Contacts of the helix formed by residues 743 - 761 (chain B) in PDB entry 1LV5
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 PHE 743 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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668B ASP* 3.4 23.6 - - - +
670B ASN* 3.1 26.7 - - - -
671B LEU* 3.6 33.9 - - + -
674B ALA* 5.2 1.3 - - + -
681B ILE* 4.3 20.9 - - + -
684B LYS* 5.4 8.5 - - + -
739B TYR* 3.2 51.6 + + + +
740B PHE* 3.3 12.8 - - + +
742B SER* 1.3 86.9 - - - +
744B PRO* 1.3 57.0 - - - +
745B GLY 3.1 9.9 + - - -
746B VAL* 3.3 23.8 + - + +
747B LYS 3.4 8.7 + - - -
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Residues in contact with PRO 744 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
668B ASP* 4.2 2.7 - - - +
670B ASN* 5.2 3.6 - - + -
740B PHE 3.2 11.2 - - - +
741B GLU* 3.6 11.2 - - - +
742B SER 3.2 11.2 - - - +
743B PHE* 1.3 85.6 - - - +
745B GLY* 1.3 58.5 + - - +
747B LYS* 4.6 6.0 - - + +
748B ARG* 3.1 45.3 + - - +
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Residues in contact with GLY 745 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B ALA* 3.9 11.0 - - - +
668B ASP* 2.6 30.8 + - - -
744B PRO* 1.3 75.2 - - - +
746B VAL* 1.3 54.7 - - - +
748B ARG* 3.5 15.9 + - - +
749B TYR* 2.7 37.1 + - - +
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Residues in contact with VAL 746 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B LEU* 3.5 38.4 - - + -
666B ALA* 4.3 7.0 - - + -
668B ASP* 3.1 12.6 + - + +
671B LEU* 4.0 18.8 - - + -
713B VAL* 3.8 23.1 - - + -
739B TYR* 6.1 0.4 - - + -
740B PHE* 3.9 13.2 - - + -
743B PHE* 3.3 18.6 + - + +
745B GLY* 1.3 76.6 - - - +
747B LYS* 1.3 65.1 + - - +
749B TYR* 3.3 1.2 + - - +
750B MET* 2.9 33.3 + - + +
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Residues in contact with LYS 747 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
740B PHE* 3.3 48.4 - - + +
743B PHE 3.4 6.6 + - - +
744B PRO* 4.6 6.3 - - + +
745B GLY 3.4 0.2 - - - -
746B VAL* 1.3 79.4 - - - +
748B ARG* 1.3 63.7 + - - +
750B MET* 3.2 8.9 - - - +
751B GLU* 3.1 42.7 + - + +
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Residues in contact with ARG 748 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B ALA 5.6 1.8 + - - -
744B PRO* 3.1 50.5 + - - +
745B GLY* 3.3 16.1 + - - +
746B VAL 3.2 0.8 - - - -
747B LYS* 1.3 76.8 - - - +
749B TYR* 1.3 67.7 + - - +
751B GLU* 2.7 29.7 + - - +
752B ASN* 2.8 32.7 + - - +
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Residues in contact with TYR 749 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B LEU* 3.9 8.7 - - + -
665B ILE* 3.5 24.2 - - + +
666B ALA* 3.5 22.0 - - + +
745B GLY 2.7 21.8 + - - +
746B VAL 3.7 1.1 - - - +
748B ARG* 1.3 74.4 - - - +
750B MET* 1.3 85.2 + - + +
752B ASN* 3.1 8.5 + - + +
753B ILE* 2.7 59.3 + - + +
792B MET 3.9 3.8 + - - -
795B PRO* 3.1 37.1 - - - +
796B ILE* 3.4 19.8 - - + +
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Residues in contact with MET 750 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B LEU* 3.8 18.8 - - + -
713B VAL* 3.0 29.4 - - - +
714B TYR* 4.4 7.2 - - + -
740B PHE* 5.6 2.2 - - + -
746B VAL* 2.9 29.9 + - + +
747B LYS* 3.2 11.9 - - - +
749B TYR* 1.3 105.9 - - + +
751B GLU* 1.3 61.2 - - + +
753B ILE* 3.2 15.9 - - - +
754B VAL* 3.5 12.5 - - - +
792B MET* 3.1 48.2 - - + +
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Residues in contact with GLU 751 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
730A LYS* 5.8 11.7 - - - -
747B LYS* 3.1 40.7 + - + +
748B ARG* 2.7 20.6 + - - +
750B MET* 1.3 78.5 - - + +
752B ASN* 1.3 64.8 + - - +
753B ILE 3.3 0.9 + - - -
754B VAL* 3.4 14.1 + - - +
755B GLN* 3.4 19.4 + - + +
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Residues in contact with ASN 752 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
748B ARG* 2.8 37.7 + - - +
749B TYR* 3.7 11.2 - - + +
751B GLU* 1.3 81.9 - - - +
753B ILE* 1.3 56.2 + - - +
754B VAL 3.4 0.2 - - - -
755B GLN* 3.5 10.9 + - - +
756B GLU* 3.0 27.4 + - - +
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Residues in contact with ILE 753 (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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749B TYR* 2.7 48.3 + - + +
750B MET* 3.2 17.9 - - - +
752B ASN* 1.3 70.7 - - - +
754B VAL* 1.3 65.7 + - - +
756B GLU* 3.3 29.0 - - - +
757B ALA* 2.8 27.7 + - - +
763B VAL* 4.4 5.4 - - + -
791B ALA 3.0 31.4 - - - +
792B MET* 3.6 17.7 - - + +
795B PRO* 4.1 11.0 - - + -
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Residues in contact with VAL 754 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
750B MET 3.5 14.8 - - - +
751B GLU* 3.4 7.9 + - - +
753B ILE* 1.3 76.2 - - + +
755B GLN* 1.3 70.5 + - - +
757B ALA* 3.2 2.0 + - - +
758B LYS* 2.9 34.4 + - - +
776B ILE* 3.6 13.9 - - + +
788B GLU* 3.3 61.0 - - + +
791B ALA* 3.9 10.3 - - + -
792B MET* 4.2 4.3 - - + -
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Residues in contact with GLN 755 (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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730A LYS* 4.0 31.5 - - - +
751B GLU* 3.4 15.5 + - + +
752B ASN* 3.7 13.2 - - - +
753B ILE 3.3 0.2 - - - -
754B VAL* 1.3 84.7 - - - +
756B GLU* 1.3 56.6 + - - +
758B LYS* 3.2 32.0 + - - +
759B GLN* 3.1 26.9 + - - +
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Residues in contact with GLU 756 (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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752B ASN 3.0 17.9 + - - +
753B ILE* 3.3 28.0 - - - +
754B VAL 3.1 0.2 - - - -
755B GLN* 1.3 74.5 - - - +
757B ALA* 1.3 66.8 + - - +
758B LYS 3.1 1.8 - - - -
759B GLN* 3.7 7.6 - - - +
760B LYS* 2.8 54.7 + - + +
762B TYR 4.6 6.1 - - - +
763B VAL* 5.0 5.2 - - - -
764B THR* 5.3 4.0 + - - -
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Residues in contact with ALA 757 (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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753B ILE 2.8 17.9 + - - +
754B VAL 3.5 5.8 - - - +
756B GLU* 1.3 75.0 - - - +
758B LYS* 1.3 54.9 + - - +
761B GLY* 2.5 38.7 + - - -
762B TYR 3.2 16.1 + - - +
763B VAL* 3.7 20.2 - - + +
773B LEU* 4.6 6.7 - - + -
776B ILE* 4.2 14.8 - - + +
791B ALA* 3.8 12.1 - - + -
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Residues in contact with LYS 758 (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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754B VAL* 2.9 20.7 + - - +
755B GLN* 3.2 35.8 + - - +
757B ALA* 1.3 80.4 - - - +
759B GLN* 1.3 63.6 + - - +
761B GLY* 3.4 7.4 + - - -
776B ILE* 3.5 38.2 - - + +
777B THR* 4.2 18.5 - - + +
784B ARG* 5.1 13.6 - - - +
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Residues in contact with GLN 759 (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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755B GLN 3.1 16.2 + - - +
756B GLU* 3.1 8.2 + - - +
758B LYS* 1.3 79.8 - - - +
760B LYS* 1.3 87.3 + - - +
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Residues in contact with LYS 760 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
756B GLU* 2.8 40.8 + - + +
759B GLN* 1.3 101.2 - - - +
761B GLY* 1.3 61.2 + - - +
762B TYR* 3.3 49.4 + - + +
764B THR* 5.8 1.8 + - - -
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Residues in contact with GLY 761 (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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757B ALA 2.5 21.6 + - - -
758B LYS* 3.4 8.0 + - - -
760B LYS* 1.3 73.7 - - - +
762B TYR* 1.3 61.4 + - - +
772B TYR* 3.8 10.0 - - - +
773B LEU* 3.4 22.4 + - - -
774B PRO* 4.7 1.2 - - - +
776B ILE* 5.3 4.5 - - - -
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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