Contacts of the helix formed by residues 116 - 121 (chain P) in PDB entry 2X86
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 SER 116 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115P SER* 1.3 85.9 + - - +
117P ALA* 1.3 52.7 + - - +
118P ALA* 2.9 24.5 + - - +
119P THR* 2.7 35.9 + - - +
140P PHE* 4.1 15.5 - - - -
144P LYS* 4.2 12.5 - - - +
166P ARG* 3.3 8.1 - - - +
167P TYR 3.8 6.3 - - - -
400P NAP 3.6 10.7 - - - -
402P BMA 3.3 15.6 + - - -
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Residues in contact with ALA 117 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116P SER* 1.3 70.0 + - - +
118P ALA* 1.3 59.6 + - - +
119P THR 3.0 5.4 - - - -
120P TYR* 3.0 24.3 + - + -
166P ARG* 3.6 4.8 - - - +
167P TYR 3.0 19.0 + - - +
168P PHE* 3.6 46.0 - - + -
273P GLN* 2.9 20.5 + - - +
276P THR* 5.2 4.2 - - + +
402P BMA 5.6 0.9 - - - +
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Residues in contact with ALA 118 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81P THR* 5.5 2.9 - - + -
116P SER* 2.9 17.1 + - - +
117P ALA* 1.3 79.4 - - - +
119P THR* 1.3 59.9 + - - +
120P TYR 3.1 0.2 - - - -
121P GLY* 3.1 17.0 + - - -
136P PRO* 3.5 12.9 - - - +
137P LEU 4.4 1.6 + - - -
138P ASN* 5.1 7.0 - - - +
140P PHE* 4.1 21.8 - - + -
141P GLY* 4.4 7.4 - - - -
273P GLN* 3.7 17.9 + - - +
401P ADP 6.0 0.2 - - - +
402P BMA 4.5 7.6 + - - +
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Residues in contact with THR 119 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
115P SER* 4.2 0.2 - - - +
116P SER 2.7 23.6 + - - +
117P ALA 4.2 0.5 - - - -
118P ALA* 1.3 78.1 - - - +
120P TYR* 1.3 58.2 + - - +
134P GLU* 3.3 9.3 - - - -
135P LYS 2.8 25.1 + - - -
136P PRO* 3.4 13.0 - - - +
141P GLY 3.9 5.2 - - - +
144P LYS* 3.9 11.2 - - + -
145P PHE* 3.5 38.1 - - - +
148P ASP* 4.2 8.5 - - - +
166P ARG* 3.2 28.1 + - - -
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Residues in contact with TYR 120 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117P ALA* 3.0 26.4 + - + +
119P THR* 1.3 79.5 - - - +
121P GLY* 1.3 67.3 + - - +
122P GLY 3.4 1.8 + - - +
123P ARG* 3.8 14.2 + - - -
127P PHE* 3.4 40.8 + + + -
128P ILE 3.2 41.4 - - - -
129P GLU* 3.3 1.6 + - - -
133P TYR* 3.6 30.0 - - + +
134P GLU* 4.4 2.7 - - + -
135P LYS* 3.9 7.8 + - - +
166P ARG* 3.1 34.9 + - - -
168P PHE* 3.9 12.3 - + - -
234P ASN* 2.6 29.2 + - - -
273P GLN* 4.3 0.4 - - - +
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Residues in contact with GLY 121 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118P ALA 3.1 15.0 + - - -
119P THR 3.3 0.2 - - - -
120P TYR* 1.3 82.0 - - - +
122P GLY* 1.3 66.9 + - - +
135P LYS* 3.4 21.9 - - - +
136P PRO* 4.1 0.7 - - - -
137P LEU* 3.7 28.3 - - - +
273P GLN* 3.3 8.5 - - - +
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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