Contacts of the helix formed by residues 165 - 186 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163D HIS 3.7 0.8 + - - -
164D MET* 1.3 73.7 - - - +
166D LEU* 1.3 60.9 - - - +
168D ALA* 3.5 12.1 + - - +
169D ARG* 3.5 23.3 + - - +
1002E T 3.1 37.7 + - - -
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Residues in contact with LEU 166 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123D GLU* 5.6 2.7 - - - +
151D PRO* 4.1 22.6 - - + +
153D ALA* 4.1 21.3 - - + -
154D GLU* 4.8 3.4 - - + +
163D HIS* 3.6 48.7 + - + +
164D MET* 2.7 8.8 + - + +
165D GLY* 1.3 72.3 - - - +
167D ALA* 1.3 62.6 + - - +
168D ALA 3.5 0.3 + - - -
169D ARG* 3.8 26.8 + - + +
170D MET* 3.5 20.2 + - + +
1002E T 3.4 1.2 + - - -
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Residues in contact with ALA 167 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146D VAL 6.1 0.4 - - - +
149D LEU 4.6 6.5 - - - +
151D PRO* 3.9 25.0 - - + +
166D LEU* 1.3 76.5 - - - +
168D ALA* 1.3 59.1 + - - +
170D MET* 3.8 7.4 - - + +
171D MET* 3.2 33.3 + - + +
210D THR* 6.2 2.2 - - + -
211D GLY* 4.6 10.8 - - - +
1176D ARG* 4.7 12.8 - - - +
1002E T 3.1 10.8 + - - +
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Residues in contact with ALA 168 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165D GLY* 3.7 9.6 - - - +
166D LEU 3.3 0.4 - - - -
167D ALA* 1.3 76.7 - - - +
169D ARG* 1.3 59.5 + - - +
171D MET* 3.4 3.3 + - - +
172D SER* 2.9 29.3 + - - -
211D GLY 4.0 11.4 - - - +
212D GLY* 3.8 16.7 - - - -
213D ASN 5.3 0.8 + - - +
214D ALA* 5.1 1.4 - - - +
1002E T 3.0 26.4 + - + +
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Residues in contact with ARG 169 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D MET* 4.8 9.9 + - - +
165D GLY* 3.5 20.3 + - - +
166D LEU* 3.8 33.7 + - + +
168D ALA* 1.3 77.5 - - - +
170D MET* 1.3 58.5 + - - +
172D SER* 3.5 7.7 + - - -
173D GLN* 3.0 28.5 + - - +
176D ARG* 4.5 3.9 + - - +
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Residues in contact with MET 170 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122D GLY* 4.1 2.7 - - - -
123D GLU* 3.6 49.8 - - + +
126D LEU* 3.9 13.5 - - + -
149D LEU* 3.6 26.0 - - + +
151D PRO* 4.3 10.1 - - + -
166D LEU* 3.5 15.5 + - + +
167D ALA* 3.8 15.9 - - + +
169D ARG* 1.3 77.1 - - - +
171D MET* 1.3 85.6 + - + +
173D GLN* 3.3 15.1 + - - +
174D ALA* 2.9 26.9 + - - +
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Residues in contact with MET 171 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D LEU* 3.5 33.2 - - + -
146D VAL* 4.4 18.6 - - + -
149D LEU* 3.4 30.5 - - + -
167D ALA* 3.2 19.1 + - + +
168D ALA 3.4 2.9 + - - +
170D MET* 1.3 84.9 - - + +
172D SER* 1.3 65.0 + - - +
174D ALA* 3.2 3.7 + - + +
175D MET* 3.0 43.9 + - + +
191D PHE* 4.8 3.8 - - + -
211D GLY* 3.5 29.6 - - - +
214D ALA* 4.2 6.5 - - + -
215D LEU* 5.6 9.2 - - + +
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Residues in contact with SER 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168D ALA 2.9 18.5 + - - -
169D ARG* 3.6 10.3 - - - -
171D MET* 1.3 77.6 - - - +
173D GLN* 1.3 62.4 + - - +
175D MET* 3.6 2.9 + - - +
176D ARG* 3.4 32.0 + - - +
214D ALA* 3.5 22.0 - - - +
218D TYR* 5.1 1.9 + - - -
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Residues in contact with GLN 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D GLU* 6.3 1.8 - - - +
169D ARG 3.0 14.5 + - - +
170D MET* 3.5 14.3 + - - +
171D MET 3.2 0.2 - - - -
172D SER* 1.3 74.6 - - - +
174D ALA* 1.3 66.6 + - - +
176D ARG* 3.2 30.4 + - - +
177D LYS* 3.3 33.8 + - + +
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Residues in contact with ALA 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126D LEU* 3.8 33.4 - - + -
170D MET 2.9 13.8 + - - +
171D MET* 3.2 9.8 + - - +
173D GLN* 1.3 76.6 - - - +
175D MET* 1.3 63.7 + - + +
177D LYS* 3.1 7.8 + - - +
178D LEU* 2.8 43.3 + - + +
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Residues in contact with MET 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61D ILE* 4.1 17.7 - - - -
171D MET* 3.0 30.9 + - - +
172D SER 3.9 3.1 - - - +
173D GLN 3.3 0.2 - - - -
174D ALA* 1.3 85.4 - - + +
176D ARG* 1.3 65.0 + - - +
178D LEU* 4.4 6.1 - - + -
179D ALA* 3.0 29.5 + - - +
191D PHE* 3.8 28.9 - - + -
214D ALA* 3.8 14.6 - - + -
215D LEU* 3.9 26.0 - - + +
218D TYR* 3.4 40.2 - - + -
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Residues in contact with ARG 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D ARG* 4.5 5.5 + - - +
172D SER* 3.4 17.6 + - - +
173D GLN* 3.2 42.5 + - + +
175D MET* 1.3 79.1 - - - +
177D LYS* 1.3 63.5 + - + +
179D ALA* 4.1 7.3 + - - +
180D GLY 4.4 3.3 + - - -
218D TYR* 3.6 21.5 + - - +
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Residues in contact with LYS 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D GLU* 3.5 19.5 + - - +
130D ASP* 3.4 28.1 + - - +
134D ARG* 5.0 1.2 - - - +
173D GLN* 3.3 26.9 + - + +
174D ALA* 3.1 8.8 + - - +
176D ARG* 1.3 82.5 - - + +
178D LEU* 1.3 63.8 + - + +
180D GLY* 4.1 1.2 + - - -
181D ASN* 3.7 22.9 + - - +
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Residues in contact with LEU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61D ILE* 4.9 2.0 - - + -
126D LEU* 4.5 9.9 - - + +
129D CYS* 4.1 11.4 - - + +
130D ASP* 3.6 42.6 - - + +
133D ALA* 4.8 4.9 - - + -
174D ALA* 2.8 39.4 + - + +
175D MET* 4.1 6.5 - - + +
177D LYS* 1.3 74.1 - - + +
179D ALA* 1.3 67.3 + - - +
181D ASN* 2.9 4.7 + - - +
182D LEU* 2.8 37.9 + - + +
189D LEU* 3.8 25.1 - - + -
191D PHE* 4.3 11.9 - - + -
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Residues in contact with ALA 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLY 4.6 1.9 - - - +
61D ILE* 4.4 13.1 - - + +
175D MET 3.0 17.7 + - - +
176D ARG 4.4 3.6 - - - +
178D LEU* 1.3 76.2 - - - +
180D GLY* 1.3 61.9 + - - +
182D LEU* 3.5 4.3 + - - +
183D LYS* 3.2 22.5 + - - +
218D TYR* 4.0 23.6 - - + -
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Residues in contact with GLY 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ARG 4.4 4.6 + - - -
177D LYS 4.1 3.5 + - - -
178D LEU 3.2 1.0 - - - -
179D ALA* 1.3 78.3 - - - +
181D ASN* 1.3 64.9 + - - +
183D LYS* 3.4 5.2 + - - +
184D GLN* 3.1 37.0 + - - +
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Residues in contact with ASN 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D ASP* 2.8 26.1 - - - +
133D ALA* 4.0 19.4 - - + +
134D ARG* 3.2 31.3 + - + +
177D LYS* 3.7 10.0 + - - +
178D LEU 2.9 8.2 + - - +
180D GLY* 1.3 76.3 - - - +
182D LEU* 1.3 61.9 + - - +
184D GLN* 3.7 7.0 + - - +
185D SER* 3.0 30.0 + - - -
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Residues in contact with LEU 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D GLY* 3.3 10.2 - - - +
60D ARG 4.9 0.7 - - - +
61D ILE* 3.7 24.0 - - + -
133D ALA* 4.0 15.9 - - + -
141D ILE* 4.8 2.9 - - + -
178D LEU* 2.8 29.7 + - + +
179D ALA* 3.8 4.7 - - - +
181D ASN* 1.3 75.9 - - - +
183D LYS* 1.3 60.3 + - - +
185D SER 3.5 0.3 + - - -
186D ASN 3.0 7.8 + - - -
187D THR* 2.9 67.6 + - + +
189D LEU* 3.7 39.0 - - + -
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Residues in contact with LYS 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D MET 4.6 5.4 - - - -
59D GLY* 3.5 19.2 + - - +
60D ARG* 3.5 35.4 - - - +
179D ALA 3.2 14.8 + - - +
180D GLY* 3.4 5.4 + - - +
182D LEU* 1.3 80.7 - - - +
184D GLN* 1.3 62.4 + - + +
186D ASN* 3.1 21.9 + - - +
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Residues in contact with GLN 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180D GLY* 3.1 26.5 + - - +
181D ASN* 4.4 7.1 + - - +
182D LEU 3.4 0.2 - - - -
183D LYS* 1.3 79.3 - - + +
185D SER* 1.3 58.9 + - - +
186D ASN* 5.4 0.4 - - - +
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Residues in contact with SER 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133D ALA 2.5 30.7 + - - -
134D ARG* 4.2 5.2 + - - -
136D GLY* 4.0 22.7 + - - +
138D VAL 4.9 2.6 - - - +
139D ASP* 5.6 1.4 - - - +
181D ASN 3.0 15.1 + - - -
182D LEU 4.1 0.2 - - - -
183D LYS 3.1 0.4 - - - -
184D GLN* 1.3 77.8 - - - +
186D ASN* 1.3 70.4 + - - +
187D THR* 3.1 15.9 + - - -
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Residues in contact with ASN 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38D GLU* 3.2 28.8 + - - +
58D MET* 3.4 51.0 - - - +
59D GLY* 3.6 6.6 + - - -
138D VAL 5.4 0.2 - - - -
139D ASP* 4.1 3.6 - - - +
182D LEU 3.0 7.0 + - - -
183D LYS* 3.1 14.6 + - - +
184D GLN 3.4 0.2 - - - -
185D SER* 1.3 81.3 - - - +
187D THR* 1.3 58.1 + - - +
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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
------------------------------------------------------------
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