Contacts of the strand formed by residues 784 - 792 (chain A) in PDB entry 3NKO
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 784 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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594A TYR* 3.7 40.8 - - + +
768A THR* 4.0 8.7 - - + -
769A SER 3.5 13.2 - - - +
771A LEU* 3.9 8.4 - - - +
777A ALA 5.9 0.4 - - - +
780A CYS* 4.2 14.8 - - + -
782A GLY 4.1 9.0 - - - +
783A PRO* 1.3 81.3 - - - +
785A SER* 1.3 60.5 + - - +
834A TYR* 4.1 7.2 - - + -
837A THR* 4.7 10.3 - - + -
839A ARG* 5.1 4.3 - - + -
844A ILE* 4.8 3.1 - - + -
847A LEU* 3.6 37.0 - - + +
1020A EDO 3.7 10.9 - - - -
1028A EDO 3.3 18.2 + - - +
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Residues in contact with SER 785 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A ARG* 2.9 13.2 + - - -
768A THR* 3.3 4.4 - - - +
769A SER* 2.8 45.8 + - - +
770A CYS 4.3 1.1 - - - -
771A LEU* 3.8 25.6 - - - +
784A LEU* 1.3 75.4 - - - +
786A VAL* 1.3 63.0 + - - +
1020A EDO 3.6 10.0 + - - -
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Residues in contact with VAL 786 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A ARG* 3.9 2.5 - - - +
766A ILE* 3.7 20.2 - - + -
767A ILE 3.4 8.1 - - - +
768A THR* 3.9 2.2 - - + +
785A SER* 1.3 77.1 + - - +
787A SER* 1.3 64.7 + - - +
788A SER* 3.8 3.8 - - - +
822A VAL* 3.8 13.0 - - + -
834A TYR* 3.2 26.5 - - - +
847A LEU* 3.5 40.4 - - + +
850A TYR* 3.2 31.0 - - + +
852A HIS* 5.1 0.2 + - - -
1020A EDO 2.9 12.0 + - - +
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Residues in contact with SER 787 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A TYR* 5.8 1.0 - - - -
723A ARG* 3.1 21.3 + - - +
767A ILE* 2.8 36.9 + - - +
786A VAL* 1.3 74.6 - - - +
788A SER* 1.3 63.6 + - - +
789A PHE* 4.6 7.8 - - - -
850A TYR* 5.2 0.7 - - - -
852A HIS* 4.0 27.4 - - - +
854A TYR* 4.1 14.2 + - - -
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Residues in contact with SER 788 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
765A SER 3.2 13.9 - - - -
766A ILE* 3.6 7.2 - - - +
786A VAL* 3.8 1.6 - - - +
787A SER* 1.3 81.6 + - - +
789A PHE* 1.3 72.2 + - - +
819A THR* 3.5 8.9 + - - -
820A ALA 3.0 36.7 + - - -
822A VAL* 3.5 26.0 - - - +
825A ILE* 3.7 18.8 - - - -
852A HIS* 5.3 0.4 - - - +
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Residues in contact with PHE 789 (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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711A PHE* 5.0 0.2 - + - -
719A TYR* 4.0 12.3 - + - -
764A TYR* 3.2 6.6 - - - +
765A SER* 3.0 40.4 + - - +
767A ILE* 4.0 24.5 - - + -
787A SER* 4.6 6.5 - - - -
788A SER* 1.3 86.1 - - - +
790A ILE* 1.3 67.2 + - - +
791A LEU* 3.8 19.7 - - + -
815A MET* 3.2 63.5 - - + -
816A LYS* 4.5 0.7 - - + -
818A HIS 3.5 5.2 - - - +
819A THR* 4.1 2.9 - - - -
820A ALA* 4.1 1.6 - - - +
825A ILE* 3.9 1.7 - - - +
854A TYR* 3.2 34.5 - + - -
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Residues in contact with ILE 790 (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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430A LYS* 3.8 23.0 + - + +
733A ILE* 4.0 12.1 - - + -
762A HIS* 3.6 35.8 - - + -
763A TYR 3.7 2.9 - - - -
764A TYR* 4.5 0.4 - - - +
789A PHE* 1.3 77.3 - - - +
791A LEU* 1.3 60.4 + - - +
792A PRO* 3.7 2.8 - - - +
818A HIS* 3.0 30.3 + - - +
820A ALA* 3.6 22.7 - - + -
824A ASP* 3.8 11.9 - - + -
825A ILE* 3.7 21.1 - - + -
828A LEU* 3.6 25.4 - - + -
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Residues in contact with LEU 791 (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 PHE* 3.7 23.6 - - + -
707A VAL* 4.1 23.3 - - + -
708A TRP* 4.4 18.4 - - + -
711A PHE* 5.5 2.9 - - + -
762A HIS* 3.0 7.9 - - - -
763A TYR 2.9 37.4 + - - +
764A TYR 6.3 0.2 - - - -
765A SER* 6.5 0.4 - - - -
789A PHE* 3.8 24.9 - - + -
790A ILE* 1.3 73.9 - - - +
792A PRO* 1.3 70.3 - - + +
814A LEU* 5.1 4.9 - - + +
815A MET* 3.9 39.5 - - + -
818A HIS* 4.2 8.1 - - + -
1023A EDO 5.7 0.2 - - - +
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Residues in contact with PRO 792 (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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427A HIS* 5.1 9.6 - - + +
704A PHE* 3.4 10.0 - - - -
761A THR 3.8 0.4 - - - +
762A HIS* 3.5 20.4 - - + +
790A ILE 3.7 0.9 - - - +
791A LEU* 1.3 87.0 - - + +
793A HIS* 1.3 60.4 + - - +
794A ARG* 3.3 19.0 + - + -
799A GLU* 4.0 9.2 - - - +
814A LEU* 5.1 2.9 - - + -
818A HIS* 3.7 43.1 - - + +
1023A EDO 2.7 34.4 + - - +
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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