Contacts of the helix formed by residues 142 - 148 (chain T) in PDB entry 2A2Q
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 142 (chain T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129T ASP* 4.2 18.5 - - - -
130T GLU 2.8 15.9 - - - -
131T ARG* 4.0 2.2 - - - +
132T THR* 3.7 2.0 - - - -
140T PHE 3.8 1.6 + - - -
141T LEU* 1.3 75.9 - - - +
143T LEU* 1.3 64.0 + - - +
144T ARG* 3.4 6.8 + - - +
145T ASP* 3.0 41.9 + - - +
146T VAL* 3.2 13.9 + - - +
1015T CL 3.9 10.1 - - - -
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Residues in contact with LEU 143 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T ASN* 3.7 16.6 - - - +
19T PHE* 4.7 2.7 - - + -
106T THR* 5.8 0.7 - - + -
107T ASN 5.7 0.2 - - - +
108T LEU* 3.9 22.2 - - + -
130T GLU* 2.6 45.9 + - + +
132T THR* 3.6 19.9 - - + +
142T SER* 1.3 73.3 - - - +
144T ARG* 1.3 59.2 + - - +
146T VAL* 3.2 1.3 + - - -
147T PHE* 2.8 61.5 + - + +
151T LEU* 3.9 14.6 - - + -
153T TYR* 4.0 6.1 - - - +
191T ALA* 4.1 9.2 - - + -
1015T CL 3.7 6.7 - - + +
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Residues in contact with ARG 144 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142T SER* 3.2 4.6 + - - +
143T LEU* 1.3 76.7 - - - +
145T ASP* 1.3 63.2 + - - +
148T GLY* 2.7 56.1 + - - +
149T LYS* 4.9 1.4 - - - +
151T LEU* 2.9 52.9 + - + +
152T ILE* 3.8 4.8 - - - +
153T TYR* 3.9 3.6 - - - -
171T ASN 3.1 23.9 + - - -
172T THR* 3.0 25.9 + - - +
173T ASN* 3.0 20.4 + - - +
1015T CL 3.4 14.9 - - + +
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Residues in contact with ASP 145 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136T ARG* 5.3 0.9 + - - -
140T PHE 4.9 0.3 - - - +
141T LEU* 3.6 30.3 - - + +
142T SER* 3.0 41.8 + - - +
144T ARG* 1.3 80.1 - - - +
146T VAL* 1.3 61.4 + - - +
148T GLY* 4.5 1.7 + - - -
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Residues in contact with VAL 146 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19T PHE* 3.7 29.4 - - + -
67T VAL* 4.3 10.5 - - + -
68T LYS* 5.3 2.4 + - - -
103T TYR* 3.6 22.7 + - + -
132T THR* 3.8 19.7 - - + +
134T VAL* 4.2 10.5 - - + -
141T LEU* 3.9 20.2 - - + -
142T SER 3.2 14.3 + - - +
143T LEU* 3.2 6.5 + - - +
144T ARG 3.1 0.6 - - - -
145T ASP* 1.3 79.1 - - - +
147T PHE* 1.3 63.3 + - + +
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Residues in contact with PHE 147 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19T PHE* 3.8 27.6 - + - -
103T TYR* 3.3 61.2 + + - -
106T THR* 4.4 2.7 - - + -
108T LEU* 4.3 5.6 - - + -
143T LEU* 2.8 54.9 + - + +
146T VAL* 1.3 77.5 - - + +
148T GLY* 1.3 63.7 + - - +
149T LYS* 3.2 2.4 + - - +
150T ASP* 3.0 18.7 + - + +
151T LEU* 3.6 20.9 - - + +
193T ILE* 3.6 28.3 - - + -
196T ARG* 3.9 13.9 - - - -
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Residues in contact with GLY 148 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144T ARG* 2.7 51.7 + - - -
145T ASP 4.5 1.5 + - - -
146T VAL 3.6 1.0 - - - -
147T PHE* 1.3 71.2 - - - +
149T LYS* 1.3 57.8 + - - -
151T LEU* 3.0 14.7 + - - +
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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