Contacts of the strand formed by residues 634 - 639 (chain A) 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 634 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A ASN 5.8 3.1 - - - -
593A GLY 2.9 17.0 + - - +
594A LYS* 3.7 35.8 - - + +
595A GLN 3.1 23.4 + - - +
632A GLY 4.3 0.2 + - - -
633A VAL* 1.3 70.8 - - - +
635A LEU* 1.3 61.1 + - - +
636A THR* 3.7 8.0 + - - +
665A ASN 4.7 9.9 - - - +
666A GLY 5.6 0.9 - - - -
667A SER* 3.8 28.3 + - - -
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Residues in contact with LEU 635 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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578A VAL* 5.3 3.4 - - + -
582A PHE* 5.2 4.5 - - + -
595A GLN* 3.4 22.9 - - + +
597A VAL* 3.8 26.5 - - + -
621A GLN 5.3 0.7 - - - +
624A MET* 3.8 42.4 - - + +
625A ALA* 4.1 8.5 - - + +
628A ALA* 3.8 18.2 - - + -
633A VAL* 3.4 4.1 + - + -
634A LYS* 1.3 73.8 - - - +
636A THR* 1.3 62.9 + - - +
637A LEU* 4.0 22.2 - - + -
663A THR* 4.1 16.6 - - + +
664A ILE 4.4 8.8 - - - +
667A SER* 5.4 0.2 - - - -
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Residues in contact with THR 636 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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595A GLN 2.9 11.3 + - - -
596A GLN* 3.1 17.3 - - + +
597A VAL 2.9 25.1 + - - -
634A LYS* 3.7 10.2 + - - +
635A LEU* 1.3 74.0 - - - +
637A LEU* 1.3 73.4 + - - +
667A SER* 2.1 39.2 + - - +
668A ILE 4.2 5.8 - - - +
669A ARG* 4.1 21.5 - - + -
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Residues in contact with LEU 637 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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597A VAL* 3.2 28.0 - - + +
599A VAL* 5.1 10.8 - - + -
621A GLN* 3.5 40.8 - - + +
624A MET* 4.8 7.2 - - - -
635A LEU* 4.0 22.6 + - + -
636A THR* 1.3 82.2 - - - +
638A PHE* 1.3 59.5 + - - +
639A HIS* 3.9 17.6 - - + +
663A THR* 3.6 30.5 + - + +
667A SER 4.8 3.0 + - - -
668A ILE* 4.0 4.9 - - + +
669A ARG* 3.2 23.4 + - - +
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Residues in contact with PHE 638 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173A VAL* 3.7 26.5 - - + -
288A TRP* 3.5 30.5 - + - -
533A ILE* 3.8 9.6 - - + -
596A GLN* 3.5 18.8 - - - +
597A VAL 2.8 12.2 + - - +
598A MET* 3.2 40.0 - - + +
599A VAL* 3.1 26.6 + - - +
636A THR 4.1 0.2 + - - -
637A LEU* 1.3 71.4 - - - +
639A HIS* 1.3 64.3 + - - +
669A ARG* 3.2 39.3 - - + -
671A THR* 3.3 30.3 - - - -
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Residues in contact with HIS 639 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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599A VAL* 4.0 9.0 - - + +
601A TYR* 2.7 31.3 + - + -
621A GLN* 3.5 13.0 + - - -
637A LEU* 3.9 14.7 - - + +
638A PHE* 1.3 72.5 - - - +
640A GLY* 1.3 62.8 + - - +
645A VAL* 3.6 29.0 - - + +
659A GLN* 3.4 30.0 + - - -
663A THR* 6.0 0.6 - - - +
664A ILE* 6.1 1.2 - - - +
668A ILE* 3.9 29.7 - - + +
669A ARG 2.7 20.1 + - - +
670A VAL* 4.5 2.4 - - + +
671A THR* 2.9 28.5 + - - -
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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