 28.5 - - + +
689E PHE* 3.8 5.4 - - - -
690E ARG* 3.2 26.5 + - - +
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Residues in contact with GLY 608 (chain B).
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* 1.3 75.2 - - - +
609B GLN* 1.3 62.4 + - - +
617B ILE* 4.4 2.0 - - - -
618B LYS 3.7 4.0 - - - -
619B VAL* 4.8 0.9 - - - -
687B PHE* 3.3 31.3 - - - -
688E VAL 3.0 11.5 + - - -
689E PHE* 3.3 6.3 - - - +
690E ARG 2.9 26.0 + - - -
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Residues in contact with GLN 609 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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608B GLY* 1.3 74.4 - - - +
610B ARG* 1.3 69.3 + - + +
617B ILE* 3.0 12.0 - - - +
618B LYS* 2.8 61.9 + - + +
620B ASN* 2.8 31.7 - - - +
690E ARG* 3.9 40.9 + - + +
691E THR 5.2 4.7 + - - +
692E ALA* 5.9 3.3 - - - +
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Residues in contact with ARG 610 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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609B GLN* 1.3 91.9 + - + +
611B GLY* 1.3 65.5 + - - +
616B SER 4.9 2.2 - - - -
617B ILE* 5.0 0.7 - - - -
618B LYS* 3.3 14.4 - - - +
610E ARG* 2.8 58.0 - - + +
611E GLY 4.2 11.3 + - - +
612E GLU 4.9 1.4 + - - -
613E ASP* 3.8 8.5 + - - +
614E GLY* 3.8 32.7 + - - +
690E ARG 4.7 3.4 + - - +
692E ALA* 4.1 27.2 - - + +
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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