Contacts of the helix formed by residues 184 - 192 (chain A) in PDB entry 1T0R
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 ASP 184 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31A GLU 3.9 2.8 - - - +
32A GLU* 3.5 23.0 + - - +
33A MET* 3.6 6.7 - - - +
35A GLY* 3.7 24.4 - - - +
37A ARG* 2.9 30.4 + - - -
183A ARG* 1.3 75.6 - - - +
185A SER* 1.3 65.1 + - - +
186A VAL 3.3 3.6 + - - -
187A ALA* 2.6 35.8 + - - +
188A VAL* 2.9 18.7 + - - +
257A MET* 4.5 0.5 - - - +
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Residues in contact with SER 185 (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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33A MET 2.8 21.0 + - - -
34A SER 3.7 8.5 + - - -
113A ARG* 4.1 7.0 - - - +
114A MET* 3.0 43.4 - - - +
117A PHE 4.1 11.7 - - - -
118A ALA* 3.4 13.6 - - - +
123A ASN* 4.9 1.1 + - - -
183A ARG 3.8 0.6 + - - -
184A ASP* 1.3 69.3 - - - +
186A VAL* 1.3 64.8 + - - +
188A VAL* 2.9 17.2 + - - +
189A SER* 3.1 11.3 + - - -
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Residues in contact with VAL 186 (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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34A SER 3.5 8.4 + - - +
35A GLY 3.2 24.5 - - - +
36A ALA* 4.6 0.7 - - - +
37A ARG* 3.7 13.5 - - - +
44A TRP* 3.4 40.8 - - + -
118A ALA* 6.0 4.0 - - + -
119A LYS 6.1 1.3 - - - +
123A ASN* 5.8 4.0 - - - +
184A ASP* 3.3 1.8 + - - +
185A SER* 1.3 79.1 + - - +
187A ALA* 1.3 60.3 + - - +
189A SER* 2.7 26.2 + - - +
190A ILE* 3.4 13.8 - - + +
241A SER* 4.7 4.7 - - - +
245A LEU* 4.2 20.0 - - + -
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Residues in contact with ALA 187 (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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37A ARG* 4.6 0.2 - - - +
183A ARG* 3.7 22.2 - - + -
184A ASP* 2.6 32.1 + - - +
186A VAL* 1.3 72.4 - - - +
188A VAL* 1.3 60.7 + - - +
190A ILE* 3.2 2.9 + - - +
191A MET* 2.9 34.3 + - - +
257A MET* 3.4 33.2 - - + -
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Residues in contact with VAL 188 (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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110A ALA* 3.9 24.9 - - + +
113A ARG* 5.0 3.8 - - + -
114A MET* 4.0 16.2 - - + -
179A MET 4.2 7.2 - - - -
180A MET* 3.7 20.2 - - + +
183A ARG* 3.4 32.5 - - + +
184A ASP 2.9 9.6 + - - +
185A SER* 2.9 8.9 + - - +
187A ALA* 1.3 75.7 - - - +
189A SER* 1.3 63.4 + - - +
192A LEU* 3.0 45.3 + - + +
193A THR* 3.5 1.0 + - - -
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Residues in contact with SER 189 (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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114A MET* 3.6 22.8 - - - -
123A ASN* 4.5 4.7 - - - -
185A SER 3.1 8.0 + - - -
186A VAL* 2.7 22.6 + - - -
188A VAL* 1.3 77.0 - - - +
190A ILE* 1.3 55.9 + - - +
193A THR* 3.0 27.2 - - - -
194A PHE 3.1 4.0 + - - -
237A GLN 3.7 19.7 - - - -
238A GLY* 3.0 12.5 - - - -
241A SER* 3.0 23.5 + - - -
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Residues in contact with ILE 190 (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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186A VAL* 3.4 18.6 - - + +
187A ALA 3.2 5.5 + - - +
188A VAL 3.1 0.6 - - - -
189A SER* 1.3 82.0 - - - +
191A MET* 1.3 69.7 + - + +
194A PHE* 3.2 10.1 + - + +
195A ALA* 3.0 23.7 + - - +
238A GLY* 4.6 0.7 - - - +
241A SER* 4.5 5.8 - - - -
242A LEU* 3.3 33.7 - - + -
245A LEU* 4.1 22.9 - - + -
254A ALA* 4.8 1.8 - - - -
257A MET* 4.1 25.8 - - + -
258A VAL* 3.6 32.1 - - + +
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Residues in contact with MET 191 (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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179A MET* 3.4 51.9 - - + +
183A ARG* 3.5 39.3 - - - +
187A ALA* 2.9 19.0 + - - +
190A ILE* 1.3 71.2 - - - +
192A LEU* 1.3 60.0 + - - +
195A ALA* 3.2 21.1 - - - +
196A PHE* 3.4 5.9 + - - +
257A MET* 3.8 41.5 - - + +
260A VAL* 3.7 22.0 - - + -
261A ALA* 3.5 18.4 - - + +
265A SER* 5.2 0.5 + - - -
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Residues in contact with LEU 192 (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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107A ALA* 5.0 5.6 - - + +
110A ALA* 4.0 12.6 - - + -
111A GLU* 4.7 9.2 - - - +
134A GLU* 5.7 0.2 - - - +
175A PHE* 6.1 0.7 - - + -
176A PHE* 5.5 1.8 - - + -
179A MET* 4.4 8.2 + - + +
180A MET* 3.6 51.8 - - + -
188A VAL* 3.0 21.1 + - + +
191A MET* 1.3 75.4 - - - +
193A THR* 1.3 72.2 + - - +
196A PHE* 3.0 44.7 + - + +
197A GLU* 3.0 30.9 + - + +
502A AZI 4.8 4.3 - - - +
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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