Contacts of the helix formed by residues 738 - 755 (chain A) in PDB entry 3LZI
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 PRO 738 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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736A SER 3.6 7.1 - - - +
737A THR* 1.3 90.9 - - + +
739A LYS* 1.3 68.3 + - - +
741A VAL* 3.0 18.1 + - + -
742A GLN* 2.9 19.6 + - - +
778A SER 3.4 13.0 - - - +
779A ILE* 3.4 23.8 - - - +
780A ALA 3.2 24.9 - - - +
781A SER* 4.1 1.8 - - - +
782A VAL* 5.8 1.3 - - + -
875A THR* 3.9 30.3 - - + +
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Residues in contact with LYS 739 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A PRO* 5.4 6.5 - - + -
292A TYR* 3.3 36.8 + - + +
295A GLU* 5.2 7.3 + - - -
296A PHE* 6.5 0.7 - - - -
737A THR 3.4 2.4 + - - -
738A PRO* 1.3 69.3 - - - +
740A ALA* 1.3 63.9 + - - +
742A GLN* 3.1 32.6 + - - +
743A LYS* 3.1 14.0 + - - +
777A ILE* 5.2 2.2 + - + +
778A SER* 3.3 19.5 + - - +
780A ALA 4.7 0.4 + - - -
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Residues in contact with ALA 740 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A LYS* 1.3 74.9 - - - +
741A VAL* 1.3 57.3 + - - +
743A LYS* 3.6 10.3 - - - +
744A ALA* 2.9 27.2 + - - +
767A PHE* 4.1 5.4 - - + -
774A LEU* 4.2 28.0 - - + -
778A SER* 2.9 36.4 + - - +
779A ILE* 4.3 2.2 - - + -
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Residues in contact with VAL 741 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
737A THR* 3.9 7.9 - - + -
738A PRO* 3.0 25.0 + - + +
740A ALA* 1.3 76.9 - - - +
742A GLN* 1.3 59.6 + - - +
744A ALA* 4.3 4.5 - - - +
745A LEU* 2.8 42.6 + - + +
767A PHE* 4.7 4.0 - - + -
771A PHE* 4.5 18.8 - - + -
779A ILE* 4.9 4.3 - - + -
875A THR* 3.3 47.3 - - - +
876A PHE* 4.1 11.7 - - + -
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Residues in contact with GLN 742 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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731A GLU 4.2 0.4 - - - +
732A THR* 3.5 31.7 + - - +
733A GLN 4.9 0.4 - - - -
734A LYS 2.8 29.9 + - - +
735A SER* 4.2 5.5 - - - +
737A THR* 3.5 26.6 + - + +
738A PRO 2.9 17.3 + - - +
739A LYS* 3.1 26.5 + - - +
741A VAL* 1.3 75.4 - - - +
743A LYS* 1.3 57.0 + - - +
745A LEU* 4.9 0.2 - - - -
746A LYS* 2.9 32.6 + - - +
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Residues in contact with LYS 743 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
739A LYS 3.1 9.5 + - - +
740A ALA* 3.6 12.8 - - + +
742A GLN* 1.3 81.4 - - - +
744A ALA* 1.3 61.0 + - - +
746A LYS* 3.8 5.5 - - - +
747A GLU* 3.2 23.9 + - - +
763A TYR* 4.6 2.8 + - - +
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Residues in contact with ALA 744 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740A ALA 2.9 18.9 + - - +
741A VAL 3.8 3.1 - - - +
743A LYS* 1.3 74.6 - - - +
745A LEU* 1.3 59.4 + - - +
747A GLU 3.5 0.5 + - - -
748A CYS* 2.9 31.7 + - - -
763A TYR* 3.6 16.1 - - + +
767A PHE* 3.5 36.3 - - + -
876A PHE* 3.8 15.3 - - + -
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Residues in contact with LEU 745 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
731A GLU* 3.8 28.3 - - + -
732A THR* 3.6 16.6 - - + +
737A THR* 4.7 1.8 - - + -
741A VAL* 2.8 38.5 + - + +
744A ALA* 1.3 70.9 - - - +
746A LYS* 1.3 60.7 + - - +
748A CYS* 3.4 3.7 - - - +
749A ILE* 2.8 33.4 + - - +
875A THR 4.0 7.0 - - - +
876A PHE* 3.8 35.2 - - + +
879A PRO* 4.1 4.3 - - + -
880A LEU* 3.9 17.0 - - + +
883A PHE* 3.6 23.6 - - + -
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Residues in contact with LYS 746 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A LEU* 3.8 30.9 - - + +
727A ILE* 4.0 13.5 - - + -
732A THR* 3.4 13.6 - - + +
733A GLN* 5.5 2.0 - - - +
742A GLN 2.9 18.9 + - - +
743A LYS* 3.8 6.3 - - - +
745A LEU* 1.3 77.4 - - - +
747A GLU* 1.3 51.6 + - - +
749A ILE* 3.1 6.6 + - - +
750A ARG* 2.6 35.8 + - + +
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Residues in contact with GLU 747 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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743A LYS 3.2 15.2 + - - +
744A ALA 4.0 0.2 - - - +
746A LYS* 1.3 77.6 - - - +
748A CYS* 1.3 55.7 - - - +
750A ARG* 2.7 48.4 + - - -
751A ARG* 2.8 50.1 + - - +
763A TYR* 3.7 36.6 - - + +
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Residues in contact with CYS 748 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
744A ALA 2.9 23.8 + - - +
745A LEU* 3.4 7.6 - - - +
747A GLU* 1.3 77.4 - - - +
749A ILE* 1.3 62.1 + - - +
751A ARG* 3.4 2.9 + - - +
752A MET* 3.1 28.7 + - - +
760A LEU* 3.7 29.3 - - + +
763A TYR* 3.8 18.6 - - - -
764A PHE* 5.1 3.4 - - - -
876A PHE* 3.9 24.9 - - - -
880A LEU* 4.0 19.3 - - + -
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Residues in contact with ILE 749 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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701A PHE* 4.2 10.1 - - + -
709A ALA* 3.9 22.0 - - + -
725A LEU* 4.2 4.3 - - + -
727A ILE* 4.2 18.2 - - + -
730A LEU* 3.8 20.0 - - + -
732A THR* 4.1 16.2 - - + -
745A LEU 2.8 23.5 + - - +
746A LYS* 3.5 4.5 - - - +
748A CYS* 1.3 71.3 - - - +
750A ARG* 1.3 66.6 + - - +
752A MET* 3.0 11.0 + - - +
753A LEU* 3.0 34.0 + - + +
883A PHE* 3.8 33.7 - - + -
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Residues in contact with ARG 750 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725A LEU* 3.9 21.7 - - + +
746A LYS* 2.6 21.3 + - + +
747A GLU* 2.7 46.2 + - - +
749A ILE* 1.3 72.2 - - - +
751A ARG* 1.3 73.0 + - - +
753A LEU 3.3 0.3 + - - -
754A GLN* 2.9 75.1 + - - +
755A GLU* 3.0 33.8 + - - +
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Residues in contact with ARG 751 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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747A GLU* 2.8 41.3 + - - +
748A CYS* 3.8 4.5 - - - +
750A ARG* 1.3 90.6 - - - +
752A MET* 1.3 55.1 + - - +
755A GLU* 2.9 17.6 + - - +
756A GLY 2.7 35.4 + - - +
759A SER* 3.0 43.8 + - - +
760A LEU* 4.1 11.7 - - - +
762A GLU* 3.9 16.4 + - - +
763A TYR* 3.6 41.9 - - - +
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Residues in contact with MET 752 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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697A GLY* 3.3 6.1 - - - -
698A ILE* 3.0 29.3 + - + +
701A PHE* 3.6 31.6 - - + -
748A CYS 3.1 21.8 + - - +
749A ILE* 3.0 16.2 + - - +
751A ARG* 1.3 76.2 - - - +
753A LEU* 1.3 62.1 + - + +
756A GLY* 3.8 10.2 + - - -
760A LEU* 3.7 20.0 - - + -
880A LEU* 4.8 4.0 - - - -
883A PHE* 4.2 14.1 - - - +
884A THR* 4.1 19.1 - - + -
887A ALA* 3.8 21.3 - - + -
889A LEU* 3.9 20.9 - - + -
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Residues in contact with LEU 753 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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691A PRO* 3.8 7.8 - - - +
697A GLY* 3.2 8.0 - - - -
698A ILE* 3.9 8.3 - - + -
699A GLY* 3.1 28.5 + - - +
700A GLY* 3.7 18.4 - - - +
701A PHE* 3.7 32.3 - - + -
709A ALA* 4.0 7.9 - - + +
710A LEU 3.5 16.8 - - - +
711A ASN* 3.4 36.4 - - + +
725A LEU* 4.0 12.6 - - + -
749A ILE* 3.0 19.9 + - + +
750A ARG 4.0 2.2 - - - +
752A MET* 1.3 79.6 - - + +
754A GLN* 1.3 60.2 + - + +
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Residues in contact with GLN 754 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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692A PRO* 3.5 19.1 - - + +
695A SER* 2.9 26.2 + - - -
697A GLY* 3.7 2.9 - - - -
711A ASN* 2.8 35.8 + - - +
723A PRO* 3.8 27.7 + - - +
725A LEU* 4.2 6.0 - - + +
750A ARG* 2.9 54.7 + - + +
753A LEU* 1.3 81.0 - - + +
755A GLU* 1.3 67.4 + - + +
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Residues in contact with GLU 755 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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695A SER* 4.8 2.0 - - - -
696A LYS* 3.3 21.5 + - - +
697A GLY 3.6 4.0 - - - -
750A ARG* 3.0 36.7 + - - +
751A ARG* 2.9 18.5 + - - +
754A GLN* 1.3 85.5 - - + +
756A GLY* 1.3 59.4 + - - +
759A SER* 2.7 37.8 + - - +
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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
------------------------------------------------------------
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