Contacts of the helix formed by residues 734 - 750 (chain A) in PDB entry 1L8A
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 ILE 734 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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731A SER 3.2 9.2 + - - +
733A SER* 1.3 80.8 - - - +
735A LEU* 1.3 65.5 + - - +
736A ARG 3.2 2.9 - - - -
737A HIS* 2.8 22.2 + - + +
738A VAL* 3.1 8.6 + - + +
800A SER* 3.5 42.0 - - - +
801A THR* 3.6 8.3 - - - +
802A ASP* 3.5 35.2 - - + +
838A ARG* 4.0 35.0 - - + +
843A VAL* 3.8 15.5 - - + +
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Residues in contact with LEU 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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661A ALA* 3.4 34.3 - - + -
662A TYR* 3.5 29.6 - - + +
716A LEU* 4.2 3.4 - - + -
730A GLY* 3.8 21.5 - - - +
731A SER 3.2 5.1 + - - +
732A GLY 3.8 1.3 - - - +
733A SER 3.4 0.8 - - - -
734A ILE* 1.3 76.8 - - - +
736A ARG* 1.3 58.1 + - - +
738A VAL* 2.9 23.8 - - + +
739A ARG* 2.8 33.4 + - + +
755A VAL* 4.5 3.8 - - + -
756A TYR 3.7 22.0 - - - +
757A SER* 3.6 20.2 - - - +
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Residues in contact with ARG 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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661A ALA* 5.6 0.2 - - - +
662A TYR* 4.9 10.0 - - + +
694A GLU* 3.1 39.5 + - - +
695A ASN 5.4 0.8 + - - -
696A TYR* 3.7 45.6 - - + +
732A GLY 4.9 0.6 + - - -
733A SER 3.5 9.8 + - - +
735A LEU* 1.3 80.8 - - - +
737A HIS* 1.3 96.3 + - + +
739A ARG* 3.5 11.8 - - - +
740A GLU* 3.2 22.0 + - - +
838A ARG* 4.0 1.8 - - - +
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Residues in contact with HIS 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 SER 3.1 19.6 + - - -
734A ILE* 2.8 22.9 + - + +
736A ARG* 1.3 116.1 + - + +
738A VAL* 1.3 59.2 + - - +
739A ARG 3.1 1.3 - - - -
740A GLU* 3.3 15.6 + - - +
741A ALA 3.1 20.1 + - - -
838A ARG* 3.2 35.0 + - + -
843A VAL 4.7 0.7 - - - +
844A ASP* 4.7 10.3 - - + -
845A ALA* 3.5 31.5 - - - +
848A VAL* 5.2 0.7 - - - -
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Residues in contact with VAL 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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728A LEU* 4.0 11.9 - - + +
729A LEU 3.6 20.4 - - - +
730A GLY* 4.0 11.7 - - - +
734A ILE* 3.3 14.4 - - + +
735A LEU* 2.9 35.2 + - + +
737A HIS* 1.3 76.3 - - - +
739A ARG* 1.3 60.1 + - - +
741A ALA* 3.3 9.9 + - - +
742A ALA* 3.0 26.7 + - - +
755A VAL* 4.3 9.9 - - + -
800A SER* 3.8 22.9 - - - +
848A VAL* 4.3 12.8 - - + -
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Residues in contact with ARG 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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662A TYR* 3.3 17.1 + - - +
699A PRO* 4.3 14.6 - - - +
716A LEU* 3.0 39.3 - - - +
717A GLU* 2.6 41.6 + - - +
719A ILE* 5.1 1.4 - - - +
735A LEU* 2.8 23.8 + - + +
736A ARG* 3.5 15.0 - - - +
737A HIS 3.1 0.2 - - - -
738A VAL* 1.3 80.4 - - - +
740A GLU* 1.3 60.8 + - - +
742A ALA* 3.4 15.2 + - - +
743A GLU* 3.4 12.6 + - - +
755A VAL* 4.0 19.3 - - + -
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Residues in contact with GLU 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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736A ARG 3.2 10.6 + - - +
737A HIS* 3.5 18.4 - - - +
738A VAL 3.2 0.4 - - - -
739A ARG* 1.3 78.2 - - - +
741A ALA* 1.3 65.3 + - - +
743A GLU* 3.1 8.4 + - + +
744A ILE* 3.0 38.2 + - + +
845A ALA* 3.3 21.4 - - + +
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Residues in contact with ALA 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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728A LEU* 5.2 0.2 - - + -
737A HIS 3.1 10.9 + - - +
738A VAL 3.3 9.4 + - - +
740A GLU* 1.3 77.6 - - - +
742A ALA* 1.3 54.8 + - - +
744A ILE* 3.7 2.3 - - - +
745A LEU* 2.8 36.9 + - + +
845A ALA* 3.6 24.7 - - - +
848A VAL* 3.6 26.2 - - + -
849A VAL* 3.6 13.2 - - + +
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Residues in contact with ALA 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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719A ILE* 3.5 23.6 - - + +
728A LEU* 3.4 28.0 - - + +
738A VAL 3.0 9.1 + - - +
739A ARG* 3.5 11.0 - - - +
740A GLU 3.1 0.4 - - - -
741A ALA* 1.3 77.2 - - - +
743A GLU* 1.3 55.8 - - - +
745A LEU* 3.5 4.7 + - - +
746A ALA* 3.1 28.1 + - - +
751A VAL 4.5 1.0 - - - +
753A SER* 3.6 7.4 + - - +
755A VAL* 3.9 10.1 - - + -
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Residues in contact with GLU 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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719A ILE* 4.3 17.5 - - + +
739A ARG 3.4 8.5 + - - +
740A GLU* 3.1 12.6 + - + +
742A ALA* 1.3 76.2 - - - +
744A ILE* 1.3 61.1 + - + +
746A ALA* 4.3 6.7 - - - +
747A LYS* 2.8 50.2 + - + +
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Residues in contact with ILE 744 (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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740A GLU* 3.0 41.2 + - + +
741A ALA 3.7 6.5 - - - +
743A GLU* 1.3 76.1 - - + +
745A LEU* 1.3 58.9 + - - +
747A LYS* 4.5 3.8 - - - -
748A ASP* 2.8 50.8 + - - +
749A TYR* 4.3 2.5 - - + -
845A ALA* 4.4 12.3 - - + -
846A SER* 5.4 0.7 - - - +
849A VAL* 3.9 22.7 - - + -
874A PHE* 4.1 24.5 - - + -
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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
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726A VAL* 3.9 20.4 - - + -
728A LEU* 4.1 17.0 - - + -
741A ALA* 2.8 24.8 + - + +
742A ALA 3.7 4.9 - - - +
743A GLU 3.3 0.2 - - - -
744A ILE* 1.3 77.7 - - - +
746A ALA* 1.3 56.9 + - - +
749A TYR* 3.1 28.0 + - + +
751A VAL* 3.1 32.9 + - + +
753A SER* 5.3 1.1 - - - +
849A VAL* 4.1 19.3 - - + -
852A ALA* 3.7 29.4 - - + -
853A LEU* 3.7 30.1 - - + -
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Residues in contact with ALA 746 (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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719A ILE* 3.5 32.5 - - + -
720A GLU 3.9 8.9 - - - +
742A ALA 3.1 13.0 + - - +
743A GLU* 3.9 7.9 - - - +
745A LEU* 1.3 77.4 - - - +
747A LYS* 1.3 59.8 + - - +
750A GLY* 2.9 25.2 + - - -
751A VAL 3.2 15.9 - - - +
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Residues in contact with LYS 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 GLU* 2.8 34.5 + - + +
744A ILE* 4.0 2.2 - - - +
746A ALA* 1.3 80.1 - - - +
748A ASP* 1.3 72.0 + - - +
750A GLY 4.7 0.9 + - - -
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Residues in contact with ASP 748 (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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723A LYS* 5.4 2.3 + - - -
744A ILE* 2.8 37.3 + - - +
747A LYS* 1.3 88.2 - - - +
749A TYR* 1.3 80.7 + - + +
873A LYS* 3.8 24.7 + - - +
874A PHE* 5.2 0.3 - - - -
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Residues in contact with TYR 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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723A LYS* 3.2 29.5 + - - +
744A ILE* 3.8 12.8 - - + -
745A LEU* 3.1 18.1 + - + +
748A ASP* 1.3 101.3 - - + +
750A GLY* 1.3 63.0 + - - +
751A VAL* 3.0 19.1 + - + +
849A VAL* 4.1 11.9 - - + -
853A LEU* 3.8 34.8 - - + -
862A ILE* 6.1 1.3 - - + +
866A VAL* 4.0 25.8 - - + -
870A ALA* 3.7 18.5 - - - +
873A LYS* 3.7 21.4 - - - +
874A PHE* 4.0 2.0 - + - -
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Residues in contact with GLY 750 (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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721A GLY* 2.9 19.7 - - - -
722A SER* 4.6 3.4 - - - -
723A LYS* 2.8 36.5 + - - -
746A ALA 2.9 18.9 + - - -
747A LYS 4.6 0.8 + - - -
748A ASP 3.8 0.6 - - - -
749A TYR* 1.3 76.8 - - - +
751A VAL* 1.3 58.4 + - - +
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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