Contacts of the helix formed by residues 727 - 737 (chain B) in PDB entry 1UKJ
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 727 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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581B GLU* 3.7 18.4 - - - -
582B ALA* 4.4 0.2 - - - -
703B ASP 3.9 6.8 + - - -
704B LEU* 4.1 3.0 - - - +
726B GLY* 1.3 73.1 - - - -
728B GLN* 1.3 59.5 + - - +
729B ALA* 3.3 9.4 + - - +
730B LEU* 3.1 30.1 + - - +
731B VAL* 2.8 31.5 + - - +
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Residues in contact with GLN 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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581B GLU* 3.2 32.1 + - + +
582B ALA* 3.2 29.4 - - + +
727B SER* 1.3 72.0 + - - +
729B ALA* 1.3 57.2 + - - +
731B VAL* 5.3 0.2 - - - +
732B ASP* 2.9 66.6 + - - +
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Residues in contact with ALA 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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727B SER* 3.2 7.9 + - - +
728B GLN* 1.3 75.6 - - - +
730B LEU* 1.3 67.6 + - + +
732B ASP* 3.9 5.6 - - - +
733B ARG* 3.3 29.3 + - - +
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Residues in contact with LEU 730 (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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600B LEU* 4.1 20.4 - - + +
652B ARG* 6.0 0.7 - - - +
682B THR* 4.7 8.5 - - + +
703B ASP* 4.0 35.7 - - + +
704B LEU* 3.6 29.4 - - + -
727B SER* 3.1 22.5 + - - +
729B ALA* 1.3 81.9 - - + +
731B VAL* 1.3 62.6 + - - +
733B ARG* 3.4 19.4 + - - +
734B ILE* 3.2 28.4 + - - +
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Residues in contact with VAL 731 (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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582B ALA* 3.4 33.2 - - + +
583B GLY 3.5 29.4 - - - +
584B LEU* 3.8 14.8 - - + -
704B LEU* 4.3 4.7 - - + -
724B VAL* 4.6 5.6 - - + +
725B VAL* 4.2 3.6 - - - -
726B GLY* 3.5 16.6 - - - +
727B SER 2.8 25.0 + - - +
730B LEU* 1.3 69.7 - - - +
732B ASP* 1.3 67.5 + - - +
734B ILE* 3.3 6.9 + - - +
735B ARG* 3.0 24.7 + - + +
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Residues in contact with ASP 732 (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 GLN* 2.9 53.1 + - - +
729B ALA* 3.9 5.6 - - - +
730B LEU 3.3 0.2 - - - -
731B VAL* 1.3 76.3 - - - +
733B ARG* 1.3 58.8 + - - +
735B ARG* 3.1 16.4 + - - +
736B LEU* 2.8 42.5 + - + +
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Residues in contact with ARG 733 (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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599B THR* 3.8 19.7 + - - +
600B LEU* 4.2 11.6 - - + +
652B ARG* 3.3 34.4 - - - +
729B ALA* 3.3 13.8 + - - +
730B LEU* 3.6 27.6 - - - +
732B ASP* 1.3 80.3 - - + +
734B ILE* 1.3 57.1 + - + +
736B LEU* 4.6 2.2 - - - +
737B GLN* 3.0 64.9 + - - +
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Residues in contact with ILE 734 (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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584B LEU* 4.0 18.6 - - + -
595B SER* 3.6 24.0 - - - +
596B THR* 3.7 36.3 - - + +
599B THR* 3.9 19.7 - - - +
600B LEU* 5.0 5.6 - - + -
704B LEU* 4.0 17.3 - - + -
724B VAL* 4.1 15.7 - - + -
730B LEU 3.2 20.3 + - - +
731B VAL* 3.7 6.3 - - - +
733B ARG* 1.3 77.1 - - + +
735B ARG* 1.3 57.5 + - - +
738B GLY 3.0 4.3 + - - -
739B LEU* 3.0 26.3 + - - +
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Residues in contact with ARG 735 (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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562B ILE* 2.7 44.2 + - + +
563B SER* 3.4 20.1 - - - +
568B ASN* 4.2 4.2 + - - -
571B GLU* 2.8 34.4 + - - -
583B GLY 3.9 10.3 + - - -
584B LEU* 3.9 27.6 - - + +
731B VAL* 3.0 16.0 + - - +
732B ASP* 3.1 18.6 + - - +
734B ILE* 1.3 78.1 - - - +
736B LEU* 1.3 78.7 + - + +
737B GLN 3.2 2.0 + - - -
739B LEU* 3.7 6.4 - - + +
740B LYS* 3.2 24.4 + - - +
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Residues in contact with LEU 736 (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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562B ILE* 4.1 25.8 - - + -
732B ASP* 2.8 26.0 + - + +
733B ARG* 4.3 3.4 - - - +
735B ARG* 1.3 89.9 - - + +
737B GLN* 1.3 65.3 + - + +
740B LYS* 3.7 20.9 - - + +
741B ASP* 3.6 13.0 - - - +
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Residues in contact with GLN 737 (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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599B THR* 3.2 29.6 + - - +
602B ARG* 5.6 4.1 - - - +
733B ARG* 3.0 45.7 + - - +
735B ARG 3.2 0.8 - - - -
736B LEU* 1.3 88.9 - - + +
738B GLY* 1.3 68.8 + - - +
739B LEU 3.5 0.9 - - - -
741B ASP* 3.3 15.6 + - - +
742B MET* 3.2 28.8 + - - +
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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