Contacts of the helix formed by residues 731 - 743 (chain B) in PDB entry 3LZB
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 731 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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729B PRO 4.2 0.8 + - - -
730B LYS* 1.3 74.6 - - - +
732B ASN* 1.3 61.6 + - - +
733B LYS* 3.4 4.0 - - + +
734B GLU* 2.9 34.2 + - + +
735B ILE* 3.0 22.7 + - - +
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Residues in contact with ASN 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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730B LYS 3.9 3.1 - - - +
731B ALA* 1.3 72.7 - - - +
733B LYS* 1.3 60.9 + - - +
735B ILE* 3.0 16.7 + - - +
736B LEU* 2.8 36.5 + - + +
758B LEU* 3.4 45.1 + - + +
759B THR 5.4 3.7 + - - +
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Residues in contact with LYS 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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731B ALA* 3.4 3.0 - - + +
732B ASN* 1.3 76.2 - - - +
734B GLU* 1.3 59.2 + - + +
736B LEU* 3.4 11.8 + - + +
737B ASP* 3.0 40.1 + - - +
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Residues in contact with GLU 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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730B LYS* 3.9 23.9 - - + +
731B ALA* 2.9 38.6 + - + +
732B ASN 3.1 0.2 - - - -
733B LYS* 1.3 79.6 - - + +
735B ILE* 1.3 59.7 + - - +
737B ASP* 3.9 20.1 - - - +
738B GLU* 4.0 11.1 - - - +
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Residues in contact with ILE 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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725B GLU* 5.1 7.9 - - - +
730B LYS* 3.0 45.8 - - + +
731B ALA 3.0 11.1 + - - +
732B ASN* 3.0 20.1 + - - +
734B GLU* 1.3 76.1 - - - +
736B LEU* 1.3 60.5 + - - +
737B ASP 3.3 0.2 - - - -
738B GLU* 3.2 10.2 + - - +
739B ALA* 3.0 21.0 + - + +
756B ILE* 4.4 10.8 - - + -
758B LEU* 3.6 29.6 - - + -
762B VAL* 4.6 10.1 - - + -
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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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680B LEU* 5.1 1.1 - - + -
682B ILE* 4.7 11.9 - - + -
732B ASN* 2.8 27.2 + - + +
733B LYS* 3.9 8.7 - - + +
735B ILE* 1.3 70.3 - - - +
737B ASP* 1.3 67.0 + - - +
738B GLU 2.9 2.0 - - - -
739B ALA* 4.0 5.4 - - + -
740B TYR* 2.8 57.0 + - + +
756B ILE* 4.2 23.8 - - + -
758B LEU* 3.0 35.7 - - + -
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Residues in contact with ASP 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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733B LYS* 3.0 29.9 + - - +
734B GLU* 3.9 15.7 - - - +
735B ILE 3.3 0.2 - - - -
736B LEU* 1.3 78.1 - - - +
738B GLU* 1.3 68.6 + - - +
740B TYR* 3.9 10.1 - - - +
741B VAL* 3.3 22.7 + - - +
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Residues in contact with GLU 738 (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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734B GLU 4.0 11.5 - - - +
735B ILE* 3.2 12.0 + - - +
736B LEU 2.9 0.2 - - - -
737B ASP* 1.3 88.3 - - - +
739B ALA* 1.3 66.7 + - - +
741B VAL* 3.0 23.7 + - - +
742B MET* 3.1 27.4 + - + +
833B GLY 5.2 9.4 - - - +
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Residues in contact with ALA 739 (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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680B LEU* 3.8 19.3 - - + -
735B ILE* 3.0 12.7 + - + +
736B LEU* 3.8 9.0 - - - +
738B GLU* 1.3 80.4 - - - +
740B TYR* 1.3 63.0 + - - +
742B MET* 2.9 11.3 + - - +
743B ALA* 2.9 24.1 + - - +
753B LEU* 3.9 19.9 - - + +
756B ILE* 4.0 16.8 - - + -
764B LEU* 5.8 0.2 - - + -
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Residues in contact with TYR 740 (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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679B LEU* 4.7 11.6 - - + +
680B LEU* 3.6 36.6 - - + -
682B ILE* 3.9 16.9 - - + +
736B LEU* 2.8 49.2 + - + +
737B ASP* 3.9 10.5 - - - +
739B ALA* 1.3 77.7 - - - +
741B VAL* 1.3 60.0 + - + +
743B ALA* 3.5 5.1 + - - +
744B SER* 3.3 21.0 + - - -
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Residues in contact with VAL 741 (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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737B ASP 3.3 18.6 - - - +
738B GLU* 3.0 18.4 + - - +
740B TYR* 1.3 77.7 - - + +
742B MET* 1.3 61.2 + - + +
743B ALA 3.1 0.2 - - - -
744B SER* 2.6 32.5 + - - +
745B VAL* 3.7 6.8 + - - +
807B ARG* 4.8 5.4 - - - +
809B LEU* 3.7 36.1 - - + -
832B PHE* 5.9 0.2 - - + -
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Residues in contact with MET 742 (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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1B ITI 3.1 35.8 - - + -
738B GLU* 3.1 26.5 - - + +
739B ALA* 2.9 13.4 + - - +
741B VAL* 1.3 78.9 - - + +
743B ALA* 1.3 58.5 + - - +
744B SER 3.3 0.2 - - - -
745B VAL* 3.2 16.6 - - - +
752B ARG* 4.0 0.3 - - - -
753B LEU* 3.1 28.5 + - + -
764B LEU* 5.6 4.7 - - + -
832B PHE* 3.0 44.1 - - + +
833B GLY* 4.0 17.0 - - - +
834B LEU* 4.2 4.0 - - + +
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Residues in contact with ALA 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
679B LEU* 3.7 13.9 - - + +
680B LEU* 3.9 27.1 - - + -
739B ALA 2.9 13.7 + - - +
740B TYR 3.9 4.7 - - - +
742B MET* 1.3 77.8 - - - +
744B SER* 1.3 59.2 + - - +
745B VAL 3.3 1.6 - - - -
752B ARG* 2.7 29.8 + - - -
753B LEU 2.9 28.3 - - - +
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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