Contacts of the strand formed by residues 746 - 753 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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744A ASP* 3.8 17.1 + - + +
745A MET* 1.3 74.1 - - - +
747A ASP* 1.3 76.6 + - - +
748A PHE 3.2 3.8 + - - -
768A SER 3.9 2.7 - - - -
769A VAL* 4.3 18.2 - - + -
800A TYR* 3.3 3.6 - - - +
801A ASN* 2.8 49.5 + - - +
790B GLN* 4.6 6.9 + - - -
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Residues in contact with ASP 747 (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 THR* 1.3 79.9 + - - +
748A PHE* 1.3 65.1 + - - +
749A VAL* 3.3 13.1 + - + +
768A SER* 3.2 19.9 + - - -
769A VAL* 5.3 0.2 - - - +
799A THR* 3.4 9.5 - - - +
800A TYR* 3.8 3.4 - - - -
801A ASN* 2.9 27.7 + - - +
755B PRO* 6.0 0.4 - - + -
756B LYS* 4.9 2.3 - - + +
757B THR* 2.9 44.0 + - + +
790B GLN* 3.7 8.7 + - - -
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Residues in contact with PHE 748 (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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715A LEU* 3.7 27.4 - - + -
717A ILE* 4.1 22.0 - - + -
735A ILE* 4.8 2.5 - - + -
737A ALA* 4.2 14.6 - - + -
745A MET 5.0 0.7 - - - +
746A THR 3.2 1.1 - - - +
747A ASP* 1.3 75.6 - - - +
749A VAL* 1.3 65.9 + - - +
750A PHE* 3.9 22.2 - - + -
765A PRO* 5.6 4.2 - - - +
767A SER 4.5 3.4 - - - +
768A SER* 3.0 26.1 + - - +
770A VAL* 4.1 14.8 - - + -
778A ILE* 3.8 28.7 - - + -
780A GLN* 5.6 1.6 - - - -
798A LEU* 4.1 18.4 - - + -
799A THR 3.4 4.0 - - - -
800A TYR* 3.9 25.8 - + + -
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Residues in contact with VAL 749 (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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747A ASP* 3.7 10.5 - - + +
748A PHE* 1.3 82.9 - - - +
750A PHE* 1.3 60.0 + - - +
751A GLN* 3.6 32.9 - - + +
797A LYS 3.7 1.2 - - - +
798A LEU* 3.6 6.2 - - - +
799A THR* 2.8 45.6 + - + +
755B PRO* 6.5 0.9 - - + -
756B LYS* 6.4 2.2 - - + -
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Residues in contact with PHE 750 (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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717A ILE* 4.7 5.2 - - + -
719A PHE* 4.1 22.7 - + - -
735A ILE* 3.3 36.1 - - + -
748A PHE* 3.9 16.4 + + + -
749A VAL* 1.3 75.0 - - - +
751A GLN* 1.3 65.0 + - - +
752A ALA* 3.9 20.2 - - + -
762A LEU* 3.6 18.2 - - + +
780A GLN* 3.8 21.6 + - - +
782A ILE* 4.2 20.2 - - + -
796A ILE* 3.5 37.9 - - + -
797A LYS 3.8 2.0 - - - -
798A LEU* 3.7 19.3 - - + -
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Residues in contact with GLN 751 (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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749A VAL* 3.6 22.1 - - + +
750A PHE* 1.3 82.8 - - - +
752A ALA* 1.3 66.4 + - - +
762A LEU* 4.1 8.3 - - + -
796A ILE* 3.5 5.0 - - - +
797A LYS* 2.9 63.0 + - + +
799A THR* 5.4 3.8 - - - +
795B ARG* 5.5 8.8 + - - +
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Residues in contact with ALA 752 (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 PHE* 3.9 18.6 - - + -
751A GLN* 1.3 80.4 - - - +
753A ASP* 1.3 68.5 + - - +
760A LEU* 3.4 27.6 - - + +
762A LEU* 4.4 6.2 - - + +
782A ILE* 5.1 0.2 - - + -
794A MET* 4.0 20.0 - - + -
795A ARG 3.3 11.0 - - - +
796A ILE* 4.2 0.7 - - + -
797A LYS* 4.7 0.4 - - - +
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Residues in contact with ASP 753 (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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752A ALA* 1.3 79.1 - - - +
754A VAL* 1.3 69.0 + - - +
760A LEU* 4.7 1.1 - - - -
794A MET* 3.4 8.6 - - - +
795A ARG* 2.9 53.9 + - + +
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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