Contacts of the strand formed by residues 715 - 723 (chain A) in PDB entry 1GYU
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 LEU 715 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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710A TYR* 3.6 19.9 - - + -
711A SER* 3.3 3.5 + - - -
712A LYS 2.9 35.2 + - - +
713A ASN 3.2 1.2 + - - -
714A GLY* 1.3 76.9 - - - +
716A LYS* 1.3 62.2 + - - +
717A ILE* 4.0 19.3 - - + -
737A ALA* 4.4 5.4 - - + -
738A SER 3.4 17.5 - - - +
745A MET* 3.8 24.7 - - + -
748A PHE* 3.9 20.0 - - + -
770A VAL* 4.6 2.5 - - + -
798A LEU* 4.0 12.6 - - + -
800A TYR* 3.8 29.4 - - + +
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Residues in contact with LYS 716 (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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708A THR* 3.6 29.8 + - + -
710A TYR 3.3 9.9 - - - +
711A SER* 4.3 10.1 - - - +
714A GLY 4.0 1.1 + - - +
715A LEU* 1.3 75.2 - - - +
717A ILE* 1.3 67.8 + - - +
718A GLU* 4.1 13.4 - - + +
736A GLN 3.6 1.3 - - - +
737A ALA* 3.3 4.0 - - - -
738A SER* 2.9 49.9 + - - +
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Residues in contact with ILE 717 (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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708A THR* 3.7 2.1 - - - +
709A ALA* 2.8 32.6 + - + +
710A TYR* 2.8 40.2 + - + +
715A LEU* 4.0 12.8 - - + -
716A LYS* 1.3 81.1 - - - +
718A GLU* 1.3 59.3 + - - +
719A PHE* 3.9 24.2 - - + -
735A ILE* 4.1 17.3 - - + -
736A GLN 3.5 4.0 - - - +
737A ALA* 3.4 27.6 - - + -
748A PHE* 4.2 12.1 - - + -
750A PHE* 4.8 3.1 - - + -
796A ILE* 5.2 1.6 - - + -
798A LEU* 4.4 13.5 - - + -
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Residues in contact with GLU 718 (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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706A SER* 6.1 1.8 - - - -
707A ILE 3.4 9.4 - - - +
708A THR* 4.5 2.7 - - - +
716A LYS* 4.1 15.3 - - - +
717A ILE* 1.3 73.3 - - - +
719A PHE* 1.3 64.1 + - - +
720A THR* 4.1 4.9 - - + -
734A THR 3.7 0.3 - - - +
735A ILE* 3.2 5.7 - - - +
736A GLN* 2.8 46.4 + - + +
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Residues in contact with PHE 719 (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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706A SER* 3.3 7.7 - - - -
707A ILE* 2.8 44.2 + - + -
709A ALA* 3.6 27.1 - - + -
717A ILE* 3.9 12.3 + - + -
718A GLU* 1.3 81.3 - - - +
720A THR* 1.3 60.8 - - - +
721A PHE* 3.7 12.9 - + + -
733A ILE* 3.7 17.9 - - + -
734A THR 3.7 2.5 - - - -
735A ILE* 3.8 24.5 - - + -
750A PHE* 4.3 11.0 - + - -
782A ILE* 4.6 2.0 - - + -
794A MET* 4.0 20.2 - - + -
796A ILE* 4.5 6.5 - - + -
813A VAL* 4.4 3.6 - - + -
816A PHE* 3.9 37.2 - + - -
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Residues in contact with THR 720 (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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706A SER* 3.2 24.2 - - - +
718A GLU* 5.4 5.8 - - + -
719A PHE* 1.3 76.9 - - - +
721A PHE* 1.3 62.1 + - - +
732A VAL 3.7 0.4 - - - +
733A ILE* 3.3 5.9 - - - +
734A THR* 2.8 55.0 + - - +
736A GLN* 5.4 8.6 - - + +
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Residues in contact with PHE 721 (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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703A MET* 5.0 7.4 - - - +
704A ILE* 3.6 43.3 + - + +
705A PRO 3.4 26.7 - - - -
706A SER* 4.9 0.4 + - - -
707A ILE* 4.1 9.9 - - + -
719A PHE* 3.7 28.7 - - + -
720A THR* 1.3 77.9 - - - +
722A GLU* 1.3 70.0 + - - +
731A THR* 4.1 6.7 - - + -
732A VAL 3.4 3.1 - - - +
733A ILE* 3.7 26.5 - - + -
792A LEU* 5.1 0.2 - - + -
816A PHE* 3.6 37.7 - + - -
817A PRO* 3.9 16.2 - - + -
820A SER* 3.9 14.1 - - - -
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Residues in contact with GLU 722 (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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703A MET* 5.7 6.3 - - + -
704A ILE* 4.8 4.9 - - - -
721A PHE* 1.3 81.7 - - - +
723A ARG* 1.3 67.2 + - - +
731A THR* 3.6 5.2 - - - +
732A VAL* 2.8 49.2 + - + +
734A THR* 4.9 7.1 + - - -
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Residues in contact with ARG 723 (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* 4.5 12.7 - - + +
722A GLU* 1.3 79.8 - - - +
724A SER* 1.3 73.2 + - - +
725A ASN* 3.6 10.7 + - - +
728A PRO* 3.6 26.3 + - + +
729A SER* 5.3 3.0 - - - +
730A VAL 3.3 19.1 - - - +
731A THR* 3.6 18.0 + - - +
732A VAL* 5.2 0.2 - - - -
819A GLN 2.6 27.2 + - - -
820A SER 4.4 0.9 - - - -
821A TRP* 3.9 8.1 - - - +
822A GLN* 2.5 36.1 + - - +
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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