Contacts of the strand formed by residues 878 - 886 (chain A) in PDB entry 1L5G
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 GLN 878 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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799A TRP 3.6 1.0 - - - +
800A PRO 4.1 0.3 - - - -
801A TYR* 3.1 32.8 + - + +
802A LYS* 3.0 37.3 + - + +
804A ASN* 4.9 3.6 + - - -
805A ASN* 4.6 19.1 + - - -
826A MET* 5.7 7.0 - - + -
874A CYS* 4.2 1.0 - - - -
877A ALA* 1.3 73.2 - - - +
879A CYS* 1.3 60.6 + - - +
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Residues in contact with CYS 879 (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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798A GLN* 3.7 24.5 - - - -
799A TRP 3.8 2.9 - - - -
801A TYR* 4.4 2.0 - - - -
825A ASP* 3.8 10.7 - - - +
826A MET* 3.9 11.2 - - - +
874A CYS* 2.0 48.5 - - + +
877A ALA 3.4 3.2 + - - +
878A GLN* 1.3 74.0 - - - +
880A LEU* 1.3 64.4 + - - +
881A LYS* 3.6 17.4 + - - +
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Residues in contact with LEU 880 (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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797A LEU 4.0 0.3 - - - +
799A TRP* 2.8 42.2 + - + +
801A TYR* 3.7 31.0 - - + +
811A ILE* 3.7 32.3 - - + -
824A SER* 3.1 25.4 - - - +
825A ASP* 3.8 3.6 - - - +
826A MET* 3.6 34.3 - - + +
827A GLU 5.1 3.6 - - - +
828A ILE* 4.9 5.4 - - + -
879A CYS* 1.3 71.1 - - - +
881A LYS* 1.3 68.4 + - - +
882A ILE* 3.9 5.6 - - + -
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Residues in contact with LYS 881 (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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796A HIS* 4.5 20.6 - - + +
797A LEU 3.2 17.7 - - - +
798A GLN* 4.6 18.4 - - + +
823A THR 4.6 0.2 - - - -
825A ASP* 2.7 52.4 + - + +
879A CYS* 3.6 15.4 + - - +
880A LEU* 1.3 77.1 - - - +
882A ILE* 1.3 73.1 + - - +
883A VAL* 4.2 2.9 - - + +
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Residues in contact with ILE 882 (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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795A LEU 4.1 0.2 - - - +
796A HIS* 3.8 0.9 - - - -
797A LEU* 2.8 61.7 + - + +
799A TRP* 5.8 0.2 - - + -
811A ILE* 4.3 17.9 - - + -
814A TYR* 3.8 35.0 - - + -
822A CYS* 4.2 9.4 - - + -
823A THR 3.2 9.9 - - - +
824A SER* 4.0 8.5 - - - -
828A ILE* 5.1 0.4 - - + -
880A LEU* 3.9 10.1 - - + +
881A LYS* 1.3 82.1 - - - +
883A VAL* 1.3 61.5 + - - +
884A CYS* 4.0 21.7 + - - -
897A LEU* 4.5 11.2 - - + -
899A VAL* 5.3 2.0 - - + -
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Residues in contact with VAL 883 (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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794A MET* 3.9 20.0 - - + -
795A LEU 3.8 2.2 - - - +
796A HIS* 3.6 30.7 - - + +
823A THR* 2.7 63.9 + - + +
825A ASP 6.0 0.2 - - - +
881A LYS* 4.2 3.3 - - + -
882A ILE* 1.3 73.6 - - - +
884A CYS* 1.3 63.3 + - - +
885A GLN* 3.1 11.4 + - - +
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Residues in contact with CYS 884 (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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794A MET* 3.7 9.4 - - - +
795A LEU* 2.8 50.7 + - + +
797A LEU* 6.0 0.2 - - - -
820A MET* 3.4 18.6 - - + -
821A ASN 3.3 2.2 - - - -
822A CYS* 2.0 48.7 - - - -
882A ILE* 4.0 13.9 - - - -
883A VAL* 1.3 76.7 - - - +
885A GLN* 1.3 64.2 + - - +
886A VAL* 3.8 0.4 + - - -
897A LEU* 4.6 8.5 - - - -
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Residues in contact with GLN 885 (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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793A ALA 4.3 2.2 - - - -
794A MET* 4.4 12.3 - - + -
820A MET* 3.1 6.4 - - - +
821A ASN* 2.7 58.5 + - + +
822A CYS* 4.2 1.0 - - - +
823A THR* 4.4 10.3 + - - +
883A VAL* 3.1 34.3 + - + +
884A CYS* 1.3 74.6 - - - +
886A VAL* 1.3 60.9 + - - +
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Residues in contact with VAL 886 (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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782A LEU* 4.5 8.1 - - + -
790A PHE* 4.0 25.8 - - + -
792A LYS* 3.4 12.5 - - - +
793A ALA* 3.0 38.5 + - + +
795A LEU* 4.4 11.4 - - + +
819A PRO 3.5 11.7 - - - +
820A MET* 3.7 31.9 - - + -
884A CYS 4.4 5.4 - - - +
885A GLN* 1.3 76.3 - - - +
887A GLY* 1.3 71.2 + - - +
889A LEU* 4.3 16.6 - - + -
895A ALA* 5.0 2.2 - - + -
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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