Contacts of the helix formed by residues 747 - 760 (chain A) in PDB entry 5J3V
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 747 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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743A MET* 3.3 17.9 + - + +
744A GLN* 3.8 5.8 - - - +
745A PRO 3.4 0.2 - - - -
746A TYR* 1.3 77.8 - - - +
748A PRO* 1.4 63.6 - - + +
750A VAL* 2.9 22.2 + - - -
751A LEU* 2.9 44.9 + - + +
778A LEU* 4.1 28.0 - - + +
781A VAL* 5.6 0.2 - - + -
782A CYS* 3.5 33.4 - - + +
785A GLU* 4.0 20.4 - - + +
786A VAL* 4.1 14.8 - - + -
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Residues in contact with PRO 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A GLN 3.8 6.3 - - - +
745A PRO* 3.4 17.7 - - + +
746A TYR 3.5 0.9 - - - -
747A ILE* 1.4 98.0 - - + +
749A MET* 1.3 59.4 + - + +
750A VAL 3.2 1.1 + - - -
751A LEU* 4.3 1.9 + - + -
752A HIS* 3.2 33.3 + - + +
785A GLU* 5.7 4.3 - - + -
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Residues in contact with MET 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A MET* 3.6 20.0 - - + +
711A PRO* 4.2 28.5 - - + -
714A GLY* 4.0 8.1 - - - -
745A PRO 4.9 2.5 - - - +
746A TYR* 3.2 52.0 - - + +
748A PRO* 1.3 80.3 - - + +
750A VAL* 1.3 63.7 + - + +
753A GLN* 3.1 25.2 + - - +
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Residues in contact with VAL 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710A MET* 3.6 24.9 - - + +
714A GLY* 4.5 11.2 - - - -
717A LEU* 3.6 8.6 - - + +
732A ILE* 3.6 33.7 - - + -
743A MET* 6.2 0.2 - - + -
746A TYR 3.4 17.9 - - - +
747A ILE* 2.9 7.4 + - - +
748A PRO 3.2 0.4 - - - -
749A MET* 1.3 89.3 - - + +
751A LEU* 1.3 66.3 + - - +
753A GLN* 3.1 11.8 - - - +
754A LEU* 3.3 33.1 + - + +
778A LEU* 4.5 4.5 - - + -
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Residues in contact with LEU 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747A ILE* 2.9 28.6 + - + +
748A PRO* 4.3 1.3 + - + -
750A VAL* 1.3 78.3 - - - +
752A HIS* 1.3 68.2 + - + +
754A LEU* 3.1 11.6 + - + +
755A VAL* 3.0 43.6 + - + +
775A ILE* 5.7 5.6 - - + -
778A LEU* 5.5 6.0 - - + +
785A GLU 3.3 26.2 - - - +
786A VAL* 3.7 28.9 - - + -
789A MET* 3.5 36.1 - - + -
793A PHE* 5.8 1.1 - - + -
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Residues in contact with HIS 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748A PRO* 3.2 31.2 + - + +
750A VAL 3.4 0.6 - - - -
751A LEU* 1.3 82.8 - - + +
753A GLN* 1.3 68.4 + - - +
755A VAL* 3.7 5.3 + - - +
756A GLU* 3.3 21.8 + - - +
789A MET* 4.0 32.4 - - + +
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Residues in contact with GLN 753 (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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714A GLY 3.2 17.5 + - - +
717A LEU* 3.7 36.1 - - + +
748A PRO 4.9 0.2 - - - +
749A MET* 3.1 28.4 + - - +
750A VAL 3.1 12.9 - - - +
751A LEU 3.2 0.2 - - - -
752A HIS* 1.3 77.9 + - - +
754A LEU* 1.3 61.1 + - - +
756A GLU* 3.0 16.5 + - - +
757A ILE* 2.9 32.6 + - + +
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Residues in contact with LEU 754 (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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717A LEU* 4.0 15.9 - - + -
729A THR* 3.8 33.7 - - + +
732A ILE* 5.1 0.4 - - + -
750A VAL* 3.3 24.2 + - + +
751A LEU* 3.1 9.1 + - - +
753A GLN* 1.3 76.3 - - - +
755A VAL* 1.3 61.3 + - - +
757A ILE* 3.3 5.5 + - + -
758A ILE* 3.1 27.0 + - - +
771A THR* 3.4 12.7 - - + +
774A THR* 4.0 10.1 - - + -
775A ILE* 3.7 26.7 - - + -
778A LEU* 3.7 30.3 - - + -
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Residues in contact with VAL 755 (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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751A LEU* 3.0 36.8 + - + +
752A HIS* 4.0 5.8 - - - +
754A LEU* 1.3 75.5 - - - +
756A GLU* 1.3 61.0 + - - +
758A ILE* 3.4 4.1 + - - +
759A ASN* 2.7 46.5 + - - +
775A ILE* 4.3 10.1 - - + -
789A MET* 4.9 8.1 - - + -
792A GLN* 4.3 24.5 - - + +
793A PHE* 4.0 28.5 - - + -
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Residues in contact with GLU 756 (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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719A PRO* 6.4 1.3 - - - -
752A HIS 3.3 10.4 + - - +
753A GLN* 3.0 20.3 + - - +
755A VAL* 1.3 81.7 - - - +
757A ILE* 1.3 62.4 + - + +
759A ASN* 3.6 3.8 + - - +
760A ARG* 3.0 32.6 + - + +
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Residues in contact with ILE 757 (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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717A LEU* 3.7 23.3 - - + +
719A PRO* 3.7 29.8 - - + -
725A CYS* 4.6 6.1 - - - -
729A THR* 6.0 0.2 - - - +
753A GLN* 2.9 19.9 + - + +
754A LEU* 3.3 11.6 + - + +
756A GLU* 1.3 80.6 - - + +
758A ILE* 1.3 66.7 + - - +
760A ARG* 3.3 20.7 + - + +
763A THR* 4.7 5.4 + - + +
767A LEU* 4.1 26.2 - - + +
768A LEU* 3.7 12.1 - - + +
771A THR* 3.9 21.5 - - + +
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Residues in contact with ILE 758 (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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754A LEU 3.1 15.5 + - - +
755A VAL* 3.7 8.5 - - - +
756A GLU 3.3 0.2 - - - -
757A ILE* 1.3 78.2 - - - +
759A ASN* 1.3 66.1 + - - +
760A ARG 3.3 2.8 + - - +
768A LEU* 3.7 23.3 - - + +
771A THR* 3.6 17.9 - - + -
772A ALA* 4.3 8.3 - - + +
775A ILE* 3.6 26.2 - - + -
793A PHE* 3.9 17.5 - - + +
796A PRO* 3.5 36.7 - - + +
797A TRP* 4.2 26.0 - - + +
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Residues in contact with ASN 759 (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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755A VAL* 2.7 37.2 + - - +
756A GLU* 3.9 3.8 - - - +
758A ILE* 1.3 75.9 - - - +
760A ARG* 1.3 63.0 + - - +
761A PRO* 3.4 7.1 - - - +
792A GLN 3.0 28.1 + - - +
793A PHE* 4.2 4.4 - - - +
796A PRO* 3.4 23.6 - - - +
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Residues in contact with ARG 760 (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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719A PRO* 3.6 42.3 + - - +
720A GLU* 6.0 0.8 - - - +
756A GLU* 3.0 21.1 + - + +
757A ILE* 3.3 18.8 - - - +
758A ILE 3.1 5.1 - - - +
759A ASN* 1.3 78.8 - - - +
761A PRO* 1.3 82.5 + - + +
762A ASN* 4.1 1.5 - - - +
763A THR* 2.9 45.4 + - + +
768A LEU* 4.7 1.9 - - - +
56B LYS* 4.0 28.0 - - + +
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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