Contacts of the strand formed by residues 761 - 766 (chain A) in PDB entry 5FWW
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 PHE 761 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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756A ASP* 3.0 33.1 + - + +
759A GLU* 4.1 18.4 - - + -
760A GLY* 1.3 81.2 - - - +
762A MET* 1.3 58.3 - - - +
763A TYR* 3.5 32.8 - - + -
775A ARG* 3.3 48.5 - - + -
776A ALA* 3.5 16.8 - - - -
777A ALA 4.3 1.3 - - - -
778A MET* 3.6 6.8 - - - +
782A GLU* 4.7 4.9 - - - -
821A LEU* 6.3 1.1 - - + -
908A PRO* 3.4 36.6 - - + -
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Residues in contact with MET 762 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
720A TYR* 4.0 28.5 - - - -
729A ILE* 4.4 10.5 - - + -
742A LEU* 4.0 11.2 - - + -
743A VAL* 4.3 10.1 - - + -
753A LEU* 4.9 5.8 - - + -
754A ALA 3.7 4.7 - - - -
755A LEU* 3.6 21.8 - - + -
761A PHE* 1.3 72.8 - - - +
763A TYR* 1.3 64.2 + - - +
764A TRP* 3.9 25.8 - - + -
775A ARG* 3.5 5.0 - - - +
776A ALA* 2.8 42.2 + - + +
777A ALA 3.5 21.5 - - - +
778A MET* 3.9 3.6 - - + -
780A GLY* 4.0 17.5 - - - -
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Residues in contact with TYR 763 (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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753A LEU* 3.5 2.5 - - - +
754A ALA* 2.7 47.2 + - + +
756A ASP* 4.5 3.6 + - + -
761A PHE* 3.5 36.6 - - + +
762A MET* 1.3 77.1 - - - +
764A TRP* 1.3 61.3 + - - +
773A ILE* 5.2 2.2 - - + -
774A ASP 3.6 5.8 - - - +
775A ARG* 3.5 24.7 - - + -
786A LEU* 3.6 13.2 - - + -
796A LEU* 3.4 17.9 - - + +
798A ILE* 3.9 14.8 - - + -
805A LEU* 3.6 24.5 - - + -
820A MET* 3.4 53.6 + - + +
821A LEU* 5.8 0.3 - - - +
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Residues in contact with TRP 764 (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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722A ALA* 5.6 0.7 - - + -
729A ILE* 3.3 26.3 - - + +
743A VAL* 4.2 6.5 - - + -
747A LEU* 4.2 3.4 - - + +
750A PRO* 3.9 15.3 - - + -
752A ALA 3.2 16.8 - - - +
753A LEU* 3.7 13.9 - - + -
762A MET* 3.9 24.5 - - + -
763A TYR* 1.3 76.1 - - - +
765A THR* 1.3 71.6 + - - +
766A GLU* 3.6 19.0 + - + -
773A ILE* 3.4 3.3 - - - +
774A ASP* 3.0 55.6 + - + +
775A ARG 4.2 1.8 - - - -
776A ALA* 3.7 38.1 - - + -
783A ARG* 3.7 30.5 - - + -
796A LEU* 3.6 8.5 - - - +
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Residues in contact with THR 765 (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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750A PRO* 3.4 5.2 - - - +
751A ARG* 2.7 31.3 + - - +
752A ALA* 2.7 39.4 + - + +
764A TRP* 1.3 78.1 - - - +
766A GLU* 1.3 55.7 + - - +
767A TRP* 4.5 1.6 - - - -
772A LYS 3.6 4.9 - - - -
773A ILE* 4.1 8.3 - - + +
793A ALA* 3.0 50.1 + - + +
794A ASN 4.5 0.2 - - - +
796A LEU* 4.0 22.9 - - + -
807A TRP* 5.2 0.7 - - + -
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Residues in contact with GLU 766 (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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746A ASP 4.0 6.9 - - - +
747A LEU* 4.1 3.3 - - - +
748A ASP* 3.3 45.1 + - - +
749A SER 3.6 7.4 - - - +
750A PRO* 4.4 3.4 - - + -
764A TRP* 3.6 15.8 + - + -
765A THR* 1.3 73.8 - - - +
767A TRP* 1.3 63.8 + - - +
768A GLY* 3.6 3.5 - - - +
770A LYS 5.4 1.8 - - - +
771A PRO* 3.2 8.3 - - - +
772A LYS* 2.7 68.6 + - + +
774A ASP* 3.9 2.2 - - - +
783A ARG* 3.3 19.9 + - - -
791A GLY 4.7 1.0 - - - +
793A ALA 5.4 0.2 + - - -
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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
------------------------------------------------------------
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