Contacts of the helix formed by residues 185 - 197 (chain A) in PDB entry 4TMU
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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184A ALA* 1.3 74.7 - - - +
186A ASP* 1.3 60.1 + - - +
187A THR* 3.3 6.7 + - - -
188A THR* 2.9 24.1 + - - -
189A ARG* 2.9 34.8 + - - +
318A GLU* 3.0 24.0 + - - +
367A LYS* 3.2 18.1 + - - -
388A TYR* 2.7 49.2 + - + +
389A PHE* 4.1 10.1 - - + -
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Residues in contact with ASP 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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185A ASP* 1.3 76.4 - - - +
187A THR* 1.3 59.4 + - - +
189A ARG* 3.3 27.2 + - - +
190A ARG* 2.9 69.6 + - - +
388A TYR 5.6 0.6 + - - -
389A PHE* 5.9 0.4 - - - +
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Residues in contact with THR 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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185A ASP* 3.4 10.3 + - - -
186A ASP* 1.3 81.4 + - - +
188A THR* 1.3 59.6 + - - +
190A ARG* 3.6 6.3 + - - +
191A ASP* 3.0 28.9 + - + +
194A ARG* 5.3 0.5 + - - -
363A ILE* 3.7 42.6 - - + +
367A LYS* 4.0 11.7 - - - +
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Residues in contact with THR 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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149A HIS* 4.2 14.8 - - + +
152A SER* 3.9 28.3 + - - -
184A ALA* 3.9 15.7 - - + -
185A ASP* 2.9 10.7 + - - -
187A THR* 1.3 73.0 - - - +
189A ARG* 1.3 66.8 + - - +
191A ASP* 3.2 1.6 + - - +
192A ILE* 2.9 38.4 + - + +
318A GLU* 2.6 27.5 + - - +
367A LYS* 3.0 14.4 + - - -
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Residues in contact with ARG 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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44A LEU* 3.9 24.0 - - + +
46A VAL* 4.2 10.4 - - + +
184A ALA* 3.1 35.4 + - + -
185A ASP* 2.9 18.0 + - - +
186A ASP* 3.3 34.4 + - - +
188A THR* 1.3 76.1 - - - +
190A ARG* 1.3 63.2 + - + +
192A ILE* 3.0 9.7 + - - +
193A VAL* 3.0 27.8 + - + +
203A ILE* 4.8 7.9 - - + -
205A ILE* 3.5 35.5 - - - +
208A PHE* 4.5 7.7 - - - -
389A PHE 3.4 25.5 + - - -
390A GLY* 6.0 1.0 - - - -
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Residues in contact with ARG 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 ASP* 2.9 51.5 + - - +
187A THR* 4.0 5.2 - - - +
189A ARG* 1.3 76.9 - - + +
191A ASP* 1.3 62.9 + - - +
193A VAL* 3.4 8.8 + - - +
194A ARG* 3.0 47.5 + - - +
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Residues in contact with ASP 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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152A SER* 3.0 27.9 + - - +
156A HIS* 2.7 30.4 + - - -
187A THR* 3.0 21.4 + - + +
188A THR 3.6 4.3 - - - +
189A ARG 3.2 0.4 - - - -
190A ARG* 1.3 76.9 - - - +
192A ILE* 1.3 58.2 + - - +
194A ARG* 3.7 19.8 + - - +
195A LEU* 3.0 49.6 + - - +
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Residues in contact with ILE 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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44A LEU* 4.0 18.2 - - + -
148A ALA* 3.5 36.6 - - + +
149A HIS* 3.9 4.0 - - - +
151A ILE* 4.2 22.4 - - + -
152A SER* 4.8 2.5 - - - -
179A ALA* 3.8 26.9 - - + -
181A THR* 4.4 8.5 - - + -
184A ALA* 4.9 0.9 - - + -
188A THR* 2.9 33.1 + - + +
189A ARG* 3.0 9.2 + - - +
191A ASP* 1.3 74.4 - - - +
193A VAL* 1.3 66.3 + - - +
196A LEU* 3.0 33.3 + - + +
198A LEU* 4.6 2.5 - - + -
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Residues in contact with VAL 193 (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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44A LEU* 4.4 15.5 - - + -
189A ARG 3.0 15.0 + - - +
190A ARG* 3.7 9.9 - - - +
192A ILE* 1.3 74.5 - - - +
194A ARG* 1.3 58.3 + - - +
197A GLY* 2.9 25.3 + - - -
198A LEU* 3.1 39.2 + - + +
201A PRO* 4.1 24.5 - - + -
203A ILE* 4.7 8.7 - - + -
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Residues in contact with ARG 194 (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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187A THR 5.3 0.8 + - - -
190A ARG* 3.0 38.6 + - - +
191A ASP* 3.7 38.4 + - - +
193A VAL* 1.3 79.0 - - - +
195A LEU* 1.3 66.8 + - + +
197A GLY* 3.2 13.0 + - - -
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Residues in contact with LEU 195 (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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151A ILE* 3.7 32.1 - - + +
156A HIS* 3.8 20.0 - - + +
162A TYR 5.5 0.6 - - - +
163A ALA* 3.7 33.6 - - + +
165A LEU* 4.8 0.3 + - - +
166A GLY* 3.3 22.2 + - - -
191A ASP* 3.0 52.5 + - - +
194A ARG* 1.3 79.3 - - + +
196A LEU* 1.3 59.0 + - - +
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Residues in contact with LEU 196 (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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145A VAL* 4.1 22.0 - - + -
151A ILE* 4.0 20.6 - - + -
165A LEU* 3.6 31.6 - - + -
166A GLY* 3.9 4.9 - - - -
169A ARG* 3.2 23.0 - - - +
177A PHE* 4.3 13.9 - - + -
178A MET 4.9 1.1 - - - +
179A ALA* 3.8 26.5 - - + +
192A ILE* 3.0 18.0 + - + +
195A LEU* 1.3 78.5 - - - +
197A GLY* 1.3 63.4 + - - +
198A LEU* 3.5 26.0 + - + -
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Residues in contact with GLY 197 (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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166A GLY* 4.6 2.2 - - - -
169A ARG* 3.2 24.4 + - - -
193A VAL 2.9 8.6 + - - -
194A ARG 3.2 9.8 + - - -
195A LEU 3.4 0.6 - - - -
196A LEU* 1.3 77.8 - - - +
198A LEU* 1.3 66.5 + - - +
199A ASP* 3.5 3.1 + - - +
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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