Contacts of the strand formed by residues 730 - 739 (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 VAL 730 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723B ARG* 3.7 3.6 - - - -
724B SER* 3.1 39.9 + - - +
727B ASN* 2.9 38.6 + - + +
729B SER* 1.3 79.3 - - - +
731B THR* 1.3 75.9 + - - +
732B VAL* 4.1 10.3 - - + -
783B LYS* 4.3 18.8 - - + +
784B VAL 3.1 8.1 - - - +
785B LEU* 4.1 11.0 - - + -
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Residues in contact with THR 731 (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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704B ILE* 4.6 3.6 - - + -
721B PHE* 4.2 27.1 - - + -
722B GLU 3.7 13.7 - - - +
723B ARG* 3.4 18.6 + - - +
729B SER 3.9 2.3 + - - -
730B VAL* 1.3 75.7 - - - +
732B VAL* 1.3 64.9 + - - +
733B ILE* 3.7 5.7 + - + +
782B ILE 3.8 0.3 - - - +
783B LYS* 3.6 1.6 - - - -
784B VAL* 2.7 44.9 + - - +
786B ASN* 6.0 2.0 - - - +
792B LEU* 6.1 2.0 - - + -
820B SER* 3.2 29.5 + - - +
821B TRP* 5.1 0.3 - - - -
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Residues in contact with VAL 732 (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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720B THR 3.6 0.7 - - - +
721B PHE* 3.3 4.3 - - - -
722B GLU* 2.8 55.3 + - + +
724B SER* 4.7 10.8 - - - +
730B VAL* 4.1 16.2 - - + -
731B THR* 1.3 73.0 - - - +
733B ILE* 1.3 64.1 + - - +
734B THR* 3.9 8.0 + - - +
781B VAL* 3.5 29.2 - - + -
782B ILE 3.7 3.4 - - - +
783B LYS* 4.3 16.6 - - + +
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Residues in contact with ILE 733 (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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719B PHE* 3.8 32.5 - - + -
720B THR 3.3 8.3 - - - +
721B PHE* 3.7 27.4 - - + -
731B THR* 4.3 9.6 - - + +
732B VAL* 1.3 75.5 - - - +
734B THR* 1.3 63.0 + - - +
780B GLN 3.7 0.9 - - - +
781B VAL* 3.6 1.0 - - - -
782B ILE* 2.8 55.9 + - + +
784B VAL* 4.2 13.2 - - + -
792B LEU* 4.5 5.2 - - + -
794B MET* 4.0 28.3 - - + -
816B PHE* 4.3 9.0 - - + -
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Residues in contact with THR 734 (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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718B GLU 3.7 0.3 - - - +
719B PHE* 3.5 1.2 - - - -
720B THR* 2.9 47.7 + - - +
732B VAL* 3.9 7.8 + - - +
733B ILE* 1.3 74.5 - - - +
735B ILE* 1.3 61.2 + - - +
736B GLN* 3.9 15.1 - - - +
779B THR* 3.9 27.1 - - + -
780B GLN 3.7 4.7 - - - +
781B VAL* 4.4 14.8 - - + +
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Residues in contact with ILE 735 (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* 4.1 8.3 - - + -
718B GLU 3.1 9.2 - - - +
719B PHE* 3.7 25.1 - - + -
733B ILE* 4.6 0.4 - - + -
734B THR* 1.3 76.1 - - - +
736B GLN* 1.3 64.6 + - - +
737B ALA* 4.7 4.5 - - + +
748B PHE* 5.2 6.7 - - + -
750B PHE* 3.4 46.7 - - + -
778B ILE* 4.6 5.4 - - + +
779B THR* 3.3 6.2 - - - -
780B GLN* 2.8 52.0 + - + +
782B ILE* 3.8 23.1 - - + -
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Residues in contact with GLN 736 (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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716B LYS* 3.3 5.4 - - - +
717B ILE* 4.3 2.0 - - - -
718B GLU* 2.7 51.9 + - + +
720B THR* 5.3 10.2 + - + +
734B THR* 3.9 14.3 - - + +
735B ILE* 1.3 72.6 - - - +
737B ALA* 1.3 60.9 + - - +
738B SER* 3.7 2.2 + - - -
777B THR* 3.0 30.6 + - + +
778B ILE 3.4 4.7 - - - +
779B THR* 3.2 31.9 + - - +
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Residues in contact with ALA 737 (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* 4.5 2.7 - - + -
716B LYS 3.3 6.7 - - - +
717B ILE* 4.3 11.0 - - + -
735B ILE* 4.1 4.9 - - + +
736B GLN* 1.3 73.0 - - - +
738B SER* 1.3 57.6 + - - +
748B PHE* 4.0 28.5 - - + -
770B VAL* 3.6 11.7 - - + +
777B THR* 3.2 8.4 - - - -
778B ILE* 2.8 48.1 + - + +
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Residues in contact with SER 738 (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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714B GLY 4.3 0.2 - - - -
715B LEU* 3.6 7.4 - - - +
716B LYS* 2.9 56.2 + - - +
736B GLN* 3.7 2.6 + - - -
737B ALA* 1.3 73.5 - - - +
739B ASN* 1.3 58.5 + - - +
770B VAL* 3.2 9.2 - - - -
774B ASN* 3.3 21.3 + - - -
776B GLY 4.4 9.6 - - - -
777B THR* 4.5 9.9 - - - -
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Residues in contact with ASN 739 (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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714B GLY 3.2 4.5 - - - -
738B SER* 1.3 72.9 - - - +
740B SER* 1.3 59.7 + - - +
741B THR* 2.5 40.6 + - - +
743B LEU 2.9 24.9 + - - -
745B MET* 3.6 21.5 - - - +
770B VAL* 3.0 38.5 + - + +
771B PRO 3.5 15.0 + - - +
772B ALA* 3.7 2.5 - - - +
773B PHE 3.5 2.9 + - - -
774B ASN* 3.1 26.7 + - - +
776B GLY 5.0 0.8 + - - -
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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