Contacts of the strand formed by residues 740 - 746 (chain A) in PDB entry 3LJ1
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 740 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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666A PHE* 4.2 17.9 - - + -
686A GLY 6.0 2.0 - - - -
703A ARG* 3.6 39.0 - - + -
704A MET 3.4 19.1 - - - +
705A LEU* 4.2 20.6 - - + -
706A ILE* 3.8 6.8 - - - +
736A THR* 3.7 4.3 - - - +
737A THR* 2.9 34.4 + - - +
739A ARG* 1.3 91.6 - - + +
741A LEU* 1.3 62.1 + - - +
742A TYR* 3.6 31.4 - - + -
685B SER 5.3 0.2 - - - -
686B GLY* 4.4 9.4 - - - -
705B LEU* 3.5 36.6 - - + -
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Residues in contact with LEU 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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702A LYS 3.7 2.4 - - - +
704A MET* 2.9 39.3 + - + +
705A LEU 4.6 1.8 - - - +
706A ILE* 4.6 9.2 - - - -
708A PHE 4.5 2.7 - - - +
709A CYS* 4.2 22.9 - - + +
712A ALA* 3.3 33.9 - - + -
716A ILE* 5.6 3.8 - - + -
734A SER* 4.6 12.1 - - - +
735A GLU 3.9 4.7 - - - +
736A THR* 3.3 23.3 - - + +
740A PHE* 1.3 74.9 - - - +
742A TYR* 1.3 68.8 + - - +
743A ILE* 4.8 4.8 - - + +
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Residues in contact with TYR 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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666A PHE 3.2 22.5 + - - -
667A GLU* 3.4 23.7 - - + +
670A LEU* 4.0 17.7 - - + -
673A LEU* 4.0 12.3 - - + -
675A VAL* 3.9 11.4 - - + -
701A VAL* 3.7 24.9 - - + -
702A LYS 3.6 3.1 - - - -
703A ARG* 3.4 38.3 + - + -
734A SER* 3.3 9.5 + - - -
735A GLU* 2.9 41.1 + - + +
737A THR* 3.8 21.1 - - + -
740A PHE* 3.6 22.9 - - + -
741A LEU* 1.3 76.0 - - - +
743A ILE* 1.3 60.0 + - - +
744A ALA 4.2 0.4 - - - -
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Residues in contact with ILE 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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700A ALA 3.5 1.4 - - - +
701A VAL* 3.4 3.5 - - - -
702A LYS* 2.7 50.8 + - + +
704A MET* 5.1 6.7 - - - -
712A ALA* 4.5 13.9 - - + -
715A GLU* 4.3 24.7 - - + +
716A ILE* 3.9 22.9 - - + -
719A LEU* 5.3 1.3 - - + -
731A TYR* 4.0 11.0 - - + -
733A CYS 3.9 2.9 - - - -
734A SER* 3.6 14.8 - - - +
741A LEU* 4.8 8.5 - - + +
742A TYR* 1.3 74.8 - - - +
744A ALA* 1.3 62.4 + - - +
745A LEU* 3.5 30.4 - - + +
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Residues in contact with ALA 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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673A LEU* 3.4 33.4 - - + +
694A PHE* 4.9 0.7 - - + -
699A VAL* 4.2 10.5 - - + -
700A ALA 3.8 3.6 - - - -
701A VAL* 4.3 4.5 - - - +
731A TYR* 3.7 4.3 - - - -
732A TYR* 3.2 27.2 + - + -
733A CYS* 2.8 26.8 + - - +
742A TYR 4.2 0.6 - - - -
743A ILE* 1.3 72.1 - - - +
745A LEU* 1.3 66.3 + - - +
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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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1A DKI 4.4 24.7 - - - +
689A VAL* 6.2 0.4 - - + -
699A VAL* 3.1 12.6 - - - +
700A ALA* 2.8 33.2 + - + +
702A LYS* 4.6 19.5 - - + -
715A GLU* 5.4 2.7 - - - +
719A LEU* 3.9 25.1 - - + -
729A ILE* 4.4 14.1 - - + -
730A ARG 3.5 13.5 - - - +
731A TYR* 4.1 4.0 - - + -
732A TYR* 3.5 7.2 - - - -
743A ILE* 3.5 25.4 - - + +
744A ALA* 1.3 83.6 - - - +
746A GLU* 1.3 66.9 + - - +
827A SER* 5.4 2.9 - - - -
828A ASP* 5.7 3.4 - - - +
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Residues in contact with GLU 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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1A DKI 2.9 24.1 + - - -
729A ILE* 3.4 24.0 - - + +
730A ARG* 2.9 37.7 + - + +
732A TYR* 2.8 31.5 + - - -
745A LEU* 1.3 70.5 - - - +
747A LEU* 1.3 68.0 + - - +
748A CYS* 3.4 7.1 + - - -
810A ARG* 4.1 14.8 + - - -
811A PHE* 3.3 35.1 - - + -
825A LEU* 5.0 5.2 - - + +
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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