Contacts of the helix formed by residues 747 - 759 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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743B MET* 3.5 30.5 - - + +
744B GLN* 3.3 23.1 - - - +
746B TYR* 1.3 77.0 - - - +
748B PRO* 1.4 67.8 - - + +
750B VAL* 3.1 3.5 + - - +
751B LEU* 2.8 52.7 + - + +
778B LEU* 3.7 26.9 - - + +
782B CYS* 4.5 10.5 - - + -
785B GLU* 3.6 32.5 - - + +
786B VAL* 4.6 2.2 - - + -
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Residues in contact with PRO 748 (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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744B GLN 3.9 5.2 - - - +
745B PRO* 3.4 16.2 - - + +
747B ILE* 1.4 97.2 - - + +
749B MET* 1.3 59.5 + - + +
750B VAL 3.1 4.2 + - - -
751B LEU* 4.3 3.8 - - + +
752B HIS* 4.0 19.6 - - + +
753B GLN* 5.9 0.2 - - - +
785B GLU* 5.5 3.8 - - - +
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Residues in contact with MET 749 (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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710B MET* 4.2 32.8 - - - +
711B PRO* 4.3 14.4 - - + -
714B GLY* 3.9 5.0 - - - -
745B PRO 4.0 19.3 - - - +
746B TYR* 3.3 27.6 - - + +
748B PRO* 1.3 80.7 - - + +
750B VAL* 1.3 65.9 + - + +
753B GLN* 2.8 23.0 + - - -
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Residues in contact with VAL 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
710B MET* 3.7 29.6 - - + +
714B GLY* 4.3 12.3 - - - +
717B LEU* 3.8 3.3 - - + +
732B ILE* 3.6 37.5 - - + -
746B TYR 4.0 4.7 - - - +
747B ILE* 3.1 5.1 + - - +
748B PRO 3.1 0.8 - - - -
749B MET* 1.3 88.3 - - + +
751B LEU* 1.3 68.0 + - - +
752B HIS 3.2 1.8 - - - -
753B GLN* 3.0 21.8 + - - +
754B LEU* 3.2 30.5 + - + +
778B LEU* 4.4 5.6 - - + -
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Residues in contact with LEU 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
747B ILE* 2.8 36.5 + - + +
748B PRO* 4.8 2.2 - - + -
750B VAL* 1.3 76.3 - - - +
752B HIS* 1.3 60.4 + - - +
753B GLN 3.1 1.2 + - - -
754B LEU* 3.4 11.4 + - - -
755B VAL* 3.5 15.7 + - + +
775B ILE* 4.7 17.3 - - + -
778B LEU* 4.6 14.4 - - + -
785B GLU 3.4 25.6 - - - +
786B VAL* 3.6 31.4 - - + +
789B MET* 3.6 26.2 - - + +
793B PHE* 5.8 2.7 - - + -
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Residues in contact with HIS 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748B PRO* 4.0 17.2 + - + +
750B VAL 3.2 0.8 - - - -
751B LEU* 1.3 78.0 - - - +
753B GLN* 1.3 64.4 + - + +
755B VAL* 3.4 21.9 - - + +
756B GLU* 3.5 27.9 + - + +
789B MET* 5.3 11.3 - - - -
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Residues in contact with GLN 753 (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 GLY* 2.8 31.4 + - - +
717B LEU* 3.3 26.8 - - + +
718B ASN* 5.4 1.6 - - - +
749B MET* 2.8 28.8 + - - +
750B VAL 3.0 9.3 + - - +
752B HIS* 1.3 85.6 - - + +
754B LEU* 1.3 64.8 + - - +
755B VAL 3.2 1.8 - - - -
756B GLU* 3.2 10.3 + - - +
757B ILE* 3.2 26.0 + - - +
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Residues in contact with LEU 754 (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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717B LEU* 3.8 18.2 - - + -
729B THR* 3.7 32.1 - - + -
732B ILE* 5.1 0.2 - - + -
750B VAL* 3.2 29.3 + - + +
751B LEU* 3.4 5.8 + - - +
753B GLN* 1.3 77.1 - - - +
755B VAL* 1.3 57.0 + - - +
757B ILE* 3.2 8.8 + - + +
758B ILE* 2.9 26.0 + - - +
771B THR* 3.4 17.0 - - + +
774B THR* 3.7 26.5 - - + -
775B ILE* 3.8 23.8 - - + -
778B LEU* 3.8 13.0 - - + -
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Residues in contact with VAL 755 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
751B LEU* 3.5 14.8 + - + +
752B HIS* 3.4 27.8 - - + +
754B LEU* 1.3 78.9 - - - +
756B GLU* 1.3 67.3 + - + +
758B ILE* 3.3 11.9 - - - +
759B ASN* 2.9 41.1 + - - +
775B ILE* 4.3 6.0 - - + +
789B MET* 5.3 10.1 - - + +
792B GLN* 4.0 25.1 - - + +
793B PHE* 3.9 21.3 - - + -
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Residues in contact with GLU 756 (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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752B HIS* 3.5 40.5 + - + +
753B GLN* 3.2 10.3 + - - +
755B VAL* 1.3 80.1 - - + +
757B ILE* 1.3 65.2 + - + +
759B ASN* 3.5 11.9 - - - +
760B ARG* 3.4 18.2 - - - +
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Residues in contact with ILE 757 (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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717B LEU* 3.2 33.2 - - + +
719B PRO* 4.0 17.7 - - + -
725B CYS* 3.6 17.3 - - - -
729B THR* 4.9 1.3 - - + -
753B GLN* 3.2 17.4 + - + +
754B LEU* 3.2 17.0 + - + +
756B GLU* 1.3 77.8 - - + +
758B ILE* 1.3 62.8 + - - +
759B ASN 3.1 0.2 - - - -
760B ARG* 3.2 21.9 + - + +
763B THR* 3.9 5.6 + - + +
767B LEU* 4.1 23.1 - - + -
768B LEU* 3.7 9.2 - - + +
771B THR* 3.8 17.5 - - - +
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Residues in contact with ILE 758 (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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754B LEU 2.9 14.9 + - - +
755B VAL* 3.3 20.2 - - - +
757B ILE* 1.3 77.3 - - - +
759B ASN* 1.3 63.7 + - - +
760B ARG 3.3 3.7 + - - +
768B LEU* 3.7 27.2 - - + +
771B THR* 3.8 10.1 - - + -
772B ALA* 4.1 24.9 - - + +
775B ILE* 4.5 7.9 - - + -
793B PHE* 4.0 13.2 - - + +
796B PRO* 3.2 38.2 - - + +
797B TRP* 3.8 33.9 - - + +
800B SER* 5.7 0.2 - - - -
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Residues in contact with ASN 759 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
755B VAL* 2.9 31.4 + - - +
756B GLU* 3.5 8.1 - - - +
757B ILE 3.1 0.6 - - - -
758B ILE* 1.3 81.8 - - - +
760B ARG* 1.3 57.4 + - - +
761B PRO* 4.1 5.1 - - - +
792B GLN* 3.0 24.8 + - - +
795B ARG* 5.0 2.3 - - - +
796B PRO* 3.2 26.2 - - - +
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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