Contacts of the strand formed by residues 594 - 599 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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591F ILE* 3.2 30.5 + - - +
592F LYS 4.2 7.6 - - - +
593F GLY* 1.3 84.9 - - - +
595F GLN* 1.3 61.2 + - - +
633F VAL* 4.1 1.7 - - - +
634F LYS* 3.6 28.5 - - + +
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Residues in contact with GLN 595 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543F VAL* 6.0 0.2 - - - +
561F VAL 3.2 19.8 + - - -
563F PRO* 3.8 11.1 - - - +
578F VAL* 5.0 3.4 - - + -
581F LEU* 5.8 4.0 - - - +
582F PHE* 3.9 20.1 - - + -
587F TYR* 2.5 37.9 + - - -
591F ILE* 4.1 5.3 - - + +
594F LYS* 1.3 73.7 - - - +
596F GLN* 1.3 85.6 + - - +
597F VAL* 4.3 6.0 - - + +
633F VAL* 3.8 15.8 - - + +
634F LYS 3.1 10.4 + - - +
635F LEU* 3.3 14.4 - - + +
636F THR* 2.9 24.1 + - - -
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Residues in contact with GLN 596 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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531F PRO* 4.0 10.2 - - - +
560F PRO* 5.8 4.0 - - + +
561F VAL 5.2 0.2 + - - -
562F VAL* 3.7 34.1 - - + +
563F PRO* 3.6 7.6 - - - +
595F GLN* 1.3 93.2 + - - +
597F VAL* 1.3 69.8 + - - +
636F THR* 3.1 25.1 - - + +
638F PHE* 3.5 14.2 - - + +
669F ARG* 2.9 46.2 + - - +
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Residues in contact with VAL 597 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562F VAL* 4.2 2.0 - - - -
563F PRO* 3.7 13.7 - - + +
565F PHE* 3.7 33.9 - - + -
578F VAL* 4.7 9.2 - - + -
595F GLN* 4.3 10.1 - - + +
596F GLN* 1.3 80.4 - - - +
598F MET* 1.3 65.7 + - - +
599F VAL* 4.1 2.0 + - + -
624F MET* 4.1 22.2 - - + -
635F LEU* 3.7 20.4 - - + -
636F THR 2.9 5.9 + - - -
637F LEU* 3.3 19.4 - - + +
638F PHE 2.9 21.7 + - - -
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Residues in contact with MET 598 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288F TRP* 3.6 32.8 - - + -
456F ARG* 5.2 0.7 - - - +
533F ILE* 4.1 12.8 - - - -
562F VAL* 3.8 14.6 - - + +
563F PRO 3.0 14.0 + - - +
564F LEU* 3.5 28.1 - - + -
565F PHE* 3.4 22.9 + - - +
597F VAL* 1.3 75.8 - - - +
599F VAL* 1.3 65.2 + - - +
600F GLY* 5.6 0.9 - - - -
603F ASP* 5.8 2.0 - - - +
638F PHE* 3.3 44.0 - - + +
640F GLY* 3.5 28.3 - - - -
641F ARG 5.0 1.1 - - - +
671F THR* 4.9 0.4 - - - +
1001F SO4 5.9 1.1 - - - +
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Residues in contact with VAL 599 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564F LEU* 4.0 4.5 - - - -
565F PHE* 4.4 4.5 - - + +
571F LEU* 4.5 13.0 - - + -
597F VAL* 4.8 4.0 - - + -
598F MET* 1.3 81.2 - - - +
600F GLY* 1.3 59.9 + - - +
601F TYR* 4.2 5.5 - - + +
617F LEU* 3.5 32.5 - - + -
621F GLN* 4.8 4.9 - - + +
624F MET* 4.8 17.7 - - + -
637F LEU* 4.9 11.4 - - + -
638F PHE 3.0 11.0 + - - +
639F HIS* 4.2 23.8 - - + +
640F GLY* 2.8 28.1 + - - -
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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