Contacts of the strand formed by residues 869 - 874 (chain J) in PDB entry 6H25
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 869 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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637J VAL* 6.3 0.9 - - + -
836J THR* 5.6 6.7 - - - +
863J LEU* 3.4 6.2 - - - -
864J ILE* 2.9 31.8 + - + +
867J TYR* 4.6 10.7 - - + +
868J GLY* 1.3 77.7 - - - +
870J GLU* 1.3 69.6 + - - +
871J GLY 4.1 0.2 + - - -
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Residues in contact with GLU 870 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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635J PRO* 5.3 9.7 - - + +
742J ILE* 5.8 3.1 - - - +
746J ARG* 4.5 22.4 + - - -
861J VAL* 4.8 9.3 - - + +
862J VAL 3.5 8.5 - - - +
863J LEU* 4.7 16.6 - - + +
869J LEU* 1.3 83.1 - - - +
871J GLY* 1.3 57.9 + - - +
925J MET* 5.1 1.5 - - - +
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Residues in contact with GLY 871 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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861J VAL* 3.5 5.7 - - - +
862J VAL* 2.8 43.7 + - - +
869J LEU 4.1 0.2 + - - -
870J GLU* 1.3 76.6 - - - +
872J THR* 1.3 62.7 + - - -
873J VAL* 4.2 0.5 + - - +
925J MET* 3.7 25.0 - - - +
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Residues in contact with THR 872 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856J ARG* 4.5 8.8 - - - +
860J ILE 3.5 11.9 + - - -
861J VAL* 3.7 19.2 - - - +
871J GLY* 1.3 74.1 - - - -
873J VAL* 1.3 66.6 + - - +
874J PHE* 3.5 38.2 - - + -
923J ILE 4.5 8.3 + - - +
924J ARG* 5.4 0.7 - - - -
925J MET* 3.5 14.9 + - - +
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Residues in contact with VAL 873 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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859J ALA* 3.1 3.6 - - - +
860J ILE* 2.9 61.1 + - + +
862J VAL* 5.4 6.7 - - + -
871J GLY 5.6 0.7 - - - +
872J THR* 1.3 74.3 - - - +
874J PHE* 1.3 73.3 + - - +
875J PHE* 4.0 7.0 + - + +
909J VAL* 5.9 5.2 - - + -
924J ARG* 6.4 0.7 - - + -
925J MET* 3.8 16.2 - - + +
926J SER* 4.1 34.1 - - - +
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Residues in contact with PHE 874 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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856J ARG* 5.4 7.4 - - - -
858J ASN* 5.7 2.0 - - - -
859J ALA* 3.5 18.6 - - + -
872J THR* 3.5 31.4 - - + -
873J VAL* 1.3 85.6 - - - +
875J PHE* 1.3 61.2 + - - +
876J GLU* 3.5 7.6 + - + +
877J GLU* 5.1 10.9 + - + +
878J LYS* 5.3 6.4 + - - +
922J LYS* 5.7 11.4 - - + -
924J ARG* 6.0 4.3 - - - +
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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