Contacts of the strand formed by residues 740 - 746 (chain B) in PDB entry 2JIU
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 740 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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730B LEU* 3.4 3.1 - - - -
731B TRP* 2.9 71.7 + - + +
733B PRO* 5.0 6.7 - - + -
738B VAL* 4.0 18.4 - - + +
739B LYS* 1.3 70.8 - - - +
741B PRO* 1.3 86.3 - - + +
742B VAL* 3.5 8.0 + - + -
778B LEU* 4.8 12.6 - - + -
791B GLN* 5.6 1.8 - - + -
792B LEU 4.7 4.5 - - - +
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Residues in contact with PRO 741 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728B LYS* 6.5 1.3 - - + -
729B GLY 3.5 7.4 - - - +
730B LEU* 4.2 10.9 - - + -
739B LYS 3.8 6.3 - - - +
740B ILE* 1.3 96.2 - - + +
742B VAL* 1.3 59.7 + - - +
792B LEU* 3.1 46.0 + - + +
793B MET 4.0 15.0 - - - +
794B PRO* 4.6 9.0 - - + +
997B PHE* 5.1 9.4 - - + -
1001B LEU* 5.4 6.5 - - + -
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Residues in contact with VAL 742 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712B PHE* 4.8 1.8 - - + -
728B LYS* 3.9 0.3 - - - -
729B GLY 2.6 45.8 + - - +
730B LEU 4.0 2.0 - - - +
731B TRP* 3.9 31.6 - - + -
740B ILE* 4.0 2.9 - - + +
741B PRO* 1.3 77.7 - - - +
743B ALA* 1.3 62.9 + - - +
744B ILE* 3.8 17.0 - - + -
778B LEU* 3.4 31.4 - - + -
789B ILE* 3.8 14.6 - - + -
790B MET 3.3 8.1 - - - +
792B LEU* 3.0 19.0 - - - +
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Residues in contact with ALA 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718B LEU* 5.4 3.8 - - + -
726B VAL* 4.3 6.1 - - + -
727B TYR 3.3 11.9 - - - +
728B LYS* 5.4 0.2 - - - -
742B VAL* 1.3 78.8 - - - +
744B ILE* 1.3 64.5 + - - +
789B ILE* 4.7 0.2 - - - -
790B MET* 2.9 31.4 + - + +
792B LEU* 3.6 24.0 - - + -
856B PHE* 3.4 25.0 - - + -
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Residues in contact with ILE 744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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712B PHE* 4.2 15.0 - - + -
713B LYS 4.6 3.6 - - - +
714B LYS* 4.4 21.1 - - + -
725B THR 3.7 1.0 - - - +
726B VAL* 3.4 1.5 - - - -
727B TYR* 2.6 48.4 + - + +
728B LYS 4.5 1.8 - - - -
729B GLY* 4.0 19.5 - - - +
742B VAL* 3.8 23.6 - - + -
743B ALA* 1.3 71.9 - - - +
745B LYS* 1.3 62.8 + - - +
746B GLU* 4.9 0.7 - - - +
787B GLN* 3.6 42.0 - - + +
788B LEU 3.2 6.1 - - - +
789B ILE* 3.6 18.4 - - + -
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Residues in contact with LYS 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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723B PHE* 2.7 49.5 + - - +
724B GLY* 4.7 2.7 - - - -
725B THR 3.3 10.5 - - - +
726B VAL* 4.5 5.6 - - + -
743B ALA 3.6 0.4 + - - -
744B ILE* 1.3 75.2 - - - +
746B GLU* 1.3 69.4 + - - +
747B LEU* 4.8 5.8 - - - +
759B ILE* 4.6 11.4 - - + +
762B GLU* 3.0 32.0 + - - +
786B VAL 4.0 0.3 - - - +
787B GLN* 3.4 1.6 - - - -
788B LEU* 2.7 43.2 + - + +
856B PHE* 3.4 42.6 - - + -
857B GLY 3.7 4.2 - - - +
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Residues in contact with GLU 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714B LYS* 3.2 25.2 + - - -
724B GLY* 3.9 1.7 - - - -
725B THR* 2.9 35.2 + - - +
727B TYR* 3.7 24.4 + - + +
744B ILE* 5.4 0.4 - - + -
745B LYS* 1.3 82.6 - - - +
747B LEU* 1.3 71.5 + - - +
759B ILE* 4.7 2.2 - - - -
785B THR* 3.8 17.9 + - - +
786B VAL 3.6 17.5 - - - +
787B GLN* 3.0 26.9 - - + +
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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