Contacts of the helix formed by residues 893 - 898 (chain I) in PDB entry 6LTJ
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 LEU 893 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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811I PRO* 5.8 2.9 - - + -
860I TYR* 5.7 8.3 - - + -
882I GLU* 3.4 28.3 - - - +
885I ARG* 4.2 10.8 - - + +
886I MET* 3.8 30.1 - - + +
891I CYS* 3.6 6.7 - - + +
892I LYS* 1.3 73.1 - - - +
894I THR* 1.3 65.7 + - + +
895I GLN 3.0 1.3 - - - -
896I VAL* 3.0 28.6 + - + +
897I LEU* 3.0 19.2 + - + +
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Residues in contact with THR 894 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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886I MET* 3.5 55.9 - - + +
888I ASN 3.1 34.8 + - - +
889I HIS* 3.4 10.8 - - - +
891I CYS* 3.8 1.7 + - + -
893I LEU* 1.3 77.2 - - + +
895I GLN* 1.3 59.4 + - - +
897I LEU 4.2 0.5 + - - -
898I ASN* 2.4 36.1 + - - +
924I LEU* 4.1 12.8 - - + -
927I PHE* 5.4 1.6 - - - -
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Residues in contact with GLN 895 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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889I HIS 2.3 28.5 + - - -
890I HIS* 4.6 2.2 - - - +
891I CYS 3.1 13.2 - - - +
892I LYS* 2.6 47.3 + - + +
894I THR* 1.3 82.8 + - - +
896I VAL* 1.3 55.5 + - - -
898I ASN* 3.4 13.5 - - - +
899I THR* 3.5 9.1 - - - +
927I PHE* 3.7 29.7 - - + -
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Residues in contact with VAL 896 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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860I TYR* 6.2 1.6 - - + -
892I LYS* 2.6 31.0 + - + +
893I LEU* 3.0 25.4 + - + +
895I GLN* 1.3 72.4 - - - +
897I LEU* 1.3 74.1 + - + +
898I ASN 3.2 0.9 - - - -
899I THR* 3.6 13.5 - - + -
900I HIS* 3.2 36.4 + - + +
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Residues in contact with LEU 897 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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809I ILE* 3.4 26.9 - - + +
860I TYR* 4.5 3.1 - - + -
880I VAL* 3.3 44.0 - - + +
881I ASP 3.8 8.7 - - - +
882I GLU* 3.3 39.9 - - + +
886I MET* 4.7 4.7 - - - -
893I LEU* 3.0 18.9 + - + +
894I THR 4.2 2.4 + - - +
896I VAL* 1.3 81.9 - - + +
898I ASN* 1.3 66.0 + - - +
900I HIS* 3.1 42.5 + - + +
901I TYR 4.7 0.2 + - - -
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Residues in contact with ASN 898 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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880I VAL* 4.6 8.9 - - - +
886I MET* 5.3 3.3 - - - +
894I THR 2.4 27.7 + - - +
895I GLN* 3.4 15.1 - - - +
897I LEU* 1.3 81.8 - - - +
899I THR* 1.3 57.9 + - - +
900I HIS 3.1 5.3 + - - -
901I TYR 3.3 15.8 + - - +
902I VAL* 3.5 19.0 - - + +
906I ARG* 4.8 8.5 + - - +
927I PHE* 4.5 21.0 + - - +
928I LEU* 5.5 5.4 - - - +
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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
------------------------------------------------------------
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