Contacts of the helix formed by residues 1106 - 1115 (chain A) in PDB entry 3LJ1
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 ASP1106 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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996A ARG* 4.1 16.9 + - - -
1103A LEU* 2.7 64.0 + - + +
1104A SER 3.1 6.3 + - - -
1105A ASP* 1.3 71.4 - - - +
1107A GLN* 1.4 51.7 + - - +
1108A ILE 3.4 2.4 + - - -
1109A LEU* 2.7 26.1 + - + +
1110A ARG* 2.3 39.5 + - - +
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Residues in contact with GLN1107 (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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1105A ASP 3.8 5.0 + - - +
1106A ASP* 1.4 70.9 + - - +
1108A ILE* 1.3 62.3 + - + +
1110A ARG* 3.5 19.7 - - + +
1111A GLU* 3.7 15.2 - - - +
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Residues in contact with ILE1108 (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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992A LYS* 4.2 31.4 - - + +
1106A ASP* 2.9 2.2 + - - -
1107A GLN* 1.3 78.2 - - + +
1109A LEU* 1.3 79.0 + - + +
1111A GLU* 3.4 23.0 + - - +
1112A PHE* 3.6 10.6 - - + -
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Residues in contact with LEU1109 (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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989A PHE* 4.4 11.4 - - + -
992A LYS* 4.1 24.9 - - + +
993A VAL* 4.4 11.9 - - + +
996A ARG* 4.8 8.7 - - + -
1099A VAL* 3.9 22.2 - - + -
1103A LEU* 3.5 32.5 - - + +
1106A ASP* 2.7 27.6 + - + +
1108A ILE* 1.3 86.7 - - + +
1110A ARG* 1.3 64.0 + - - +
1111A GLU 3.1 2.2 - - - -
1112A PHE* 3.1 10.6 + - + +
1113A LEU* 2.9 28.5 + - - +
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Residues in contact with ARG1110 (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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1104A SER 3.1 24.0 + - - -
1105A ASP* 3.7 22.1 + - - +
1106A ASP* 2.3 46.9 + - - +
1107A GLN* 3.5 14.8 - - + +
1108A ILE 3.3 0.2 - - - -
1109A LEU* 1.3 67.9 - - - +
1111A GLU* 1.3 60.6 + - - +
1113A LEU* 4.5 0.4 - - - -
1114A TYR* 2.7 65.8 + - + +
1115A SER* 3.8 1.0 + - - -
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Residues in contact with GLU1111 (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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985A LYS* 4.9 1.6 + - - -
1107A GLN 3.7 14.0 - - - +
1108A ILE* 3.5 16.4 - - - +
1109A LEU 3.1 0.6 - - - -
1110A ARG* 1.3 81.1 - - - +
1112A PHE* 1.3 64.6 + - + +
1115A SER* 3.1 47.2 + - - +
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Residues in contact with PHE1112 (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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976A ARG* 5.0 0.5 - - - +
981A TRP* 3.2 23.9 + + + -
985A LYS* 3.5 53.3 + - + +
988A GLU* 3.9 25.1 - - + -
989A PHE* 3.6 43.3 - + + -
992A LYS* 4.0 22.0 - - + -
1108A ILE* 3.6 21.1 - - + -
1109A LEU* 3.1 12.6 + - + +
1111A GLU* 1.3 83.2 - - + +
1113A LEU* 1.3 63.5 + - - +
1115A SER 4.6 1.9 + - - +
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Residues in contact with LEU1113 (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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976A ARG* 3.7 21.0 - - - +
981A TRP* 4.9 0.2 - - - -
989A PHE* 3.8 25.8 - - + -
1096A TYR* 3.8 33.7 + - + +
1099A VAL* 4.0 10.1 - - + -
1100A LYS* 3.9 21.7 - - + +
1103A LEU 4.1 6.5 - - - +
1104A SER* 3.8 22.7 - - - +
1109A LEU 2.9 19.3 + - - +
1112A PHE* 1.3 80.6 - - - +
1114A TYR* 1.3 94.7 + - + +
1115A SER 3.7 0.4 - - - -
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Residues in contact with TYR1114 (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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973A LYS* 6.3 0.4 - - + -
976A ARG* 3.3 29.3 + - - +
1100A LYS* 3.8 29.5 + - - +
1104A SER* 3.1 42.3 - - - -
1110A ARG* 2.7 48.3 + - - +
1113A LEU* 1.3 103.7 - - + +
1115A SER* 1.3 62.5 + - - +
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Residues in contact with SER1115 (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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976A ARG* 4.1 13.7 + - - +
985A LYS* 4.0 17.1 + - - -
1110A ARG 4.2 0.3 + - - -
1111A GLU* 3.1 48.2 + - - +
1112A PHE 4.7 1.0 - - - +
1113A LEU 3.7 1.0 - - - -
1114A TYR* 1.3 81.4 - - - +
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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
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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