Contacts of the strand formed by residues 594 - 599 (chain G) in PDB entry 6V3O
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 594 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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560G PRO* 6.2 0.2 - - - +
591G ILE* 3.3 31.2 + - - +
592G LYS 4.4 7.2 - - - +
593G GLY* 1.3 84.9 - - - +
595G GLN* 1.3 60.2 + - - +
633G VAL* 4.0 2.4 - - - +
634G LYS* 3.4 40.5 - - + +
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Residues in contact with GLN 595 (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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543G VAL* 5.9 0.4 - - - +
561G VAL 3.0 21.6 + - - -
563G PRO* 3.9 9.9 - - - +
578G VAL* 5.6 4.3 - - + -
581G LEU* 5.4 4.6 - - - +
582G PHE* 3.9 19.0 - - + -
587G TYR* 2.3 38.7 + - - -
591G ILE* 4.2 4.6 - - + +
594G LYS* 1.3 74.8 - - - +
596G GLN* 1.3 84.8 + - - +
597G VAL* 4.3 4.9 - - + -
633G VAL* 3.7 17.6 - - + +
634G LYS 3.0 10.4 + - - +
635G LEU* 3.2 16.0 - - + -
636G THR* 2.9 24.7 + - - -
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Residues in contact with GLN 596 (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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531G PRO* 4.1 10.4 - - - +
560G PRO* 5.9 4.4 - - + +
562G VAL* 3.2 40.0 - - + +
595G GLN* 1.3 94.6 + - - +
597G VAL* 1.3 66.7 + - - +
636G THR* 3.2 29.4 - - + +
638G PHE* 3.5 14.7 - - + +
669G ARG* 2.9 46.8 + - - +
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Residues in contact with VAL 597 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
562G VAL* 3.7 5.6 - - - -
563G PRO* 3.8 22.9 - - + +
565G PHE* 3.8 20.6 - - + -
578G VAL* 4.5 6.3 - - + -
595G GLN* 4.3 7.6 - - + +
596G GLN* 1.3 79.3 - - - +
598G MET* 1.3 60.1 + - - +
599G VAL* 4.7 2.9 - - + -
624G MET* 3.5 37.7 - - + -
635G LEU* 3.9 10.7 - - + +
636G THR 2.9 6.1 + - - -
637G LEU* 3.3 17.2 - - + +
638G PHE* 2.8 29.7 + - - +
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Residues in contact with MET 598 (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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288G TRP* 3.6 31.0 - - + -
456G ARG* 5.0 0.9 - - - +
533G ILE* 4.1 13.0 - - + -
562G VAL* 3.6 8.2 - - + +
563G PRO 3.0 14.5 + - - +
564G LEU* 3.5 28.7 - - + -
565G PHE 3.3 23.6 + - - -
597G VAL* 1.3 76.7 - - - +
599G VAL* 1.3 66.8 + - - +
600G GLY* 5.5 1.3 - - - -
603G ASP* 5.8 0.9 - - - +
638G PHE* 3.2 48.2 - - + +
640G GLY* 3.6 26.7 - - - -
641G ARG 5.0 1.1 - - - +
671G THR* 4.9 0.4 - - - +
1002G SO4 5.8 2.2 - - - +
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Residues in contact with VAL 599 (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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564G LEU* 4.0 3.8 - - - -
565G PHE* 4.1 7.0 - - + +
571G LEU* 4.4 13.5 - - + -
597G VAL* 4.7 6.3 - - + -
598G MET* 1.3 80.4 - - - +
600G GLY* 1.3 59.2 + - - +
601G TYR* 4.2 6.1 + - + -
617G LEU* 3.5 29.8 - - + -
620G ALA* 6.0 1.6 - - + -
621G GLN* 4.7 10.3 - - + +
624G MET* 5.8 3.6 - - - -
637G LEU* 4.6 20.2 - - + -
638G PHE 3.0 10.7 + - - +
639G HIS* 4.2 21.3 - - + +
640G GLY* 2.9 26.7 + - - -
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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