Contacts of the strand formed by residues 832 - 840 (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 832 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A LYS* 3.8 22.2 - - + -
677A GLN* 4.8 0.2 - - - +
679A HIS* 3.5 48.7 - - + +
831A TYR* 1.3 92.9 - - + +
833A VAL* 1.3 67.5 + - - +
834A PHE* 5.1 3.8 - - + +
849A ILE* 4.4 11.4 - - + +
850A ILE* 3.4 2.8 - - - +
851A GLN* 3.2 48.9 + - + +
21C VAL 5.9 1.8 - - - +
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Residues in contact with VAL 833 (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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819A ALA* 4.1 4.9 - - + +
820A PHE* 4.0 38.7 - - + +
823A LEU* 3.8 35.4 - - + +
824A ARG* 4.1 16.4 - - + +
829A LEU* 5.0 0.2 - - + -
830A GLY 4.0 17.5 - - - +
831A TYR 3.4 4.6 + - - +
832A ILE* 1.3 79.8 - - - +
834A PHE* 1.3 64.5 + - - +
848A PHE* 6.4 1.8 - - + -
849A ILE 3.5 3.8 - - - -
850A ILE* 4.3 18.2 - - + -
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Residues in contact with PHE 834 (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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832A ILE* 5.5 4.5 - - + -
833A VAL* 1.3 79.2 - - - +
835A SER* 1.3 84.9 + - - +
836A GLY* 4.3 5.6 - - - -
837A PRO* 5.1 1.6 - - + -
847A ARG* 3.3 40.6 - - - -
848A PHE* 3.3 6.6 - - - +
849A ILE* 2.8 63.7 + - + +
850A ILE* 5.5 0.3 - - - +
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Residues in contact with SER 835 (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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812A ALA 5.3 0.3 + - - -
815A ILE* 4.3 8.0 + - - +
816A SER* 4.2 17.2 + - - -
819A ALA* 3.8 19.0 - - - +
833A VAL* 6.4 0.2 - - - -
834A PHE* 1.3 98.3 - - - +
836A GLY* 1.3 59.6 + - - +
846A LEU* 5.6 0.4 - - - -
847A ARG 3.2 8.3 - - - -
848A PHE* 3.7 29.8 - - - -
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Residues in contact with GLY 836 (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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812A ALA* 4.3 7.8 - - - +
815A ILE* 5.9 0.4 - - - +
834A PHE* 4.5 5.2 - - - -
835A SER* 1.3 78.8 + - - +
837A PRO* 1.3 75.2 - - - +
846A LEU* 3.4 14.6 - - - +
847A ARG* 3.1 30.0 + - - +
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Residues in contact with PRO 837 (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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808A LEU* 4.0 17.5 - - + -
809A GLU* 4.5 16.4 - - + -
812A ALA* 3.8 20.2 - - + -
834A PHE* 5.0 1.7 - - + -
836A GLY* 1.3 85.9 - - - +
838A ARG* 1.3 58.4 + - - +
839A ARG* 3.9 28.2 + - - +
845A GLY 3.4 7.2 - - - +
847A ARG* 3.4 18.6 + - - -
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Residues in contact with ARG 838 (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 5.1 1.4 + - - -
686A LEU* 3.1 34.7 - - - +
687A ARG* 4.2 21.3 - - - +
690A MET* 4.2 13.7 - - - +
691A THR* 5.9 0.8 + - - -
768A GLU* 3.6 19.2 + - - -
792A GLU* 4.0 15.8 + - - -
794A TYR* 3.7 41.6 + - + -
836A GLY 3.9 0.2 + - - -
837A PRO* 1.3 73.2 - - - +
839A ARG* 1.3 64.1 + - - +
840A ALA* 3.6 20.4 - - - +
841A ASN* 5.4 0.4 - - - +
844A GLN* 3.0 29.9 - - - +
845A GLY 2.7 10.7 + - - +
847A ARG* 3.8 27.9 - - + +
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Residues in contact with ARG 839 (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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800A GLN* 3.6 27.6 - - - +
805A ASN* 3.8 19.4 + - - +
808A LEU* 4.6 1.2 - - - +
809A GLU* 2.8 43.7 + - - +
837A PRO* 3.9 23.2 - - - +
838A ARG* 1.3 86.5 - - - +
840A ALA* 1.3 61.9 + - - +
843A ILE 3.4 3.8 - - - -
844A GLN* 2.7 26.9 + - + -
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Residues in contact with ALA 840 (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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768A GLU* 3.6 13.7 + - - +
794A TYR* 5.6 0.8 + - - -
800A GLN* 4.6 0.2 - - - -
838A ARG* 3.6 29.4 - - - +
839A ARG* 1.3 75.0 - - - +
841A ASN* 1.3 80.6 + - - +
842A GLY 3.2 2.7 - - - -
843A ILE* 2.9 19.8 + - - +
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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