Contacts of the helix formed by residues 728 - 743 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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722A ALA* 3.6 2.0 - - - +
727A ILE* 1.3 85.4 - - - +
729A ARG* 1.3 62.2 + - - +
730A LYS* 3.6 7.1 + - - +
731A GLU* 2.8 45.1 + - - +
732A ALA* 3.2 19.9 + - - +
781B PHE* 4.7 3.6 - - - -
784B ARG* 4.3 21.3 - - - +
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Residues in contact with ARG 729 (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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718A ASP* 3.0 37.3 + - + +
719A TYR* 3.3 48.0 + - + -
722A ALA* 4.1 10.2 - - + +
728A SER* 1.3 73.2 - - - +
730A LYS* 1.3 77.0 + - - +
733A ALA* 2.9 36.1 + - - +
781B PHE* 4.7 6.5 - - + -
784B ARG* 6.3 0.6 - - - +
785B SER* 4.7 4.2 + - - +
788B GLU* 4.3 21.5 + - - +
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Residues in contact with LYS 730 (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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728A SER* 3.3 7.0 + - - +
729A ARG* 1.3 98.1 - - - +
731A GLU* 1.3 66.6 + - + +
733A ALA* 3.7 2.2 + - - +
734A GLU* 3.1 47.1 + - - +
751B GLU* 5.8 12.3 - - - -
755B GLN* 4.0 27.3 - - - +
788B GLU* 6.0 2.0 - - - +
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Residues in contact with GLU 731 (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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727A ILE* 4.1 18.4 - - + +
728A SER* 2.8 42.8 + - - +
730A LYS* 1.3 77.5 - - + +
732A ALA* 1.3 68.5 + - - +
734A GLU* 3.0 9.2 + - - +
735A PHE* 2.9 23.0 + - - +
738A ARG* 5.8 0.2 - - - -
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Residues in contact with ALA 732 (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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718A ASP* 3.4 27.8 - - - +
721A LEU* 3.8 17.6 - - + +
722A ALA 3.9 5.4 - - - +
727A ILE* 3.5 19.1 - - + +
728A SER 3.2 14.9 + - - +
729A ARG 3.9 1.1 - - - +
731A GLU* 1.3 77.1 - - - +
733A ALA* 1.3 63.3 + - - +
735A PHE* 3.1 14.6 + - - +
736A ILE* 3.1 18.4 + - - +
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Residues in contact with ALA 733 (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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718A ASP* 3.8 15.0 - - + +
729A ARG* 2.9 37.4 + - - +
730A LYS* 3.7 5.6 - - - +
732A ALA* 1.3 77.7 - - - +
734A GLU* 1.3 62.3 + - + +
736A ILE* 3.4 8.2 + - - +
737A GLU* 3.3 17.7 + - - +
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Residues in contact with GLU 734 (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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730A LYS* 3.1 50.3 + - + +
731A GLU* 3.0 7.1 + - - +
733A ALA* 1.3 76.0 - - + +
735A PHE* 1.3 64.9 + - - +
736A ILE 3.1 0.4 - - - -
737A GLU* 3.1 17.3 + - - +
738A ARG* 3.1 60.3 + - - +
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Residues in contact with PHE 735 (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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685A THR* 3.9 15.9 - - + -
688A ASP* 4.0 23.8 - - + -
689A ILE* 3.2 35.9 - - + -
708A VAL* 3.8 6.7 - - + -
712A ILE* 3.6 28.0 - - + -
721A LEU* 4.1 11.0 - - + -
725A LEU* 5.3 2.5 - - + -
727A ILE* 5.7 2.5 - - + -
731A GLU 2.9 12.9 + - - +
732A ALA* 3.1 11.4 + - - +
734A GLU* 1.3 77.7 - - - +
736A ILE* 1.3 56.5 + - - +
738A ARG* 4.0 19.1 - - + +
739A TYR* 3.3 27.9 + + - +
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Residues in contact with ILE 736 (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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712A ILE* 4.1 13.0 - - + -
716A ILE* 4.0 24.2 - - + +
718A ASP* 4.3 21.1 - - + +
721A LEU* 3.5 26.9 - - + -
732A ALA 3.1 10.9 + - - +
733A ALA* 3.7 9.6 - - - +
734A GLU 3.1 0.4 - - - -
735A PHE* 1.3 77.5 - - - +
737A GLU* 1.3 64.7 + - - +
738A ARG 3.3 0.2 - - - -
739A TYR* 3.3 6.6 + - - +
740A PHE* 3.2 46.0 + - + -
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Residues in contact with GLU 737 (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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733A ALA 3.3 10.2 + - - +
734A GLU* 3.1 21.1 + - - +
736A ILE* 1.3 80.5 - - - +
738A ARG* 1.3 58.2 + - - +
740A PHE* 3.3 8.7 + - - +
741A GLU* 2.8 47.9 + - + +
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Residues in contact with ARG 738 (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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734A GLU* 3.1 53.3 + - - +
735A PHE* 4.1 17.6 - - + +
737A GLU* 1.3 76.0 + - + +
739A TYR* 1.3 65.8 + - - +
741A GLU* 2.9 27.9 + - - +
742A SER* 2.9 25.0 + - - -
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Residues in contact with TYR 739 (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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659A LEU* 4.8 5.2 - - - +
671A LEU* 6.1 0.5 - - - +
681A ILE* 4.8 3.0 - - + +
685A THR* 4.4 9.9 - - + -
709A ASN* 2.7 41.0 + - - +
712A ILE* 3.6 41.7 - - + -
713A VAL* 4.1 18.7 - - + +
735A PHE* 3.3 22.7 + + - +
736A ILE* 3.4 14.1 - - - +
737A GLU 3.2 0.4 - - - -
738A ARG* 1.3 77.8 - - - +
740A PHE* 1.3 68.1 + + - +
742A SER* 2.8 25.2 + - - -
743A PHE* 2.9 42.9 + + + -
746A VAL* 6.0 0.2 - - + -
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Residues in contact with PHE 740 (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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712A ILE* 4.0 26.5 - - + -
713A VAL* 4.9 1.6 - - + -
736A ILE* 3.2 42.3 + - + +
737A GLU* 3.3 6.9 + - - +
739A TYR* 1.3 85.2 - + + +
741A GLU* 1.3 60.4 + - - +
742A SER 3.3 0.2 - - - -
743A PHE* 3.8 17.9 - - + +
744A PRO* 3.5 22.0 - - - +
746A VAL* 4.2 15.7 - - + -
747A LYS* 4.0 29.4 - - + +
750A MET* 3.3 35.9 - - + -
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Residues in contact with GLU 741 (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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670A ASN* 4.9 1.7 + - - -
737A GLU* 2.8 44.4 + - + +
738A ARG* 2.9 37.7 + - - +
740A PHE* 1.3 79.3 - - - +
742A SER* 1.3 63.0 + - - +
744A PRO* 3.7 9.9 - - - +
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Residues in contact with SER 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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670A ASN* 2.9 28.6 + - - +
738A ARG 2.9 13.5 + - - -
739A TYR* 2.8 14.3 + - - -
741A GLU* 1.3 79.4 - - - +
743A PHE* 1.3 83.8 + - - +
744A PRO* 3.5 0.7 - - - -
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Residues in contact with PHE 743 (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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668A ASP* 2.9 27.1 - - - +
670A ASN* 4.0 7.6 - - + -
671A LEU* 3.8 42.2 - - + -
674A ALA* 5.4 1.8 - - + -
681A ILE* 4.8 19.7 - - + -
684A LYS* 5.7 4.9 - - - -
713A VAL* 6.2 0.2 - - + -
739A TYR* 2.9 53.0 + + + +
740A PHE* 3.7 13.4 - - + -
742A SER* 1.3 99.9 - - - +
744A PRO* 1.3 64.3 - - - +
745A GLY 3.4 2.2 - - - -
746A VAL* 3.3 27.2 + - + +
747A LYS 3.4 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
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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