Contacts of the strand formed by residues 843 - 852 (chain A) in PDB entry 3H44
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 ILE 843 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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768A GLU* 3.4 31.9 - - + +
794A TYR* 4.4 1.6 - - - -
796A GLN* 3.8 15.9 - - + +
798A ASP 4.6 0.7 - - - -
799A MET* 3.6 23.3 - - + +
800A GLN* 3.0 13.5 + - - -
840A ALA 2.9 23.9 + - - +
841A ASN 2.9 24.8 + - - +
842A GLY* 1.3 81.4 - - - +
844A GLN* 1.3 80.4 + - - +
1005A PHE* 3.4 46.0 - - + -
1006A PRO 3.6 12.1 - - - +
1008A VAL* 5.8 0.4 - - + -
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Residues in contact with GLN 844 (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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794A TYR* 3.2 15.0 + - - -
796A GLN* 3.6 4.5 - - - +
797A THR* 2.9 25.8 + - - +
798A ASP 3.3 17.5 + - - +
799A MET 3.8 1.0 + - - -
800A GLN* 3.6 13.4 - - + +
804A GLU* 3.3 24.4 + - - +
805A ASN* 2.7 30.4 + - - +
808A LEU* 3.2 11.9 - - + +
838A ARG 3.0 15.7 - - - +
839A ARG* 2.7 38.0 + - + -
843A ILE* 1.3 85.3 - - - +
845A GLY* 1.3 60.2 + - - +
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Residues in contact with GLY 845 (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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794A TYR* 3.5 8.2 - - - -
795A TYR 3.0 15.3 - - - -
797A THR* 3.7 10.3 - - - -
808A LEU* 3.2 16.1 - - - +
837A PRO* 3.4 0.9 - - - +
838A ARG 2.7 29.2 + - - -
844A GLN* 1.3 80.3 - - - +
846A LEU* 1.3 56.8 + - - -
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Residues in contact with LEU 846 (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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793A ILE 3.8 0.2 - - - +
794A TYR* 3.5 3.2 - - - -
795A TYR* 2.7 50.3 + - + +
797A THR* 4.9 0.4 - - - +
808A LEU* 3.7 18.7 - - + +
811A PHE* 4.1 28.7 - - + -
812A ALA* 4.4 15.7 - - + -
815A ILE* 4.1 4.9 - - + -
835A SER* 5.6 0.2 - - - -
836A GLY* 3.4 31.2 - - - +
845A GLY* 1.3 73.6 - - - -
847A ARG* 1.3 61.5 + - - +
848A PHE* 3.8 31.2 - - + -
867A LEU* 5.0 3.1 - - + -
944A LEU* 4.7 11.7 - - + -
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Residues in contact with ARG 847 (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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683A MET* 3.9 15.5 - - - +
687A ARG* 6.0 0.2 - - - +
792A GLU* 3.1 29.4 + - + +
793A ILE 3.0 12.8 - - - +
794A TYR* 4.6 4.0 - - + -
834A PHE* 3.3 33.7 - - + -
835A SER* 3.2 23.4 - - - -
836A GLY 3.1 17.7 + - - +
837A PRO 3.4 15.5 + - - -
838A ARG* 3.8 30.0 - - + +
846A LEU* 1.3 76.4 - - - +
848A PHE* 1.3 68.6 + - - +
849A ILE* 3.9 19.0 - - - +
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Residues in contact with PHE 848 (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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791A ILE* 3.7 1.7 - - + +
792A GLU* 3.2 8.0 - - - +
793A ILE* 2.9 37.1 + - + -
795A TYR* 3.8 24.9 - + - -
815A ILE* 3.9 20.9 - - + -
819A ALA* 4.5 5.6 - - + -
823A LEU* 5.2 5.6 - - + -
833A VAL* 6.4 1.6 - - + -
834A PHE 3.3 6.1 - - - +
835A SER* 3.7 23.6 - - - -
846A LEU* 3.8 15.3 - - + -
847A ARG* 1.3 75.0 - - - +
849A ILE* 1.3 67.5 + - - +
850A ILE* 4.3 6.1 - - + -
863A VAL* 3.6 44.2 - - + -
866A PHE* 4.3 18.2 - + - -
867A LEU* 4.0 15.0 - - + -
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Residues in contact with ILE 849 (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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679A HIS* 3.9 37.7 - - + +
683A MET* 3.8 36.1 - - + -
791A ILE 3.4 9.9 - - - +
792A GLU* 3.8 20.9 - - + +
832A ILE* 3.9 5.4 - - + +
833A VAL* 3.5 1.9 + - - -
834A PHE* 2.8 63.2 + - + +
847A ARG* 3.9 12.6 - - - +
848A PHE* 1.3 80.8 - - - +
850A ILE* 1.3 66.4 + - - +
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Residues in contact with ILE 850 (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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679A HIS* 4.5 5.0 - - - +
789A SER 3.9 0.5 - - - +
790A GLY* 3.5 2.3 - - - -
791A ILE* 2.9 45.1 + - + +
823A LEU* 4.7 5.8 - - + -
829A LEU* 4.2 26.2 - - + +
832A ILE 3.4 8.5 - - - +
833A VAL* 4.3 19.3 - - + -
834A PHE 5.5 0.2 - - - +
848A PHE* 5.2 4.9 - - + -
849A ILE* 1.3 83.2 - - - +
851A GLN* 1.3 66.1 + - - +
852A SER* 3.8 23.3 + - - -
859A LEU* 4.2 16.1 - - + +
863A VAL* 4.1 26.2 - - + -
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Residues in contact with GLN 851 (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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188A SER* 4.8 0.7 + - - -
192A LYS* 3.8 24.0 - - - +
677A GLN* 3.1 27.1 - - - +
678A PRO* 3.3 17.0 - - + +
679A HIS* 3.0 32.8 + - + -
786A HIS* 5.6 0.6 + - - -
788A ASN* 3.5 25.8 + - + +
789A SER 3.3 11.4 - - - +
790A GLY* 4.4 0.2 - - - -
830A GLY* 3.5 19.1 - - - -
831A TYR 4.1 3.6 + - - -
832A ILE* 3.2 28.3 + - + +
850A ILE* 1.3 74.5 - - - +
852A SER* 1.3 64.1 + - - +
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Residues in contact with SER 852 (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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188A SER* 5.3 0.9 - - - -
788A ASN* 3.0 9.7 - - - +
789A SER* 2.8 40.6 + - - -
829A LEU* 2.8 23.9 + - - -
830A GLY* 4.6 1.1 - - - -
850A ILE* 3.8 14.1 - - - -
851A GLN* 1.3 76.9 - - - +
853A GLU* 1.3 63.1 + - - +
854A LYS* 3.0 16.6 + - - +
859A LEU* 3.6 23.8 - - - +
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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