Contacts of the helix formed by residues 792 - 801 (chain A) in PDB entry 5M64
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 GLY 792 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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749A LEU* 5.7 1.8 - - - -
771A PHE* 5.9 0.2 - - - -
784A SER 3.9 8.5 - - - -
785A GLN* 3.1 18.6 - - - -
789A SER 5.7 0.2 - - - -
790A LYS 3.5 1.6 - - - -
791A TYR* 1.3 77.6 - - - +
793A ILE* 1.3 57.8 + - - -
794A VAL* 3.3 4.7 - - - -
795A HIS* 3.9 8.9 - - - +
796A SER* 2.6 37.1 + - - -
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Residues in contact with ILE 793 (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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732A ILE* 6.1 4.9 - - + -
736A LEU* 5.4 5.8 - - + -
747A ILE* 4.4 9.2 - - + -
771A PHE* 3.6 31.4 - - + -
781A LEU* 5.2 3.1 - - + -
785A GLN* 2.8 50.3 + - + +
786A TYR* 3.9 11.2 - - + -
792A GLY* 1.3 69.0 - - - -
794A VAL* 1.3 62.0 + - + +
796A SER* 3.3 6.0 + - - -
797A LEU* 2.9 66.3 + - + +
810A LEU* 6.1 2.2 - - + -
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Residues in contact with VAL 794 (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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657A TYR* 3.2 31.4 - - + +
667A ARG* 4.9 4.5 - - - +
785A GLN 4.3 1.8 - - - +
786A TYR* 3.8 28.9 - - + -
787A GLY 4.3 9.6 - - - +
792A GLY* 4.8 1.8 - - - -
793A ILE* 1.3 82.1 - - - +
795A HIS* 1.3 62.1 + - + +
797A LEU* 3.5 5.9 + - - +
798A HIS* 3.0 26.2 + - - +
806A ALA* 4.2 9.6 - - + +
809A VAL* 5.7 0.2 - - - -
810A LEU* 3.6 38.6 - - + -
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Residues in contact with HIS 795 (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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657A TYR* 3.7 16.6 - + - +
658A LEU* 4.8 8.1 - - + +
665A PRO* 3.5 30.0 - - + +
789A SER 5.7 0.4 - - - +
790A LYS* 3.1 37.6 + - + -
791A TYR* 4.3 8.6 + - - +
792A GLY* 3.5 19.4 + - - +
793A ILE 3.3 0.2 - - - -
794A VAL* 1.3 81.0 - - + +
796A SER* 1.3 63.3 + - - +
798A HIS* 3.4 6.3 + - - -
799A GLU* 2.8 35.1 + - - +
1061A SER* 3.4 27.0 - - - -
1062A HIS* 3.7 15.3 + + - -
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Residues in contact with SER 796 (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 ILE* 5.5 1.3 - - - -
749A LEU* 3.4 41.3 - - - +
791A TYR* 4.8 2.9 - - - -
792A GLY 2.6 26.2 + - - -
793A ILE* 3.3 6.9 + - - -
795A HIS* 1.3 77.2 - - - +
797A LEU* 1.3 63.2 + - - +
799A GLU* 3.2 4.5 + - - +
800A VAL* 3.1 29.8 + - - +
1062A HIS* 4.9 4.3 + - - -
1068A PHE* 3.9 16.2 - - - -
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Residues in contact with LEU 797 (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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736A LEU* 3.7 24.5 - - + -
747A ILE* 3.7 27.6 - - + -
793A ILE* 2.9 42.3 + - + +
794A VAL* 4.1 3.4 - - - +
796A SER* 1.3 73.0 - - - +
798A HIS* 1.3 63.9 + - - +
800A VAL* 3.7 4.0 - - + -
801A TYR* 3.1 53.0 + - + +
802A GLY 3.3 3.9 + - - +
806A ALA* 4.4 3.7 - - - +
809A VAL* 3.7 34.3 - - + -
810A LEU* 6.0 0.4 - - + -
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Residues in contact with HIS 798 (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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654A ASP 4.5 1.6 - - - -
657A TYR* 3.8 37.6 - + + -
658A LEU* 5.4 4.1 - - + +
794A VAL 3.0 18.1 + - - +
795A HIS* 3.5 13.9 - - - +
796A SER 3.1 0.4 - - - -
797A LEU* 1.3 78.7 - - - +
799A GLU* 1.3 85.9 + - - +
802A GLY* 3.2 26.7 - - - -
803A PRO* 3.4 40.2 - - + +
806A ALA* 3.8 8.2 - - + +
1058A THR 4.4 12.0 + - - -
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Residues in contact with GLU 799 (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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795A HIS* 2.8 26.6 + - - +
796A SER 3.2 6.1 + - - +
798A HIS* 1.3 103.5 + - - +
800A VAL* 1.3 63.5 + - - +
801A TYR 3.3 2.3 + - - -
802A GLY* 4.5 2.1 + - - -
1058A THR 4.2 8.5 - - - +
1059A LYS* 4.9 2.6 - - - -
1061A SER* 3.1 37.4 + - - +
1062A HIS* 3.9 13.7 - - + +
1068A PHE* 4.5 8.1 - - + -
1076A LEU* 5.6 0.2 - - - +
1079A LYS* 3.4 25.8 + - - -
1080A TYR* 6.1 1.1 - - - +
1173A LYS* 6.2 3.1 - - - -
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Residues in contact with VAL 800 (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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744A MET* 3.3 19.6 - - + +
747A ILE* 3.7 21.1 - - + -
796A SER 3.1 18.8 + - - +
797A LEU* 3.7 11.2 - - - -
799A GLU* 1.3 77.7 - - - +
801A TYR* 1.3 82.2 + - + +
1068A PHE* 3.5 27.1 - - + -
1072A ASN* 3.7 22.4 - - + +
1075A ALA* 5.0 4.3 - - + -
1076A LEU* 5.4 8.5 - - + +
1079A LYS* 4.5 15.1 - - - +
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Residues in contact with TYR 801 (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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736A LEU* 4.7 7.5 - - + +
739A VAL* 5.9 0.2 - - + -
740A THR* 3.2 40.2 + - + +
741A PRO* 4.8 8.7 - - + -
744A MET* 3.6 31.0 - - + -
745A PRO 4.3 8.9 + - - -
746A GLY* 4.8 2.6 - - - -
747A ILE* 4.3 10.3 - - + +
797A LEU* 3.1 47.8 + - + +
799A GLU 4.7 0.7 - - - -
800A VAL* 1.3 96.4 - - + +
802A GLY* 1.3 58.1 + - - +
805A VAL* 3.6 42.2 - - + +
809A VAL* 5.1 2.2 - - + -
1079A LYS* 6.0 2.7 - - - +
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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