Contacts of the helix formed by residues 165 - 186 (chain A) in PDB entry 3CMT
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 GLY 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A HIS 3.5 2.8 + - - -
164A MET* 1.3 75.4 - - - +
166A LEU* 1.3 62.1 + - - +
168A ALA* 3.1 7.5 + - - +
169A ARG* 3.0 32.7 + - - +
1002B T 3.3 33.5 + - - -
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Residues in contact with LEU 166 (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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123A GLU* 4.8 7.0 - - - +
151A PRO* 3.7 24.5 - - + -
153A ALA* 4.0 20.4 - - + -
163A HIS* 3.5 49.0 + - + +
164A MET 3.2 3.6 + - - +
165A GLY* 1.3 76.6 - - - +
167A ALA* 1.3 62.6 + - - +
169A ARG* 3.5 23.6 + - - +
170A MET* 3.2 21.1 + - + +
1002B T 3.6 1.0 + - - -
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Residues in contact with ALA 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A LEU 4.6 3.1 - - - +
151A PRO* 3.8 27.7 - - + +
163A HIS 5.4 0.2 + - - -
166A LEU* 1.3 76.2 - - - +
168A ALA* 1.3 59.1 + - - +
170A MET* 3.5 10.6 + - + +
171A MET* 3.0 34.6 + - + +
210A THR* 6.6 0.4 - - + -
211A GLY* 4.8 10.3 - - - -
1176A ARG* 4.8 12.1 - - - +
1002B T 3.3 11.6 + - - +
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Residues in contact with ALA 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A GLY* 3.1 10.9 + - - +
167A ALA* 1.3 76.0 - - - +
169A ARG* 1.3 58.7 + - - +
171A MET* 3.4 3.1 + - - +
172A SER* 2.9 29.2 + - - -
211A GLY 4.0 13.0 - - - +
212A GLY* 3.8 18.8 - - - +
213A ASN 5.7 0.5 + - - -
214A ALA* 5.1 1.2 - - - +
1002B T 3.2 28.1 + - + +
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Residues in contact with ARG 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A MET 4.0 9.7 + - - -
165A GLY* 3.0 23.8 + - - +
166A LEU* 3.8 30.8 - - - +
168A ALA* 1.3 75.7 - - - +
170A MET* 1.3 59.2 + - - +
172A SER* 3.5 7.6 + - - -
173A GLN* 3.0 27.7 + - - +
176A ARG* 4.5 3.9 + - - +
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Residues in contact with MET 170 (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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122A GLY* 4.1 2.5 - - - -
123A GLU* 3.6 49.1 - - + +
126A LEU* 3.9 12.3 - - + -
149A LEU* 3.6 26.7 - - + +
151A PRO* 4.4 9.0 - - + -
166A LEU* 3.2 16.7 + - + +
167A ALA* 3.6 15.7 - - + +
168A ALA 3.3 0.2 - - - -
169A ARG* 1.3 75.8 - - - +
171A MET* 1.3 86.1 + - + +
173A GLN* 3.3 15.7 + - - +
174A ALA* 2.9 27.2 + - - +
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Residues in contact with MET 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A LEU* 3.5 33.7 - - + -
146A VAL* 4.5 17.9 - - + -
149A LEU* 3.4 30.1 - - + -
167A ALA* 3.0 20.2 + - + +
168A ALA 3.5 2.7 - - - +
170A MET* 1.3 82.1 - - + +
172A SER* 1.3 65.8 + - - +
174A ALA* 3.2 3.9 + - + +
175A MET* 3.0 44.3 + - + +
191A PHE* 4.8 4.7 - - + -
211A GLY* 3.4 33.2 - - - +
214A ALA* 4.2 6.5 - - + -
215A LEU* 5.6 8.5 - - - +
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Residues in contact with SER 172 (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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168A ALA 2.9 17.7 + - - -
169A ARG* 3.6 11.0 - - - -
171A MET* 1.3 78.2 - - - +
173A GLN* 1.3 62.3 + - - +
175A MET* 3.6 3.3 + - - +
176A ARG* 3.4 31.3 + - - +
214A ALA* 3.5 21.9 - - - +
218A TYR* 5.1 2.3 + - - -
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Residues in contact with GLN 173 (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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123A GLU* 6.3 1.6 - - - +
169A ARG 3.0 12.9 + - - +
170A MET* 3.5 16.8 + - - +
172A SER* 1.3 75.8 - - - +
174A ALA* 1.3 65.6 + - - +
176A ARG* 3.2 29.8 + - - +
177A LYS* 3.2 35.0 + - + +
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Residues in contact with ALA 174 (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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126A LEU* 3.8 33.4 - - + -
170A MET 2.9 14.3 + - - +
171A MET* 3.2 9.8 + - - +
173A GLN* 1.3 76.8 - - - +
175A MET* 1.3 64.3 + - + +
177A LYS* 3.2 7.1 + - - +
178A LEU* 2.8 43.1 + - + +
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Residues in contact with MET 175 (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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61A ILE* 4.1 18.4 - - - -
171A MET* 3.0 35.6 + - + +
172A SER 3.9 2.9 - - - +
173A GLN 3.3 0.2 - - - -
174A ALA* 1.3 85.4 - - + +
176A ARG* 1.3 63.8 + - - +
178A LEU* 4.4 6.3 - - + +
179A ALA* 2.9 30.0 + - - +
191A PHE* 3.8 29.2 - - + -
214A ALA* 3.8 14.4 - - + -
215A LEU* 3.9 24.9 - - + +
218A TYR* 3.4 39.5 - - + -
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Residues in contact with ARG 176 (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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169A ARG* 4.5 5.5 + - - +
172A SER* 3.4 18.5 + - - +
173A GLN* 3.2 41.6 + - + +
174A ALA 3.3 0.2 - - - -
175A MET* 1.3 79.6 - - - +
177A LYS* 1.3 64.4 + - + +
179A ALA* 4.2 7.3 + - - +
180A GLY* 4.5 3.3 + - - -
218A TYR* 3.6 22.4 + - - +
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Residues in contact with LYS 177 (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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127A GLU* 3.5 18.9 + - - +
130A ASP* 3.4 28.5 + - - +
134A ARG* 5.0 1.0 - - - +
173A GLN* 3.2 26.7 + - + +
174A ALA* 3.2 9.2 + - - +
176A ARG* 1.3 83.2 - - + +
178A LEU* 1.3 64.6 + - + +
180A GLY* 4.2 1.4 + - - -
181A ASN* 3.7 23.4 + - - +
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Residues in contact with LEU 178 (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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61A ILE* 4.9 2.5 - - + -
126A LEU* 4.4 10.1 - - + +
129A CYS* 4.1 11.2 - - + +
130A ASP* 3.6 43.5 - - + +
133A ALA* 4.8 5.2 - - + -
174A ALA* 2.8 39.4 + - + +
175A MET* 4.1 6.7 - - + +
177A LYS* 1.3 70.6 - - + +
179A ALA* 1.3 67.0 + - - +
180A GLY 3.2 2.7 - - - -
181A ASN* 2.9 4.0 + - - -
182A LEU* 2.8 38.5 + - + +
189A LEU* 3.8 24.9 - - + -
191A PHE* 4.4 11.2 - - + -
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Residues in contact with ALA 179 (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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59A GLY 4.6 1.9 - - - +
61A ILE* 4.4 12.9 - - + +
175A MET 2.9 18.5 + - - +
176A ARG 4.5 3.4 - - - +
178A LEU* 1.3 75.9 - - - +
180A GLY* 1.3 61.9 + - - +
182A LEU* 3.5 3.8 + - - +
183A LYS* 3.2 23.0 + - - +
218A TYR* 4.0 23.3 - - + -
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Residues in contact with GLY 180 (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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176A ARG 4.5 4.4 + - - -
177A LYS 4.2 3.3 + - - -
178A LEU 3.2 0.6 - - - -
179A ALA* 1.3 76.4 - - - +
181A ASN* 1.3 67.8 + - - +
183A LYS* 3.4 6.1 + - - +
184A GLN* 3.1 35.6 + - - +
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Residues in contact with ASN 181 (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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130A ASP* 2.8 26.7 - - - +
133A ALA* 4.0 18.9 - - + +
134A ARG* 3.2 30.7 - - + +
177A LYS* 3.7 9.2 + - - +
178A LEU 2.9 8.0 + - - +
180A GLY* 1.3 77.5 - - - +
182A LEU* 1.3 59.5 + - - +
184A GLN* 3.7 7.1 + - - +
185A SER* 3.0 31.0 + - - -
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Residues in contact with LEU 182 (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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59A GLY* 3.3 11.0 - - - +
60A ARG 4.9 1.1 - - - +
61A ILE* 3.7 22.9 - - + -
133A ALA* 4.0 15.0 - - + -
141A ILE* 4.8 3.4 - - + -
178A LEU* 2.8 30.4 + - + +
179A ALA* 3.8 4.0 - - - +
181A ASN* 1.3 75.4 - - - +
183A LYS* 1.3 59.3 + - - +
185A SER 3.4 0.2 + - - -
186A ASN 3.0 7.8 + - - -
187A THR* 2.9 67.6 + - + +
189A LEU* 3.7 40.2 - - + -
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Residues in contact with LYS 183 (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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58A MET 4.6 5.2 - - - -
59A GLY* 3.5 19.4 + - - +
60A ARG* 3.5 34.3 - - - +
179A ALA 3.2 14.6 + - - +
180A GLY* 3.4 5.4 + - - +
182A LEU* 1.3 78.7 - - - +
184A GLN* 1.3 67.0 + - + +
186A ASN* 3.1 18.2 + - - +
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Residues in contact with GLN 184 (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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180A GLY* 3.1 25.6 + - - +
181A ASN* 3.7 8.3 + - - +
183A LYS* 1.3 81.1 - - + +
185A SER* 1.3 59.8 + - - +
186A ASN* 3.4 0.4 - - - +
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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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133A ALA 2.5 30.7 + - - -
134A ARG* 4.2 5.2 + - - -
136A GLY* 4.0 22.5 + - - +
138A VAL 4.9 2.1 - - - +
139A ASP* 5.6 1.4 - - - +
181A ASN 3.0 15.2 + - - -
183A LYS 3.1 0.6 - - - -
184A GLN* 1.3 78.1 - - - +
186A ASN* 1.3 70.5 + - - +
187A THR* 3.1 15.9 + - - -
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Residues in contact with ASN 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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38A GLU* 3.2 28.6 + - - +
58A MET* 3.3 49.5 - - - +
59A GLY* 3.6 7.4 + - - -
138A VAL 5.4 0.2 - - - -
139A ASP* 4.1 3.8 - - - +
182A LEU 3.0 6.9 + - - -
183A LYS* 3.1 14.7 + - - +
184A GLN 3.4 0.4 - - - -
185A SER* 1.3 80.5 - - - +
187A THR* 1.3 59.5 + - - +
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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
------------------------------------------------------------
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