Contacts of the helix formed by residues 734 - 750 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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631B THR* 4.1 4.3 - - - +
731B SER 3.2 3.6 + - - +
733B SER* 1.3 80.7 - - - +
735B LEU* 1.3 66.8 + - - +
736B ARG 3.2 1.1 - - - -
737B HIS* 2.9 24.0 + - + +
738B VAL* 3.0 9.5 + - + +
800B SER* 3.4 40.4 - - - +
801B THR* 3.5 13.2 - - - +
802B ASP* 3.5 28.3 - - + +
838B ARG* 3.9 26.2 - - + +
843B VAL* 3.6 27.8 - - + +
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Residues in contact with LEU 735 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661B ALA* 3.5 30.3 - - + -
662B TYR* 3.6 24.2 - - + +
716B LEU* 3.9 6.1 - - + -
730B GLY* 3.9 26.2 - - - +
731B SER 3.3 5.9 + - - +
732B GLY 3.8 0.9 - - - +
733B SER 3.4 0.8 - - - -
734B ILE* 1.3 76.1 - - - +
736B ARG* 1.3 58.9 + - - +
738B VAL* 2.9 6.6 + - + +
739B ARG* 2.9 36.5 + - + +
755B VAL* 4.6 3.1 - - + -
756B TYR 3.6 23.6 - - - +
757B SER* 3.5 30.1 - - - +
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Residues in contact with ARG 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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662B TYR* 4.8 10.2 + - + +
694B GLU* 2.8 26.9 + - - -
695B ASN 5.2 1.6 + - - -
696B TYR* 3.4 51.8 - - + +
732B GLY 4.8 0.6 + - - -
733B SER 3.9 6.0 + - - +
734B ILE 3.2 1.2 - - - -
735B LEU* 1.3 79.3 - - - +
737B HIS* 1.3 93.0 + - + +
739B ARG* 3.5 12.9 + - - +
740B GLU* 3.1 22.9 + - - +
838B ARG* 3.8 1.4 - - - +
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Residues in contact with HIS 737 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
733B SER 3.2 25.8 + - - -
734B ILE* 2.9 22.6 + - + +
736B ARG* 1.3 105.2 + - + +
738B VAL* 1.3 60.9 + - - +
739B ARG 3.2 0.2 - - - -
740B GLU* 3.3 16.5 + - - -
741B ALA* 3.0 22.7 + - - +
838B ARG* 3.2 42.9 + - - -
843B VAL 4.9 0.2 - - - +
844B ASP* 4.7 9.4 - - + -
845B ALA* 3.4 30.4 - - - +
848B VAL* 5.4 0.4 - - - -
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Residues in contact with VAL 738 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B LEU* 3.5 35.0 - - + +
729B LEU 3.6 25.6 - - - +
730B GLY* 4.1 7.0 - - - +
734B ILE* 3.0 15.6 + - + +
735B LEU* 2.9 11.3 + - + +
737B HIS* 1.3 78.3 - - - +
739B ARG* 1.3 57.9 + - - +
741B ALA* 3.3 9.3 + - - +
742B ALA* 3.0 24.3 + - - +
755B VAL* 4.7 7.0 - - + -
798B VAL 5.4 0.2 - - - +
799B ALA 5.4 0.2 - - - -
800B SER* 3.8 22.9 - - - -
848B VAL* 4.3 11.7 - - + -
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Residues in contact with ARG 739 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B TYR* 2.9 33.8 + - - -
699B PRO* 4.5 10.1 - - - +
716B LEU* 3.3 35.5 + - - +
717B GLU* 2.8 38.7 + - - +
735B LEU* 2.9 20.7 + - + +
736B ARG* 3.7 10.8 - - - +
738B VAL* 1.3 76.0 - - - +
740B GLU* 1.3 64.8 + - - +
742B ALA* 3.1 17.6 + - - +
743B GLU* 3.2 18.5 + - - +
755B VAL* 4.0 19.0 - - + +
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Residues in contact with GLU 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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736B ARG 3.1 14.5 + - - +
737B HIS* 3.5 19.8 - - - +
738B VAL 3.3 0.2 - - - -
739B ARG* 1.3 76.0 - - - +
741B ALA* 1.3 63.1 + - - +
743B GLU* 3.1 10.6 + - + +
744B ILE* 3.0 35.8 + - + +
845B ALA* 3.5 20.0 - - + +
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Residues in contact with ALA 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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728B LEU* 5.0 0.9 - - + -
737B HIS 3.0 13.0 + - - +
738B VAL 3.3 10.3 - - - +
740B GLU* 1.3 77.5 - - - +
742B ALA* 1.3 60.9 + - - +
744B ILE* 3.2 2.8 + - - +
745B LEU* 2.9 30.3 + - + +
845B ALA* 3.6 13.4 - - - +
848B VAL* 3.4 35.4 - - + -
849B VAL* 3.7 13.0 - - + +
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Residues in contact with ALA 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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719B ILE* 4.0 12.7 - - + +
728B LEU* 3.7 17.9 - - + +
738B VAL 3.0 10.2 + - - +
739B ARG* 3.1 11.8 + - - +
741B ALA* 1.3 76.7 - - - +
743B GLU* 1.3 56.2 + - - +
745B LEU* 3.5 4.4 + - - +
746B ALA* 3.1 28.1 + - - +
751B VAL 4.6 0.3 - - - +
753B SER* 3.7 22.6 + - - +
755B VAL* 3.8 16.6 - - + -
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Residues in contact with GLU 743 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
717B GLU* 4.4 7.3 - - - +
719B ILE* 3.2 27.7 - - - +
739B ARG 3.5 13.3 - - - +
740B GLU* 3.1 11.4 + - + +
742B ALA* 1.3 75.2 - - - +
744B ILE* 1.3 61.0 + - + +
746B ALA* 3.3 4.3 + - - +
747B LYS* 2.8 36.6 + - + +
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Residues in contact with ILE 744 (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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740B GLU* 3.0 40.7 + - + +
741B ALA 3.2 5.6 + - - +
743B GLU* 1.3 75.4 - - + +
745B LEU* 1.3 57.7 + - - +
747B LYS* 4.8 0.7 - - - -
748B ASP* 2.6 58.6 + - - +
749B TYR* 4.1 7.6 - - + -
845B ALA* 4.2 12.3 - - + -
846B SER* 5.1 1.1 - - - +
849B VAL* 3.7 24.0 - - + -
874B PHE* 4.1 24.9 - - + -
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Residues in contact with LEU 745 (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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726B VAL* 4.1 9.0 - - + -
728B LEU* 3.9 24.2 - - + -
741B ALA* 2.9 23.1 + - + +
742B ALA 3.7 3.8 - - - +
744B ILE* 1.3 77.1 - - - +
746B ALA* 1.3 57.3 + - - +
749B TYR* 3.0 27.8 + - + +
750B GLY 3.0 9.0 + - - -
751B VAL* 3.0 26.9 + - + +
753B SER* 5.4 1.1 - - - +
848B VAL 5.1 0.2 - - - +
849B VAL* 4.2 16.4 - - + -
852B ALA* 3.8 28.0 - - + -
853B LEU* 3.5 37.9 - - + -
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Residues in contact with ALA 746 (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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719B ILE* 3.6 27.4 - - + -
720B GLU 4.2 8.0 - - - +
742B ALA 3.1 17.1 + - - +
743B GLU* 3.7 7.2 - - - +
745B LEU* 1.3 77.1 - - - +
747B LYS* 1.3 59.8 + - - +
750B GLY* 3.0 24.9 + - - -
751B VAL 3.2 16.1 + - - +
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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
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743B GLU* 2.8 22.2 + - + +
744B ILE* 4.3 1.3 - - - +
746B ALA* 1.3 76.6 - - + +
748B ASP* 1.3 70.8 + - - +
750B GLY 4.8 0.7 + - - -
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Residues in contact with ASP 748 (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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744B ILE* 2.6 35.8 + - - +
747B LYS* 1.3 94.7 - - - +
749B TYR* 1.3 78.0 + - + +
750B GLY 3.8 0.2 - - - -
873B LYS* 3.3 21.8 + - - +
874B PHE* 5.4 1.0 - - - -
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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
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723B LYS* 3.4 20.2 - - - +
744B ILE* 3.8 11.9 - - + -
745B LEU* 3.0 16.2 + - - +
748B ASP* 1.3 98.8 - - + +
750B GLY* 1.3 62.0 + - - +
751B VAL* 3.1 19.7 + - + +
849B VAL* 4.0 17.3 - - + -
853B LEU* 3.7 20.4 - - + -
866B VAL* 3.7 33.7 - - + -
870B ALA* 3.6 14.9 - - - +
873B LYS* 2.9 34.6 + - - -
874B PHE* 4.0 1.1 - + - -
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Residues in contact with GLY 750 (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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721B GLY* 3.1 6.9 - - - -
722B SER 3.1 10.4 + - - -
723B LYS* 2.8 49.7 + - - -
745B LEU 3.0 2.8 + - - -
746B ALA 3.0 16.6 + - - -
747B LYS 4.6 0.6 + - - -
748B ASP 3.8 0.8 - - - -
749B TYR* 1.3 78.5 - - - +
751B VAL* 1.3 57.8 + - - +
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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