Contacts of the strand formed by residues 647 - 652 (chain G) in PDB entry 2VKZ
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 PHE 647 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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589G ARG* 5.3 2.0 - - - +
607G VAL* 4.3 9.2 - - + -
611G THR* 4.2 9.4 - - - +
616G THR* 6.3 0.2 - - - +
617G ILE 3.8 13.7 - - - +
619G LEU* 4.4 16.4 - - + -
634G ILE* 4.0 35.2 - - + -
637G VAL* 3.2 38.6 - - + -
638G VAL* 4.0 16.8 - - + -
641G ILE* 4.1 9.9 - - + -
646G THR* 1.3 80.2 + - - +
648G GLY* 1.3 79.5 + - - +
649G ILE* 4.7 2.0 - - + -
675G PRO* 3.3 12.4 + - + -
676G ILE* 3.5 14.2 - - + -
677G GLN* 3.0 24.9 + - - -
678G PHE* 3.8 10.0 - - - -
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Residues in contact with GLY 648 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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617G ILE 3.4 6.3 + - - -
618G GLU* 4.1 3.6 - - - -
619G LEU* 2.7 32.1 + - - +
647G PHE* 1.3 81.0 - - - +
649G ILE* 1.3 65.5 + - - +
676G ILE* 4.6 1.8 - - - -
678G PHE* 3.2 28.6 - - - -
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Residues in contact with ILE 649 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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618G GLU* 4.7 2.7 - - - -
619G LEU* 3.7 16.2 - - + +
630G MET* 4.1 17.3 - - + -
634G ILE* 3.2 36.3 - - + -
647G PHE* 4.7 3.1 - - + -
648G GLY* 1.3 80.8 - - - +
650G ASN* 1.3 62.0 + - - +
651G LEU* 3.9 27.6 - - + -
665G LEU* 5.6 0.2 - - + -
666G ILE* 4.3 17.3 - - + -
676G ILE* 3.3 26.5 - - + -
678G PHE* 3.1 9.4 + - - +
679G LEU* 3.3 8.3 - - - +
680G THR* 2.9 26.1 + - - -
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Residues in contact with ASN 650 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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596G GLY* 4.0 19.9 - - - -
618G GLU* 4.0 12.4 - - + +
619G LEU 3.0 13.0 + - - +
620G ALA* 4.3 2.2 - - - +
621G GLY* 2.7 36.8 + - - +
649G ILE* 1.3 71.3 - - - +
651G LEU* 1.3 63.2 + - - +
652G ILE* 3.7 7.1 - - - +
680G THR* 3.4 18.6 - - + +
682G GLY 4.4 0.2 + - - -
3051G FMN 2.7 58.4 + - - -
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Residues in contact with LEU 651 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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621G GLY* 4.1 5.6 - - - -
630G MET* 5.2 5.8 - - - -
649G ILE* 3.9 13.7 - - + -
650G ASN* 1.3 84.8 - - - +
652G ILE* 1.3 64.2 + - - +
658G MET* 3.7 24.2 - - + -
659G LEU* 3.9 18.4 - - + -
661G TRP* 5.4 1.1 - - + -
662G GLY* 4.2 9.6 - - - -
663G ILE* 3.6 38.4 - - + +
666G ILE* 3.9 17.3 - - + -
679G LEU* 3.9 13.2 - - + -
680G THR 3.0 7.0 + - - +
681G ILE* 3.4 8.5 - - + +
682G GLY* 2.9 24.8 + - - -
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Residues in contact with ILE 652 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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598G THR* 5.4 0.4 - - + -
622G GLY* 4.1 13.9 - - - +
650G ASN* 3.7 20.0 - - - +
651G LEU* 1.3 76.6 - - - +
653G TYR* 1.3 65.8 + - - +
654G VAL* 3.3 18.4 - - + +
655G ASN* 3.3 27.3 + - + +
658G MET* 2.8 33.1 - - + +
659G LEU* 3.6 9.8 - - - +
681G ILE* 5.5 0.2 - - - -
682G GLY 3.5 5.6 - - - +
683G ALA* 3.5 16.2 - - + -
3051G FMN 3.9 20.0 - - + +
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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