Contacts of the strand formed by residues 734 - 739 (chain A) in PDB entry 6F3T
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 THR 734 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710A HIS* 3.4 13.9 + - - -
729A GLY* 3.8 0.7 - - - -
730A SER 3.3 23.7 + - - -
732A ASP* 2.7 35.0 + - - +
733A ASN* 1.3 86.0 - - - +
735A VAL* 1.3 62.7 + - - +
736A ARG* 3.5 10.4 + - - +
772A THR* 4.0 17.7 - - + -
773A TYR 3.0 11.7 - - - +
774A MET* 4.3 19.5 - - + -
775A THR* 3.6 3.5 + - - -
780A VAL* 5.5 0.5 + - - +
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Residues in contact with VAL 735 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A ILE* 4.8 12.3 - - + -
727A ALA* 4.9 1.1 - - + -
728A SER 3.2 13.7 - - - +
729A GLY* 4.2 1.8 - - - -
734A THR* 1.3 75.9 - - - +
736A ARG* 1.3 63.6 - - - +
737A LEU* 4.2 20.4 - - + -
772A THR* 3.4 2.6 - - - -
773A TYR* 2.6 54.9 + - + +
775A THR* 3.7 19.9 - - + +
780A VAL* 3.9 26.2 - - + -
783A LEU* 4.3 15.5 - - + -
793A ALA* 4.8 3.6 - - + -
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Residues in contact with ARG 736 (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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709A GLY* 3.2 27.8 + - - -
710A HIS* 3.3 33.5 + - + +
711A THR* 4.8 5.5 - - - +
726A LEU 3.6 1.4 - - - +
727A ALA* 3.4 4.2 - - - -
728A SER* 2.9 43.3 + - - +
732A ASP* 3.7 8.1 + - - -
734A THR* 3.5 16.3 + - - +
735A VAL* 1.3 79.7 - - - +
737A LEU* 1.3 63.9 + - - +
738A TRP* 3.7 16.5 - - - +
769A LEU* 3.9 22.7 - - + +
771A GLY 3.3 4.5 - - - +
772A THR* 3.3 39.8 + - + +
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Residues in contact with LEU 737 (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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458A LEU* 4.4 8.5 - - + -
459A PRO* 3.8 32.3 - - + -
461A ILE* 4.2 12.1 - - + -
725A ILE* 4.2 13.5 - - + -
726A LEU 3.4 1.8 - - - -
727A ALA* 3.7 23.6 - - + -
735A VAL* 4.2 10.8 - - + -
736A ARG* 1.3 80.5 - - - +
738A TRP* 1.3 56.7 + - - +
769A LEU* 3.6 4.7 - - - +
770A LEU* 2.8 42.9 + - + -
771A GLY 3.0 8.9 + - - +
773A TYR* 3.5 35.2 - - + +
785A PHE* 5.5 0.4 - - + -
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Residues in contact with TRP 738 (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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693A VAL* 4.8 3.3 - - + +
707A LEU* 3.7 57.3 - - + +
708A LYS 3.6 27.8 - - - -
709A GLY* 4.5 4.0 - - - -
710A HIS* 4.7 6.3 - + - -
725A ILE* 3.3 9.0 - - - +
726A LEU* 2.8 55.4 + - + +
728A SER* 3.0 24.3 + - - -
736A ARG* 3.7 30.1 + - + -
737A LEU* 1.3 72.8 - - - +
739A ASP* 1.3 62.9 + - - +
740A ALA* 3.1 2.5 + - - -
765A SER 3.7 17.9 - - - -
768A LEU* 3.2 9.4 - - + +
769A LEU* 3.8 33.7 - - + -
770A LEU* 3.9 4.3 - - - -
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Residues in contact with ASP 739 (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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454A GLY* 5.8 0.7 - - - -
455A PRO* 3.4 29.6 - - - +
724A GLU 4.0 5.1 - - - +
738A TRP* 1.3 69.6 - - - +
740A ALA* 1.3 61.8 + - - +
741A ILE* 3.3 12.5 + - - +
742A LYS* 3.2 41.0 + - + +
743A ALA* 3.1 21.6 + - - +
767A GLU 5.0 1.1 - - - +
768A LEU* 2.8 26.8 + - - +
770A LEU* 3.8 18.1 - - + +
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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