Contacts of the strand formed by residues 746 - 753 (chain B) in PDB entry 1GYW
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 746 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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744B ASP* 4.0 21.7 + - + +
745B MET* 1.3 78.8 - - - +
747B ASP* 1.4 73.3 + - - +
748B PHE 3.2 3.6 + - - -
768B SER 3.8 4.5 - - - -
769B VAL* 4.3 14.6 - - + -
800B TYR* 3.4 2.3 - - - -
801B ASN* 2.8 47.4 + - - +
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Residues in contact with ASP 747 (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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746B THR* 1.4 79.9 + - - +
748B PHE* 1.3 63.4 - - - +
749B VAL* 3.5 11.9 + - - +
768B SER* 3.4 16.9 + - - -
769B VAL* 5.2 0.6 - - - +
799B THR* 3.6 7.4 + - - +
800B TYR* 3.9 2.9 - - - -
801B ASN* 3.6 18.8 - - - +
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Residues in contact with PHE 748 (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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715B LEU* 4.0 29.8 - - + -
717B ILE* 4.8 3.4 - - + -
735B ILE* 5.2 2.0 - - + -
737B ALA* 4.0 22.2 - - + -
745B MET* 4.9 2.5 - - + +
746B THR 3.2 1.7 - - - +
747B ASP* 1.3 75.3 - - - +
749B VAL* 1.3 69.5 + - - +
750B PHE* 4.0 29.4 - + + -
765B PRO* 5.6 6.8 - - + +
767B SER 5.0 1.7 - - - +
768B SER* 3.1 29.5 + - - +
770B VAL* 3.8 17.3 - - + -
778B ILE* 3.6 26.5 - - + -
780B GLN* 5.4 1.6 - - - -
798B LEU* 4.5 12.6 - - + -
799B THR 3.4 5.8 - - - -
800B TYR* 4.0 26.5 - + + -
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Residues in contact with VAL 749 (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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747B ASP 3.7 9.0 - - - +
748B PHE* 1.3 85.5 - - - +
750B PHE* 1.3 71.6 + - - +
751B GLN* 4.3 18.2 - - + +
797B LYS 3.3 6.8 - - - +
798B LEU* 3.4 2.9 - - - -
799B THR* 2.8 47.6 + - - +
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Residues in contact with PHE 750 (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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717B ILE* 4.5 5.6 - - + -
719B PHE* 4.2 11.0 - + - -
735B ILE* 3.4 41.3 - - + -
748B PHE* 4.0 11.9 - + + -
749B VAL* 1.3 77.8 - - - +
751B GLN* 1.3 64.4 - - - +
752B ALA* 3.8 20.2 - - + -
762B LEU* 3.6 22.3 - - + +
780B GLN* 3.5 22.8 + - - +
782B ILE* 3.9 20.6 - - + -
796B ILE* 3.6 41.1 - - + -
797B LYS 3.6 1.6 - - - -
798B LEU* 3.6 18.6 - - + -
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Residues in contact with GLN 751 (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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749B VAL* 4.3 17.1 - - + +
750B PHE* 1.3 81.0 - - - +
752B ALA* 1.3 63.1 + - - +
762B LEU* 4.5 6.3 - - + -
796B ILE* 3.2 8.8 - - - +
797B LYS* 3.0 69.0 + - + +
799B THR* 5.3 4.9 + - - +
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Residues in contact with ALA 752 (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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750B PHE* 3.8 21.3 - - + -
751B GLN* 1.3 76.3 - - - +
753B ASP* 1.3 63.5 + - - +
760B LEU* 3.1 19.9 - - + +
762B LEU* 4.8 14.3 - - + +
782B ILE* 4.5 6.5 - - + -
794B MET* 4.1 19.1 - - - -
795B ARG 3.3 9.0 - - - +
796B ILE* 4.5 0.2 - - + -
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Residues in contact with ASP 753 (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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752B ALA* 1.3 76.6 - - - +
754B VAL* 1.3 80.0 + - - +
760B LEU* 3.5 5.1 - - - +
794B MET* 3.3 6.1 - - - +
795B ARG* 3.0 39.7 + - + +
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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