Contacts of the helix formed by residues 724 - 729 (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 ALA 724 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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722B TYR 3.6 1.4 + - - -
723B ARG* 1.3 75.7 - - - +
725B PRO* 1.3 67.9 - - + +
726B GLU* 3.4 29.8 - - + +
727B LEU* 2.9 25.4 + - + +
728B ILE* 3.2 9.4 + - - +
738B ILE* 4.0 18.8 + - + +
741B TRP* 3.4 26.3 - - + +
742B SER* 5.1 1.0 + - - -
828B ARG* 4.1 0.4 - - - +
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Residues in contact with PRO 725 (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 3.7 0.4 - - - -
724B ALA* 1.3 87.2 - - + +
726B GLU* 1.3 59.7 + - - +
728B ILE* 3.2 14.4 + - + +
729B PHE* 2.9 42.3 + - + -
741B TRP* 3.5 40.2 - - + -
766B LEU* 4.6 9.2 - - + -
769B ILE* 4.7 4.9 - - + -
784B MET* 3.0 35.9 - - + -
823B TYR* 4.3 5.6 - - + -
828B ARG* 3.9 4.3 - - - +
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Residues in contact with GLU 726 (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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724B ALA* 3.4 12.2 - - - +
725B PRO* 1.3 74.8 - - - +
727B LEU* 1.3 61.5 + - - +
729B PHE* 3.5 4.3 + - - +
730B GLY 3.3 3.6 + - - -
731B ALA* 2.8 31.8 + - + +
734B TYR* 4.2 15.9 - - + +
735B THR 5.4 0.5 + - - -
737B SER* 4.2 1.7 + - - -
738B ILE* 3.2 24.4 - - + +
784B MET* 3.5 40.2 - - + +
825B PRO* 3.9 16.7 - - + +
828B ARG* 2.8 43.1 + - - -
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Residues in contact with LEU 727 (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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715B SER* 3.9 12.9 + - - +
717B ILE* 3.6 29.8 - - + +
718B CYS* 3.9 19.3 - - + -
723B ARG* 3.3 25.5 + - + +
724B ALA 2.9 23.6 + - - +
726B GLU* 1.3 76.6 - - - +
728B ILE* 1.3 59.8 + - - +
730B GLY* 2.8 20.3 + - - -
731B ALA 4.4 1.8 - - - +
734B TYR* 3.5 44.6 - - + -
738B ILE* 4.1 22.9 - - + -
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Residues in contact with ILE 728 (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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215A SER* 5.1 1.2 + - - -
216A TYR* 3.5 29.4 - - + +
723B ARG* 3.9 34.8 + - + +
724B ALA 3.6 9.6 - - - +
725B PRO* 3.2 10.5 + - + +
727B LEU* 1.3 76.5 - - - +
729B PHE* 1.3 59.2 + - - +
730B GLY* 3.0 4.2 + - - -
762B GLY* 4.0 13.9 - - - +
765B GLN* 3.6 31.4 - - + +
766B LEU* 3.9 28.7 - - + -
769B ILE* 4.2 21.5 - - + -
788B TYR* 4.9 0.7 - - - -
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Residues in contact with PHE 729 (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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216A TYR* 3.6 34.5 - + - -
725B PRO* 2.9 27.6 + - + +
726B GLU* 3.9 5.4 - - - +
727B LEU 3.1 0.4 - - - -
728B ILE* 1.3 75.1 - - - +
730B GLY* 1.3 57.9 + - - +
731B ALA 3.5 0.2 - - - -
766B LEU* 3.7 31.6 - - + -
776B PRO* 5.3 9.4 - - + -
781B ILE* 5.3 24.0 - - + -
784B MET* 3.8 29.6 - - + -
785B ASN* 3.2 19.1 - - + +
788B TYR* 2.8 42.3 - - + -
790B GLU 5.1 4.9 - - - -
793B PHE* 5.7 3.8 - + - -
823B TYR* 5.9 0.9 - + - -
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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