Contacts of the helix formed by residues 720 - 727 (chain B) in PDB entry 3KUL
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 720 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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719B GLY* 1.3 70.5 - - - -
721B LEU* 1.3 59.1 + - - +
722B ASP* 3.2 20.0 - - - -
723B THR* 3.2 14.5 + - - -
724B PHE* 3.0 29.9 + - - +
764B ARG* 2.8 24.7 + - - +
766B VAL 3.5 7.0 - - - -
767B LEU* 4.0 8.3 - - - +
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Residues in contact with LEU 721 (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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719B GLY 3.6 1.2 + - - -
720B SER* 1.3 70.2 - - - +
722B ASP* 1.3 67.2 + - - +
724B PHE* 4.1 3.6 - - + -
725B LEU* 3.1 43.3 + - + +
740B MET* 4.2 13.5 - - + -
741B LEU* 5.6 0.2 - - + -
744B VAL* 4.9 4.0 - - + -
763B ALA* 3.4 18.8 + - + +
766B VAL* 2.9 38.6 + - + +
768B VAL* 3.7 24.7 - - + -
774B CYS* 4.0 13.9 - - - -
827B VAL* 4.8 4.3 - - + -
831B VAL* 3.5 28.3 - - + -
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Residues in contact with ASP 722 (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 SER* 3.2 20.1 - - - -
721B LEU* 1.3 75.9 - - - +
723B THR* 1.3 71.9 + - - +
725B LEU* 3.4 3.7 + - - +
726B ARG* 3.0 55.2 + - - +
763B ALA* 3.6 20.0 + - + +
764B ARG* 3.4 25.9 + - - +
830B GLU* 4.1 9.8 - - - +
835B GLY* 4.0 11.8 - - - -
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Residues in contact with THR 723 (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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718B ASN 5.3 0.7 + - - -
719B GLY* 5.6 0.2 - - - -
720B SER* 3.2 19.6 + - - -
722B ASP* 1.3 91.1 + - - +
724B PHE* 1.3 62.4 + - - +
726B ARG* 3.5 24.6 - - - +
727B THR* 2.9 40.5 + - - +
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Residues in contact with PHE 724 (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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718B ASN* 3.5 49.4 - - + +
720B SER 3.0 19.7 + - - +
721B LEU* 3.7 7.6 - - + +
722B ASP 3.4 0.2 - - - -
723B THR* 1.3 78.2 + - - +
725B LEU* 1.3 71.7 + - + +
727B THR* 3.2 4.8 + - - -
728B HIS* 2.7 53.6 + + - +
732B PHE* 3.5 38.1 - + - -
740B MET* 4.5 6.7 - - + -
768B VAL* 4.2 18.6 - - + -
772B LEU* 3.7 22.4 - - + -
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Residues in contact with LEU 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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721B LEU* 3.1 35.1 + - + +
722B ASP* 3.9 3.8 - - - +
724B PHE* 1.3 81.0 - - + +
726B ARG* 1.3 65.4 + - - +
728B HIS* 3.2 10.5 + - - +
729B ASP* 3.3 12.8 + - - -
732B PHE* 3.8 24.0 - - + -
737B LEU* 3.8 21.5 - - + -
740B MET* 4.2 6.7 - - - -
830B GLU 4.6 1.3 - - - +
831B VAL* 3.7 46.9 - - + +
834B TYR* 3.4 29.4 - - + +
835B GLY 4.8 0.9 - - - +
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Residues in contact with ARG 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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722B ASP* 3.0 49.4 + - - +
723B THR* 3.3 35.1 + - - +
725B LEU* 1.3 77.9 - - - +
727B THR* 1.3 60.1 + - + +
728B HIS 3.3 1.0 + - - -
729B ASP* 4.2 14.2 - - - +
830B GLU* 5.7 0.2 + - - -
834B TYR 3.4 18.8 + - - +
835B GLY 2.8 23.3 + - - +
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Residues in contact with THR 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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723B THR* 2.9 24.5 + - - +
724B PHE* 3.2 9.4 + - - -
726B ARG* 1.3 79.0 - - + +
728B HIS* 1.3 80.7 + - - +
729B ASP 3.7 1.8 - - - -
731B GLN* 4.1 5.0 + - - -
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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