Contacts of the strand formed by residues 730 - 739 (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 VAL 730 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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723A ARG* 3.3 9.4 - - - -
724A SER* 3.2 35.8 + - - +
727A ASN* 2.9 33.2 + - + +
728A PRO 3.3 0.8 - - - -
729A SER* 1.3 83.5 - - - +
731A THR* 1.3 63.5 + - - +
732A VAL* 4.3 17.7 - - + -
783A LYS* 4.9 10.5 - - + -
784A VAL 3.5 4.3 - - - +
785A LEU* 4.2 23.6 - - + -
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Residues in contact with THR 731 (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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704A ILE* 4.9 0.9 - - + -
721A PHE* 4.2 29.2 - - + -
722A GLU 3.6 12.6 - - - +
723A ARG* 3.0 25.3 + - - +
729A SER 4.0 1.6 + - - -
730A VAL* 1.3 73.7 - - - +
732A VAL* 1.3 64.5 + - - +
733A ILE* 4.0 3.9 + - + +
782A ILE 4.0 1.0 - - - +
783A LYS* 3.7 0.3 - - - -
784A VAL* 2.9 49.9 + - - +
786A ASN* 6.2 0.3 - - - +
792A LEU* 5.9 1.1 - - + -
820A SER* 3.1 26.6 + - - +
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Residues in contact with VAL 732 (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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720A THR 3.7 0.5 - - - +
721A PHE* 3.3 5.0 - - - +
722A GLU* 2.8 51.0 + - + +
724A SER* 5.6 3.6 - - - +
730A VAL* 4.3 13.2 - - + -
731A THR* 1.3 73.3 - - - +
733A ILE* 1.3 65.5 + - - +
734A THR* 4.2 6.6 + - - +
781A VAL* 3.8 26.7 - - + -
782A ILE 3.8 2.9 - - - -
783A LYS* 4.0 27.6 - - + +
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Residues in contact with ILE 733 (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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719A PHE* 3.8 30.7 - - + -
720A THR 3.2 9.9 - - - +
721A PHE* 3.7 28.3 - - + -
731A THR* 4.2 9.2 - - + +
732A VAL* 1.3 77.5 - - - +
734A THR* 1.3 66.6 + - - +
735A ILE* 4.0 1.7 + - + -
780A GLN 3.9 0.3 - - - +
781A VAL* 3.5 2.4 - - - +
782A ILE* 2.8 66.1 + - + +
784A VAL* 3.9 17.7 - - + -
792A LEU* 4.7 4.0 - - + -
794A MET* 4.1 9.0 - - + -
816A PHE* 4.3 8.5 - - + -
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Residues in contact with THR 734 (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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718A GLU 3.6 0.7 - - - +
719A PHE* 3.5 4.2 - - - -
720A THR* 3.0 42.1 + - - +
732A VAL* 4.1 7.8 + - - +
733A ILE* 1.3 75.3 + - - +
735A ILE* 1.4 60.8 + - - +
736A GLN* 4.1 17.5 + - - +
779A THR* 4.0 26.5 - - + -
780A GLN 3.6 4.0 - - - +
781A VAL* 4.4 14.3 - - + +
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Residues in contact with ILE 735 (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* 4.0 9.9 - - + -
718A GLU 3.2 9.0 - - - +
719A PHE* 3.5 26.9 - - + -
733A ILE* 4.4 2.9 - - + -
734A THR* 1.4 74.4 - - - +
736A GLN* 1.3 67.4 + - - +
737A ALA* 4.6 2.5 - - + +
748A PHE* 4.8 8.7 - - + -
750A PHE* 3.3 48.0 - - + -
778A ILE* 4.7 3.8 - - + +
779A THR* 3.3 8.0 - - - +
780A GLN* 2.8 56.6 + - + +
782A ILE* 4.1 19.1 - - + -
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Residues in contact with GLN 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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716A LYS* 3.4 3.8 - - - +
717A ILE* 3.4 2.0 - - - -
718A GLU* 2.9 55.9 + - + +
720A THR* 5.2 10.3 + - + +
734A THR* 4.1 16.9 - - - +
735A ILE* 1.3 77.5 + - - +
737A ALA* 1.3 60.7 + - - +
738A SER* 5.0 1.5 + - - -
777A THR* 3.7 24.5 + - + +
778A ILE 3.3 5.4 + - - +
779A THR* 2.6 30.0 + - - +
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Residues in contact with ALA 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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715A LEU* 4.1 9.6 - - + -
716A LYS 3.2 5.2 - - - -
717A ILE* 3.6 22.7 - - + -
735A ILE* 4.1 4.5 - - + +
736A GLN* 1.3 73.5 - - - +
738A SER* 1.3 59.0 + - - +
748A PHE* 4.2 17.5 - - + -
770A VAL* 3.8 7.4 - - + +
777A THR* 3.1 11.1 - - - -
778A ILE* 2.9 40.6 + - + -
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Residues in contact with SER 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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715A LEU* 3.5 9.0 - - - +
716A LYS* 2.9 56.8 + - - +
718A GLU* 5.3 1.6 + - - -
736A GLN* 5.0 2.0 + - - -
737A ALA* 1.3 73.4 - - - +
739A ASN* 1.3 61.3 + - - +
740A SER 4.1 0.6 + - - -
770A VAL* 3.5 6.7 - - - -
774A ASN* 3.6 19.5 + - - -
776A GLY 4.5 4.5 - - - -
777A THR* 4.8 11.0 - - - -
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Residues in contact with ASN 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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714A GLY 3.3 4.5 - - - -
738A SER* 1.3 75.1 - - - +
740A SER* 1.3 59.4 + - - +
741A THR* 2.8 31.6 + - - -
743A LEU 2.7 24.6 + - - -
744A ASP* 3.6 2.6 - - - +
745A MET* 3.3 25.2 - - - +
770A VAL* 2.8 33.6 + - + +
771A PRO 3.3 17.5 + - - +
772A ALA* 3.7 2.0 - - - +
773A PHE 3.5 1.4 + - - -
774A ASN* 3.1 27.2 + - - +
776A 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