Contacts of the helix formed by residues 166 - 181 (chain B) in PDB entry 2NYM
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 PRO 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164B GLU 3.1 1.5 - - - +
165B ASP* 1.3 95.0 - - - +
167B ARG* 1.3 54.3 - - - +
168B GLU 3.2 0.2 - - - -
169B ARG* 2.3 57.8 + - + +
170B ASP* 2.4 34.8 + - - +
213B GLU* 3.8 16.2 - - - +
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Residues in contact with ARG 167 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B LEU* 3.5 24.7 - - - +
118B GLU 5.0 0.4 + - - -
121B TRP* 3.0 58.2 - - + +
164B GLU* 2.6 40.3 + - - +
165B ASP* 2.1 20.8 + - - -
166B PRO* 1.3 76.8 - - - +
168B GLU* 1.3 57.1 + - - +
170B ASP* 3.5 5.8 + - - +
171B PHE* 3.1 28.5 + - - -
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Residues in contact with GLU 168 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B MSE 3.3 2.6 - - - +
95B ARG* 2.4 33.7 + - - -
97B LEU* 5.7 3.9 - - - +
118B GLU* 3.3 18.4 - - - +
121B TRP* 3.9 16.0 - - + -
124B LEU* 5.0 4.3 - - - -
128B TYR* 2.9 26.2 + - + +
160B LEU* 4.4 10.2 - - - +
163B SER 5.4 1.9 + - - +
164B GLU* 3.2 32.1 + - + +
165B ASP 3.2 2.4 + - - -
166B PRO 2.7 3.4 + - - -
167B ARG* 1.3 79.2 - - - +
169B ARG* 1.3 67.1 + - + +
171B PHE* 3.4 4.5 + - - +
172B LEU* 3.1 28.9 + - + +
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Residues in contact with ARG 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
160B LEU 5.2 0.2 - - - +
161B PHE* 4.3 17.0 - - + +
162B ASP 4.4 0.4 - - - +
163B SER* 3.8 35.5 + - - +
164B GLU 3.7 7.2 + - - +
165B ASP* 4.2 4.2 + - - +
166B PRO* 2.3 42.9 + - + +
168B GLU* 1.3 67.2 - - + +
170B ASP* 1.3 56.5 + - - +
172B LEU* 2.4 41.0 + - + -
173B LYS* 2.9 10.8 + - - -
209B ASN* 3.6 23.4 + - - +
210B GLY* 4.1 14.1 - - - +
212B ALA* 5.9 0.4 - - - +
213B GLU* 3.0 51.0 + - + -
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Residues in contact with ASP 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B PRO* 2.4 53.8 + - - +
167B ARG* 3.6 7.2 - - - +
169B ARG* 1.3 69.0 - - - +
171B PHE* 1.3 67.1 + - + +
173B LYS* 3.3 21.0 + - - +
174B THR* 3.2 23.2 + - - -
213B GLU* 4.6 5.4 - - - +
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B TRP* 4.0 20.6 - + - -
125B GLN* 4.1 17.5 - - + -
128B TYR* 3.2 41.5 - + + -
129B GLU* 3.9 23.3 - - + -
132B LEU* 3.8 23.5 - - + +
167B ARG* 3.1 23.8 + - - -
168B GLU 3.6 8.1 - - - +
169B ARG 2.6 4.6 + - - -
170B ASP* 1.3 78.7 - - + +
172B LEU* 1.3 54.6 + - - +
174B THR* 3.0 7.6 + - - -
175B THR* 2.7 38.5 + - - -
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Residues in contact with LEU 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B TYR* 3.2 28.0 - - + +
157B LEU* 3.4 32.3 - - + +
160B LEU* 3.5 40.8 - - + +
161B PHE* 3.9 22.2 - - + +
168B GLU* 3.1 23.8 - - + +
169B ARG* 2.4 28.4 + - - +
171B PHE* 1.3 68.1 - - - +
173B LYS* 1.3 63.7 + - - +
175B THR* 3.1 5.5 + - - -
176B LEU* 2.8 28.4 + - - +
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Residues in contact with LYS 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B PHE* 4.3 4.1 - - - -
169B ARG 2.9 6.1 + - - +
170B ASP* 3.3 26.9 + - - +
172B LEU* 1.3 78.4 - - - +
174B THR* 1.3 67.9 + - - +
177B HIS* 3.1 24.0 + - + +
213B GLU* 4.4 20.6 - - + +
216B GLU* 2.9 43.4 + - - +
217B ILE* 3.6 30.1 - - + +
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Residues in contact with THR 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.5 32.5 - - + -
170B ASP 3.2 8.9 + - - -
171B PHE* 3.0 9.4 + - - -
173B LYS* 1.3 85.3 - - - +
175B THR* 1.3 68.0 + - - +
177B HIS* 2.9 18.3 + - + +
178B ARG* 3.0 29.4 + - + +
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Residues in contact with THR 175 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B PHE* 5.1 1.6 - - + -
128B TYR* 4.6 12.3 + - - -
131B PHE* 3.7 36.6 - - + -
132B LEU* 4.2 19.0 - - + +
157B LEU* 4.2 14.1 - - + -
171B PHE 2.7 24.0 + - - -
172B LEU* 3.7 7.2 - - - -
174B THR* 1.3 77.0 - - - +
176B LEU* 1.3 63.9 + - - +
178B ARG* 3.3 3.3 + - - +
179B ILE* 3.0 38.0 + - + +
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Residues in contact with LEU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B VAL* 4.7 8.7 - - + -
157B LEU* 4.4 15.7 - - + +
158B LEU* 3.5 20.9 - - + -
161B PHE* 3.2 32.3 - - + -
172B LEU 2.8 18.2 + - - +
175B THR* 1.3 74.5 - - - +
177B HIS* 1.3 64.3 + - - +
179B ILE* 3.9 8.7 - - + +
180B TYR* 3.0 20.7 + - + +
190B ILE* 3.5 42.8 - - + -
194B ILE* 4.5 3.6 - - + -
214B LEU* 4.4 4.5 - - + -
217B ILE* 3.5 17.3 - - + -
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Residues in contact with HIS 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B LYS* 3.1 21.0 + - + +
174B THR* 2.9 15.8 + - + +
176B LEU* 1.3 77.1 - - - +
178B ARG* 1.3 66.7 + - + +
180B TYR* 3.0 11.4 + + + +
181B GLY* 3.0 21.6 + - - -
217B ILE* 4.6 21.1 - - + -
220B SER* 3.8 33.7 - - - -
221B ILE* 5.9 1.3 - - + -
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Residues in contact with ARG 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B LEU* 3.6 26.4 - - + +
135B LEU 5.8 2.2 - - - +
136B GLU* 2.7 47.2 + - + +
174B THR* 3.0 19.6 + - + +
175B THR* 4.0 3.8 - - - +
177B HIS* 1.3 85.4 - - + +
179B ILE* 1.3 61.3 + - + +
181B GLY* 3.4 4.5 + - - +
182B LYS* 3.3 40.2 - - + +
183B PHE* 4.7 0.2 - - - -
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Residues in contact with ILE 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B PHE* 4.5 6.3 - - + -
149B ILE* 4.4 8.1 - - + -
153B PHE* 4.0 22.0 - - + -
154B VAL* 5.2 6.5 - - + -
157B LEU* 4.0 18.4 - - + -
175B THR* 3.0 41.1 + - + +
176B LEU* 3.9 7.9 - - + +
178B ARG* 1.3 78.3 - - + +
180B TYR* 1.3 63.1 + - - +
183B PHE* 2.9 51.3 + - + +
186B LEU* 4.1 20.4 - - + +
190B ILE* 5.2 3.8 - - + -
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Residues in contact with TYR 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176B LEU* 3.0 18.9 + - + +
177B HIS* 3.0 9.8 + + - +
179B ILE* 1.3 78.2 - - - +
181B GLY* 1.3 60.5 + - - +
182B LYS 3.3 2.9 + - - -
183B PHE 4.3 2.8 + - - -
186B LEU* 5.9 0.7 - - - -
187B ARG* 3.0 82.7 + - + +
190B ILE* 3.7 30.5 - - + -
191B ARG* 3.1 31.5 + - + -
217B ILE* 5.5 2.0 - - + -
221B ILE* 3.4 48.3 - - + +
225B PHE* 5.1 1.6 - - - -
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Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177B HIS* 3.0 15.3 + - - -
178B ARG* 3.4 3.5 + - - -
179B ILE 3.2 0.8 - - - -
180B TYR* 1.3 80.0 - - - +
182B LYS* 1.3 69.8 + - - +
184B LEU* 5.6 0.7 - - - -
187B ARG* 4.0 18.1 + - - -
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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