Contacts of the strand formed by residues 752 - 759 (chain A) in PDB entry 1L4Z
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 LYS 752 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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547A ASP* 6.5 0.2 - - + -
548A CYS 4.1 2.7 - - - +
549A GLY 3.4 17.3 - - - +
550A LYS* 4.1 10.3 - - + +
666A CYS* 3.3 34.5 - - + -
747A CYS 3.9 0.2 - - - +
748A PHE* 3.1 11.3 - - - -
749A GLU* 2.6 44.2 + - - +
751A ASP* 1.3 95.9 + - - +
753A TYR* 1.3 59.4 + - - +
754A ILE* 3.9 17.2 + - + -
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Residues in contact with TYR 753 (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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549A GLY* 2.7 37.2 + - - -
551A PRO* 3.8 18.2 - - + -
555A PRO* 4.1 17.1 - - + +
557A LYS* 3.6 31.6 + - - +
573A TRP* 4.2 15.7 - + - -
575A TRP* 3.5 35.4 - + + -
665A ALA* 4.5 2.8 - - - +
666A CYS* 3.5 13.0 + - - +
681A PHE* 4.4 12.7 - + - -
746A VAL* 4.1 15.7 - - + -
747A CYS* 3.8 3.4 - - - -
748A PHE* 3.3 46.5 - + + -
752A LYS* 1.3 72.2 - - - +
754A ILE* 1.3 62.8 + - - +
755A LEU 4.1 0.2 + - - -
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Residues in contact with ILE 754 (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 CYS* 3.3 22.2 - - + +
667A LEU 3.7 3.6 - - - +
668A PRO* 3.5 37.2 - - + -
746A VAL* 3.2 3.0 - - - -
747A CYS 2.8 39.1 + - - +
749A GLU* 3.9 36.3 - - + +
752A LYS* 4.6 15.7 - - + -
753A TYR* 1.3 76.7 - - - +
755A LEU* 1.3 66.1 + - - +
756A GLN* 3.2 17.6 + - - +
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Residues in contact with LEU 755 (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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591A THR* 3.8 35.9 - - + +
593A ILE* 4.2 18.2 - - + -
599A LEU* 4.2 13.0 - - + -
665A ALA* 4.4 10.7 - - + +
666A CYS 2.8 17.7 + - - +
667A LEU* 4.3 9.9 - - + -
668A PRO* 3.2 25.1 - - - +
744A PRO* 5.1 1.3 - - + -
745A LEU 3.9 5.2 - - - +
746A VAL* 4.1 8.8 - - + +
753A TYR 4.1 1.4 + - - -
754A ILE* 1.3 69.1 - - - +
756A GLN* 1.3 58.4 + - - +
757A GLY 3.6 14.4 - - - +
758A VAL* 4.7 3.8 - - + -
777A VAL* 3.0 32.9 - - + +
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Residues in contact with GLN 756 (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 PRO* 3.4 23.1 - - - +
672A TYR* 3.6 29.3 - - - +
674A VAL* 3.3 27.3 - - + +
725A LEU* 3.7 16.1 - - + +
745A LEU* 3.0 9.4 + - + +
747A CYS* 3.6 30.3 + - + +
754A ILE* 3.2 31.1 + - - +
755A LEU* 1.3 73.5 - - - +
757A GLY* 1.3 59.0 + - - +
776A ARG* 3.8 0.9 - - - +
777A VAL* 3.0 25.7 + - - +
778A SER* 4.3 4.9 + - - -
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Residues in contact with GLY 757 (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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725A LEU* 4.7 3.8 - - - -
744A PRO* 3.8 0.9 - - - +
745A LEU* 3.0 39.7 + - - +
755A LEU* 3.6 6.1 - - - +
756A GLN* 1.3 80.1 - - - +
758A VAL* 1.3 60.0 + - - -
774A TYR* 4.1 10.3 - - - -
775A VAL 3.1 11.2 - - - -
777A VAL* 3.4 8.0 - - - +
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Residues in contact with VAL 758 (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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591A THR* 5.6 3.1 - - - +
599A LEU* 3.8 35.4 - - + +
600A THR 4.3 11.7 - - - +
601A ALA* 4.4 4.5 - - + +
647A ILE* 4.3 12.1 - - + -
742A GLY* 3.5 32.5 - - - +
743A GLY 3.5 3.1 - - - +
744A PRO* 5.0 0.2 - - - -
755A LEU* 4.7 3.1 - - + -
757A GLY* 1.3 76.8 - - - +
759A THR* 1.3 69.1 + - - +
760A SER* 3.1 2.6 + - - -
774A TYR* 3.3 3.4 - - - -
775A VAL* 3.0 37.3 + - + +
777A VAL* 4.1 7.9 - - + -
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Residues in contact with THR 759 (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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601A ALA* 4.5 1.4 - - - +
682A ILE* 4.5 4.4 - - + +
739A GLY* 4.5 15.2 - - - +
740A ASP 3.2 26.0 - - - +
742A GLY* 2.7 29.1 + - - -
743A GLY* 2.7 21.4 + - - -
744A PRO 3.9 6.9 + - - -
757A GLY 4.1 0.6 + - - -
758A VAL* 1.3 70.8 - - - +
760A SER* 1.3 67.0 + - - +
761A TRP 3.9 0.2 + - - -
764A GLY* 3.8 24.2 - - - +
774A TYR* 3.3 27.8 - - + -
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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
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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