Contacts of the helix formed by residues 761 - 774 (chain B) in PDB entry 1J1C
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 SER 761 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A ASP* 5.1 3.4 - - - -
216A TYR 4.6 0.2 - - - -
218A CYS 3.5 32.3 - - - -
219A SER* 3.9 6.3 - - - -
223A ARG* 6.1 0.4 - - - +
760B ASP* 1.3 78.3 - - - +
762B GLY* 1.3 64.1 + - - +
763B VAL* 2.9 30.9 - - - +
764B ASP* 3.1 11.3 + - - +
765B GLN* 3.1 27.8 + - - +
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Residues in contact with GLY 762 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TYR* 3.3 19.1 + - - -
218A CYS 4.6 1.2 + - - -
223A ARG* 5.6 1.6 - - - +
728B ILE* 4.0 21.6 - - - +
761B SER* 1.3 73.8 - - - +
763B VAL* 1.3 56.2 + - - +
765B GLN* 3.2 12.7 + - - +
766B LEU* 2.9 31.9 + - - +
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Residues in contact with VAL 763 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A PHE* 5.0 11.4 - - + -
203A SER* 4.7 11.9 - - - +
216A TYR* 3.3 33.6 + - + +
217A ILE* 3.7 22.2 - - + -
218A CYS 5.8 0.7 - - - +
761B SER* 2.9 23.1 - - - +
762B GLY* 1.3 75.7 - - - +
764B ASP* 1.3 67.2 + - - +
766B LEU* 3.3 2.6 + - - +
767B VAL* 3.0 33.2 + - - +
790B GLU* 4.8 4.9 - - - +
793B PHE* 3.8 16.1 - - + -
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Residues in contact with ASP 764 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 3.2 25.7 + - - +
67A PHE* 4.5 4.3 - - - -
183A LYS* 5.1 6.8 + - - -
219A SER* 5.4 0.2 + - - -
758B PRO 4.2 2.5 - - - +
759B GLY* 3.8 15.4 - - - -
760B ASP* 4.0 13.4 + - - +
761B SER* 3.1 21.6 + - - +
763B VAL* 1.3 90.3 - - - +
765B GLN* 1.3 63.3 + - - +
767B VAL* 3.2 8.8 + - - +
768B GLU* 3.1 26.0 + - - +
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Residues in contact with GLN 765 (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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720B ARG* 3.8 14.0 - - - +
721B TYR* 4.4 16.2 - - - +
723B ARG* 4.7 13.3 - - - +
728B ILE* 3.6 28.8 - - + +
757B PHE* 3.8 19.1 - - + +
758B PRO 3.8 6.7 - - - -
759B GLY* 3.2 25.7 - - - +
760B ASP 4.7 1.4 - - - -
761B SER 3.1 21.9 + - - +
762B GLY* 3.5 9.8 - - - +
764B ASP* 1.3 77.6 - - - +
766B LEU* 1.3 63.1 + - - +
768B GLU* 3.2 4.9 + - - +
769B ILE* 3.0 29.3 + - + +
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Residues in contact with LEU 766 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A TYR* 3.6 35.9 - - + -
725B PRO* 4.6 6.3 - - + -
728B ILE* 3.9 26.0 - - + -
729B PHE* 3.7 37.2 - - + -
762B GLY 2.9 15.3 + - - +
763B VAL 3.7 4.9 - - - +
765B GLN* 1.3 75.8 - - - +
767B VAL* 1.3 57.8 + - - +
769B ILE* 3.3 14.9 + - + +
770B ILE* 2.8 42.3 + - + +
793B PHE* 3.9 17.5 - - + -
823B TYR* 5.8 3.1 - - + -
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Residues in contact with VAL 767 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 3.7 35.2 - - - +
67A PHE* 3.5 33.9 - - + -
763B VAL 3.0 20.9 + - - +
764B ASP 3.4 8.5 - - - +
766B LEU* 1.3 76.4 - - - +
768B GLU* 1.3 58.8 + - - +
770B ILE* 3.3 6.7 + - - +
771B LYS* 2.8 43.3 + - + +
793B PHE* 3.5 14.1 - - + -
794B PRO* 6.1 0.4 - - + -
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Residues in contact with GLU 768 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 4.5 8.1 - - - -
756B ILE 4.4 5.6 - - - +
757B PHE* 3.7 18.0 - - + -
758B PRO* 3.3 36.5 - - + +
764B ASP 3.1 8.5 + - - +
765B GLN 3.5 7.4 - - - +
767B VAL* 1.3 81.2 - - - +
769B ILE* 1.3 61.3 + - - +
771B LYS* 3.1 49.6 + - - +
772B VAL* 3.5 15.4 + - - +
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Residues in contact with ILE 769 (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 ARG 5.0 1.8 - - - +
725B PRO* 4.7 5.6 - - + -
728B ILE* 4.2 24.9 - - + -
741B TRP* 3.8 25.4 - - + -
757B PHE* 3.5 32.1 - - + -
765B GLN* 3.0 20.0 + - + +
766B LEU* 3.5 15.9 - - + +
768B GLU* 1.3 74.6 - - - +
770B ILE* 1.3 53.9 + - - +
772B VAL* 3.1 3.1 + - - +
773B LEU* 2.7 46.4 + - + +
823B TYR* 3.7 28.3 - - + +
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Residues in contact with ILE 770 (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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766B LEU* 2.8 28.2 + - + +
767B VAL* 3.7 5.4 - - - +
769B ILE* 1.3 73.6 - - + +
771B LYS* 1.3 63.3 + - + +
774B GLY* 2.6 29.9 + - - -
775B THR* 3.7 27.8 - - - +
776B PRO* 4.0 17.7 - - + -
793B PHE* 3.9 39.0 - - + -
794B PRO 4.2 5.2 - - - +
796B ILE* 3.6 19.3 - - + +
823B TYR* 3.4 21.3 - - + +
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Residues in contact with LYS 771 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A SER* 3.8 25.0 + - - +
767B VAL* 2.8 21.9 + - + +
768B GLU* 3.1 44.6 + - - +
769B ILE 3.2 0.2 - - - -
770B ILE* 1.3 79.3 - - - +
772B VAL* 1.3 53.1 + - + +
796B ILE* 4.2 18.3 - - + +
797B LYS 4.2 4.0 - - - +
799B HIS* 2.7 35.1 + - + +
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Residues in contact with VAL 772 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756B ILE* 4.7 9.4 - - + +
757B PHE* 4.0 15.0 - - + -
768B GLU 3.5 13.0 + - - +
769B ILE 3.1 5.4 + - - +
770B ILE 3.1 0.2 - - - -
771B LYS* 1.3 80.9 - - + +
773B LEU* 1.3 61.7 + - + +
774B GLY 3.4 0.2 - - - -
798B ALA* 4.4 1.0 - - - +
799B HIS* 3.1 34.1 + - + +
801B TRP* 3.8 42.0 + - + -
804B VAL* 3.9 28.0 - - + -
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Residues in contact with LEU 773 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
741B TRP* 4.0 19.7 - - + -
757B PHE* 4.8 3.4 - - + -
769B ILE* 2.7 25.4 + - + +
772B VAL* 1.3 79.8 - - + +
774B GLY* 1.3 59.3 + - - +
775B THR 5.2 0.3 - - - +
798B ALA* 4.0 13.0 - - - +
801B TRP* 3.4 37.9 - - + +
821B LEU* 3.3 27.1 - - + +
822B GLU* 4.4 0.4 - - - -
823B TYR* 3.6 44.2 - - + +
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Residues in contact with GLY 774 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
770B ILE* 2.6 26.9 + - - -
772B VAL 3.4 1.6 - - - -
773B LEU* 1.3 77.1 - - - +
775B THR* 1.3 61.6 + - - -
796B ILE 3.6 10.5 - - - -
797B LYS 3.9 0.9 - - - -
798B ALA* 3.9 15.4 - - - +
823B TYR* 2.5 31.5 + - - -
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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
------------------------------------------------------------
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