Contacts of the helix formed by residues 1084 - 1090 (chain C) in PDB entry 4DAJ
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 LEU1084 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078C ILE* 3.8 35.2 - - + +
1081C ASN* 2.9 36.4 + - + +
1082C ALA 3.5 0.2 - - - -
1083C LYS* 1.3 77.8 - - + +
1085C LYS* 1.3 67.3 + - - +
1086C PRO 3.3 0.7 - - - -
1087C VAL* 2.8 19.6 + - + +
1088C TYR* 2.9 12.9 + - + +
1099C LEU* 5.5 9.0 - - + -
1103C VAL* 5.0 5.4 - - + -
1108C GLU* 4.3 21.3 - - + +
1111C VAL* 4.3 9.4 - - + +
1112C ALA* 4.0 23.6 - - + +
1118C LEU* 4.2 19.5 - - + -
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Residues in contact with LYS1085 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1078C ILE* 3.9 5.8 + - - +
1079C LEU* 4.3 30.7 - - + +
1081C ASN 3.4 16.4 + - - +
1082C ALA* 4.8 0.9 - - - +
1084C LEU* 1.3 77.4 - - - +
1086C PRO* 1.3 72.2 - - + +
1088C TYR* 3.3 6.8 + - - +
1089C ASP* 2.9 37.3 + - + +
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Residues in contact with PRO1086 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1082C ALA 3.6 18.4 - - - +
1083C LYS* 3.8 5.6 - - - +
1084C LEU 3.4 4.0 - - - -
1085C LYS* 1.3 105.6 - - + +
1087C VAL* 1.3 58.4 + - - +
1089C ASP* 3.6 5.1 + - + +
1090C SER* 3.0 27.7 + - - -
1122C GLN* 3.3 18.8 - - - +
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Residues in contact with VAL1087 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1083C LYS 3.7 18.4 - - - +
1084C LEU* 2.8 16.3 + - + +
1086C PRO* 1.3 71.9 - - - +
1088C TYR* 1.3 58.9 + - - +
1090C SER* 2.9 19.6 + - - -
1091C LEU* 3.0 36.7 - - + +
1099C LEU* 4.0 13.2 - - + -
1118C LEU* 4.0 33.7 - - + -
1121C LEU* 4.4 9.0 - - + -
1122C GLN* 3.5 31.4 - - + +
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Residues in contact with TYR1088 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258C GLU* 4.1 13.2 + - - -
1075C VAL* 3.7 23.7 - - + +
1078C ILE* 3.7 40.6 - - + -
1079C LEU* 4.2 24.9 - - + -
1084C LEU 2.9 6.7 + - - +
1085C LYS* 3.7 6.3 - - - +
1087C VAL* 1.3 78.6 - - - +
1089C ASP* 1.3 66.6 + - + +
1090C SER 3.4 0.3 + - - -
1091C LEU* 3.5 6.4 + - - +
1096C ARG* 3.3 57.0 + - + +
1099C LEU* 4.1 16.8 - - + +
1100C ILE* 4.0 26.9 - - + +
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Residues in contact with ASP1089 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1079C LEU* 6.4 0.9 - - + -
1085C LYS* 2.9 25.6 + - + +
1086C PRO* 4.1 5.6 - - + +
1088C TYR* 1.3 82.0 - - + +
1090C SER* 1.3 60.3 + - - +
1091C LEU 3.2 2.3 + - - +
1096C ARG* 3.6 19.7 + - - +
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Residues in contact with SER1090 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1086C PRO 3.0 15.0 + - - -
1087C VAL* 2.9 17.0 + - - -
1088C TYR 3.3 0.2 - - - -
1089C ASP* 1.3 75.2 - - - +
1091C LEU* 1.3 61.8 + - - +
1122C GLN* 4.1 25.5 - - - +
1124C LYS* 3.2 27.7 + - - +
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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