Contacts of the helix formed by residues 728 - 743 (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 SER 728 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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781A PHE* 4.0 7.9 - - - -
784A ARG* 4.8 25.4 - - - +
722B ALA* 3.9 0.9 - - - -
727B ILE* 1.3 85.5 - - - +
729B ARG* 1.3 64.6 + - - +
730B LYS* 3.8 10.5 + - - +
731B GLU* 3.1 34.9 + - - +
732B ALA* 2.9 14.7 + - - +
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Residues in contact with ARG 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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754A VAL* 6.1 1.0 - - - +
781A PHE* 3.5 8.3 - - + -
784A ARG* 5.8 2.3 - - - +
788A GLU* 4.4 23.2 + - - -
718B ASP* 3.9 22.8 + - + +
719B TYR* 3.5 50.2 + - + -
722B ALA* 3.9 11.7 - - - -
728B SER* 1.3 70.9 - - - +
730B LYS* 1.3 104.4 + - - +
732B ALA* 2.8 3.5 + - - +
733B ALA* 2.7 43.2 + - - +
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Residues in contact with LYS 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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751A GLU* 6.6 0.4 - - + -
755A GLN* 4.3 22.4 - - - +
758A LYS* 5.7 3.1 - - - +
728B SER* 3.8 11.1 + - - +
729B ARG* 1.3 110.4 - - - +
731B GLU* 1.3 59.0 + - - +
733B ALA* 3.4 2.1 + - - +
734B GLU* 2.7 69.4 + - + +
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Residues in contact with GLU 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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727B ILE* 3.6 32.0 - - + +
728B SER* 3.1 34.2 + - - +
729B ARG 3.1 0.4 - - - -
730B LYS* 1.3 83.0 + - - +
732B ALA* 1.3 64.3 + - - +
733B ALA 3.2 0.2 - - - -
734B GLU* 3.5 20.9 + - - +
735B PHE* 3.4 19.6 + - - +
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Residues in contact with ALA 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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718B ASP* 2.9 31.6 - - - +
721B LEU* 3.2 27.5 - - + +
722B ALA* 3.3 26.9 - - + +
727B ILE* 3.8 9.2 - - - +
728B SER 2.9 5.2 + - - +
729B ARG 2.8 8.2 + - - +
731B GLU* 1.3 78.1 - - - +
733B ALA* 1.3 60.3 + - - +
735B PHE 3.8 0.2 + - - -
736B ILE* 3.2 13.7 + - - +
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Residues in contact with ALA 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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718B ASP* 3.8 24.0 - - + +
729B ARG* 2.7 26.6 + - - +
730B LYS 3.8 4.0 - - - +
732B ALA* 1.3 78.7 - - - +
734B GLU* 1.3 63.0 + - - +
735B PHE 3.3 0.4 - - - -
736B ILE* 4.0 5.8 - - - +
737B GLU* 3.2 26.3 + - - +
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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* 2.7 53.8 + - + +
731B GLU* 3.5 26.7 - - - +
732B ALA 3.4 0.4 - - - -
733B ALA* 1.3 79.5 - - - +
735B PHE* 1.3 59.9 + - - +
737B GLU* 3.7 4.0 + - - +
738B ARG* 2.8 35.1 + - - +
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Residues in contact with PHE 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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685B THR* 4.4 9.6 - - + -
688B ASP* 3.0 39.9 - - + -
689B ILE* 3.3 32.3 - - + -
708B VAL* 4.0 15.0 - - + -
712B ILE* 5.1 1.1 - - + -
721B LEU* 4.3 16.2 - - + -
725B LEU* 6.4 0.2 - - + -
727B ILE* 5.5 4.3 - - + -
731B GLU 3.4 13.5 + - - +
732B ALA 4.1 3.8 - - - +
734B GLU* 1.3 76.6 - - - +
736B ILE* 1.3 59.8 + - - +
738B ARG* 2.6 43.2 + - + +
739B TYR* 2.7 41.4 + + - +
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Residues in contact with ILE 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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712B ILE* 3.4 26.2 - - + -
716B ILE* 4.2 13.5 - - + +
717B SER* 3.9 24.9 - - - +
718B ASP* 3.9 12.6 - - + +
721B LEU* 3.2 26.7 - - + -
732B ALA 3.2 16.2 + - - +
733B ALA* 4.0 4.9 - - - +
735B PHE* 1.3 77.9 - - - +
737B GLU* 1.3 64.9 + - - +
739B TYR* 3.2 4.2 + - - +
740B PHE* 3.1 36.7 + - + -
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Residues in contact with GLU 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 ALA 3.2 16.0 + - - +
734B GLU* 4.0 5.2 - - - +
735B PHE 3.1 0.6 - - - -
736B ILE* 1.3 78.8 - - + +
738B ARG* 1.3 65.0 + - - +
740B PHE* 3.4 5.0 + - - +
741B GLU* 3.1 42.4 + - + +
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Residues in contact with ARG 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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688B ASP* 4.3 15.8 + - - -
734B GLU* 2.8 29.5 + - - +
735B PHE* 2.6 36.9 + - + +
737B GLU* 1.3 70.8 - - + +
739B TYR* 1.3 61.1 + - - +
741B GLU* 3.0 21.5 + - - +
742B SER* 3.1 17.4 + - - -
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Residues in contact with TYR 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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659B LEU* 5.3 1.6 - - - +
681B ILE* 4.6 6.0 - - + +
685B THR* 3.8 8.9 + - - -
708B VAL 4.8 0.2 - - - -
709B ASN* 2.5 48.6 + - - +
712B ILE* 3.1 51.4 - - + -
713B VAL* 3.9 14.9 - - + +
735B PHE* 2.7 37.7 + + - +
736B ILE 3.2 2.2 - - - +
738B ARG* 1.3 78.1 - - - +
740B PHE* 1.3 63.1 + + - +
742B SER* 3.6 3.5 + - - -
743B PHE* 3.2 57.4 + + - +
746B VAL* 6.1 0.7 - - + -
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Residues in contact with PHE 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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712B ILE* 3.0 47.8 - - + -
713B VAL* 4.3 2.7 - - - -
736B ILE* 3.1 32.4 + - + +
737B GLU* 3.4 5.4 + - - +
739B TYR* 1.3 82.4 - + - +
741B GLU* 1.3 64.6 + - - +
742B SER 3.1 1.6 - - - -
743B PHE* 3.3 6.9 - - + -
744B PRO* 3.2 24.1 - - - +
746B VAL* 3.9 16.2 - - + -
747B LYS* 3.3 57.6 - - + +
750B MET* 5.6 1.8 - - + -
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Residues in contact with GLU 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 GLU* 3.1 39.3 + - + +
738B ARG* 3.0 11.6 + - - +
740B PHE* 1.3 78.7 - - - +
742B SER* 1.3 61.2 + - - +
744B PRO* 3.6 11.4 - - - +
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Residues in contact with SER 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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670B ASN* 3.2 33.6 + - - +
738B ARG 3.1 14.9 + - - -
739B TYR* 3.8 5.8 - - - -
741B GLU* 1.3 81.3 - - - +
743B PHE* 1.3 72.1 + - - +
744B PRO* 3.2 8.7 - - - +
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Residues in contact with PHE 743 (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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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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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