Contacts of the strand formed by residues 700 - 706 (chain v) in PDB entry 6FF7
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 700 (chain v).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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639v SER* 4.1 4.5 - - - -
698v PRO 5.3 0.2 - - - +
699v VAL* 1.3 77.3 - - - +
701v LEU* 1.3 61.0 + - - +
702v PHE* 4.0 3.9 - - + +
713v LEU 3.1 6.9 - - - +
714v ALA* 4.2 0.9 - - - -
715v MET* 2.9 39.0 + - + +
740v GLU 4.9 12.1 - - - +
741v PHE* 5.7 3.8 - - - -
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Residues in contact with LEU 701 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639v SER* 4.0 12.1 - - - -
640v LEU 3.1 22.7 - - - +
641v CYS* 3.7 25.2 - - + +
665v ASN* 5.1 4.0 - - + +
666v ILE 4.8 6.7 - - - +
667v GLY* 6.1 1.3 - - - -
700v LYS* 1.3 70.5 - - - +
702v PHE* 1.3 59.4 + - - +
712v VAL* 5.6 4.3 - - + -
713v LEU 3.5 5.6 - - - -
714v ALA* 4.2 11.2 - - + +
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Residues in contact with PHE 702 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641v CYS* 5.6 2.0 - - - -
700v LYS* 5.1 3.8 - - + +
701v LEU* 1.3 75.2 - - - +
703v ARG* 1.3 63.6 + - - +
704v VAL* 3.8 1.2 + - - +
712v VAL* 3.5 4.7 - - - +
713v LEU* 2.9 34.6 + - - +
742v ALA* 3.6 42.0 - - + +
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Residues in contact with ARG 703 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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641v CYS* 6.1 3.6 - - + -
642v ILE 5.1 9.9 - - - +
643v VAL* 6.0 4.3 - - + -
702v PHE* 1.3 73.8 - - - +
704v VAL* 1.3 61.7 + - - +
710v GLU* 5.8 4.5 - - + -
711v ALA 3.4 8.7 - - - +
712v VAL* 4.8 1.1 - - - +
743v SER* 5.3 3.2 - - - -
744v GLY 4.9 6.9 + - - -
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Residues in contact with VAL 704 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702v PHE 3.8 2.6 + - - +
703v ARG* 1.3 73.6 - - - +
705v ARG* 1.3 62.5 + - - +
710v GLU* 3.2 8.2 - - - +
711v ALA* 2.9 35.6 + - + +
713v LEU* 5.7 7.2 - - + +
742v ALA* 6.2 3.6 - - + -
743v SER* 5.4 2.7 - - - +
744v GLY* 5.0 15.9 - - - +
754v ILE* 5.3 11.9 - - + -
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Residues in contact with ARG 705 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704v VAL* 1.3 78.7 - - - +
706v MET* 1.3 60.9 + - - +
708v GLY 6.2 0.2 - - - +
709v GLN 3.3 12.6 - - - +
710v GLU* 4.7 3.8 - - + -
744v GLY* 5.7 2.6 - - - -
752v GLU* 4.3 15.1 - - - +
753v GLY 5.2 4.9 + - - +
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Residues in contact with MET 706 (chain v).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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704v VAL 4.3 0.2 - - - -
705v ARG* 1.3 75.2 - - - +
707v GLN* 1.3 61.1 + - + +
708v GLY 2.9 11.7 + - - -
709v GLN* 2.9 25.4 + - - +
710v GLU* 4.6 2.0 - - - +
711v ALA* 5.3 7.7 - - + +
752v GLU* 5.3 5.2 - - + -
767v LEU* 5.9 6.5 - - + -
770v LEU* 6.3 3.1 - - + -
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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