Contacts of the helix formed by residues 972 - 976 (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 972 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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914I LEU* 4.1 39.5 - - + -
916I ASN* 6.2 3.4 - - - +
918I LEU* 4.2 21.8 - - + +
921I LEU* 4.0 14.8 - - + -
922I TRP* 3.1 17.9 - - - -
969I HIS 5.4 10.1 - - - +
970I LYS* 3.0 1.5 - - - -
971I VAL* 1.3 85.7 - - + +
973I ARG* 1.3 65.1 + - - +
976I LEU* 3.1 36.5 - - + +
978I ARG* 5.1 5.6 - - - +
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Residues in contact with ARG 973 (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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970I LYS* 2.8 47.6 + - + +
972I LEU* 1.3 77.6 - - - +
974I PRO* 1.4 60.1 - - + +
976I LEU 2.5 37.8 + - - +
977I LEU* 3.4 39.1 - - - +
978I ARG* 3.1 41.0 + - + +
979I ARG* 4.6 5.7 - - - +
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Residues in contact with PRO 974 (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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776I ILE 4.7 0.2 - - - +
922I TRP* 3.5 21.8 - - + -
939I PHE* 4.4 31.0 - - + -
942I TRP* 6.0 2.5 - - + -
970I LYS* 3.4 29.4 - - - +
971I VAL* 4.6 1.3 - - - -
973I ARG* 1.4 91.5 - - + +
975I PHE* 1.3 70.8 + - + +
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Residues in contact with PHE 975 (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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774I ASN 4.8 2.0 - - - -
775I GLY* 4.1 17.7 - - - -
776I ILE* 2.9 53.1 - - + +
777I LEU* 3.7 2.2 - - - -
922I TRP* 3.3 35.7 - + + -
925I LEU* 3.8 8.3 - - + -
928I LEU* 5.9 1.1 - - + -
932I ILE* 4.2 22.0 - - + -
935I SER* 3.9 25.1 - - - -
936I CYS* 4.3 17.7 - - + -
939I PHE* 5.8 2.7 - + - -
973I ARG 3.2 0.2 - - - -
974I PRO* 1.3 85.1 - - + +
976I LEU* 1.3 71.5 + - - +
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Residues in contact with LEU 976 (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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778I ALA* 3.3 32.1 - - + +
910I THR* 4.0 14.4 - - + -
912I THR* 5.1 8.3 - - + -
914I LEU* 5.9 4.9 - - + -
921I LEU* 3.6 39.7 - - + -
922I TRP* 4.8 1.1 - - + -
925I LEU* 4.5 5.6 - - + -
972I LEU* 3.1 34.0 + - + +
973I ARG* 2.5 30.8 + - - +
975I PHE* 1.3 86.1 - - - +
977I LEU* 1.3 64.3 + - - +
978I ARG* 3.4 6.1 + - - +
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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