Contacts of the strand formed by residues 708 - 712 (chain B) in PDB entry 5TWV
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 LEU 708 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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706B GLY 3.7 2.5 + - - +
707B GLN* 1.3 73.8 - - - +
709B THR* 1.3 60.4 + - - +
876B LEU* 5.3 15.7 - - + -
884B VAL* 4.0 7.2 - - + -
897B ALA* 4.2 12.1 - - + -
898B ASP* 3.4 30.0 + - + +
899B TRP* 3.0 27.4 + - - +
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Residues in contact with THR 709 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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703B ILE* 4.6 10.7 - - + +
707B GLN* 3.1 36.8 + - - +
708B LEU* 1.3 70.3 - - - +
710B MET* 1.3 71.9 + - - +
711B ILE* 5.5 0.3 - - - +
884B VAL 3.8 9.0 + - - -
885B VAL* 4.0 8.2 - - + +
886B LEU* 3.2 26.6 + - - +
897B ALA* 5.6 1.1 - - - -
899B TRP 3.3 7.0 - - - +
900B ILE 5.0 0.7 - - - -
901B ILE* 4.1 17.9 - - + +
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Residues in contact with MET 710 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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708B LEU 4.2 0.4 - - - -
709B THR* 1.3 81.1 - - - +
711B ILE* 1.3 62.4 + - - +
712B VAL* 5.3 3.8 - - + +
886B LEU* 3.3 11.0 - - + +
888B THR* 4.6 13.7 - - + -
894B LEU* 5.5 12.1 - - + -
897B ALA* 5.3 10.4 - - + +
899B TRP 3.3 9.4 + - - +
900B ILE* 4.5 15.9 - - + -
901B ILE* 3.0 26.5 + - - +
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Residues in contact with ILE 711 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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710B MET* 1.3 74.5 - - - +
712B VAL* 1.3 62.1 + - - +
719B LYS* 5.5 8.9 - - + +
722B LEU* 6.2 4.0 - - + -
886B LEU 3.4 6.4 + - - -
887B VAL* 3.6 19.2 - - + +
888B THR* 2.8 27.5 + - - +
901B ILE* 3.6 5.6 - - + +
903B MET* 5.9 4.7 - - + +
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Residues in contact with VAL 712 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B MET* 4.2 3.8 - - + -
711B ILE* 1.3 74.0 - - - +
713B GLY* 1.3 59.4 + - - +
719B LYS* 5.5 6.5 - - - +
888B THR* 3.5 16.4 - - + +
889B HIS* 5.5 3.4 - - - -
890B LYS 5.7 2.0 - - - +
901B ILE 3.8 9.1 + - - +
902B ALA* 5.2 5.8 - - + -
903B MET* 3.0 32.5 + - - +
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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