Contacts of the helix formed by residues 172 - 188 (chain B) in PDB entry 2NP5
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 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B PRO 3.2 6.2 - - - +
169B ALA 3.2 17.0 - - - +
170B LEU 3.4 6.3 - - - +
171B TYR* 1.4 91.0 - - - +
173B PRO* 1.4 78.2 - - + +
174B GLU* 4.6 4.0 - - + +
175B TYR* 3.0 20.0 + - + +
176B LEU* 3.0 19.1 + - - +
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Residues in contact with PRO 173 (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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94B PRO 4.4 4.7 - - - +
95B LEU* 3.4 47.3 - - + +
96B ASP* 5.5 0.2 - - - -
171B TYR 4.7 0.2 - - - +
172B PRO* 1.4 86.3 - - + +
174B GLU* 1.3 57.2 + - - +
176B LEU* 3.3 5.4 + - + +
177B GLU* 2.9 38.9 + - - +
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Residues in contact with GLU 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PRO* 3.3 4.1 - - + +
173B PRO* 1.3 79.4 - - - +
175B TYR* 1.3 56.1 + - - +
177B GLU* 3.4 19.5 + - - +
178B HIS* 3.0 28.4 + - - +
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Residues in contact with TYR 175 (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 0.7 - - + -
170B LEU 4.1 10.3 - - - -
171B TYR* 4.0 35.0 - + - -
172B PRO* 3.0 29.8 + - + +
174B GLU* 1.3 75.5 - - - +
176B LEU* 1.3 62.3 + - + +
178B HIS* 3.3 14.2 + + + +
179B ALA* 2.9 39.6 + - + +
131D ARG* 3.6 15.2 + - - -
147D GLU 4.4 1.4 + - - -
148D THR* 4.1 22.2 + - + +
151D ALA* 3.2 26.8 - - + +
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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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93B LEU* 4.2 11.9 - - + +
94B PRO* 3.8 40.4 - - + +
95B LEU* 3.7 16.8 - - + -
160B LEU* 3.9 46.2 - - + +
164B ALA* 4.2 1.6 - - + -
171B TYR* 3.6 32.3 - - + +
172B PRO 3.0 13.3 + - - +
173B PRO* 3.6 7.6 - - + +
175B TYR* 1.3 74.8 - - - +
177B GLU* 1.3 57.9 + - - +
179B ALA* 3.4 4.4 + - - +
180B LEU* 2.9 30.0 + - - +
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Residues in contact with GLU 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 3.5 34.1 - - + -
90B SER* 5.0 0.2 - - - +
93B LEU* 5.4 0.9 - - - -
95B LEU* 4.0 29.3 - - + +
173B PRO* 2.9 23.2 + - - +
174B GLU* 3.8 24.2 - - + +
175B TYR 3.3 0.4 - - - -
176B LEU* 1.3 74.0 - - - +
178B HIS* 1.3 58.8 + - - +
180B LEU* 3.3 2.7 + - - -
181B ASP* 2.9 30.0 + - - +
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Residues in contact with HIS 178 (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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174B GLU 3.0 17.2 + - - +
175B TYR* 3.6 17.0 - + + +
177B GLU* 1.3 76.3 - - - +
179B ALA* 1.3 62.4 + - - +
181B ASP* 3.2 10.6 + - - +
182B ILE* 3.0 46.0 + - + +
145D GLU* 3.4 19.3 + - - -
148D THR* 3.1 32.4 + - + -
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Residues in contact with ALA 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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160B LEU* 3.9 26.0 - - + -
175B TYR* 2.9 29.7 + - + +
176B LEU* 3.8 4.0 - - - +
178B HIS* 1.3 72.9 - - - +
180B LEU* 1.3 62.9 + - - +
182B ILE 3.3 1.7 + - - -
183B GLN* 2.9 20.8 + - - +
148D THR* 3.9 18.8 - - + -
151D ALA* 5.9 1.1 - - + -
152D LEU* 3.6 21.1 - - + +
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Residues in contact with LEU 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 3.8 30.1 - - + +
89B MSE 3.6 34.1 - - + -
90B SER* 3.8 12.6 - - - +
93B LEU* 3.9 15.3 - - + -
153B LEU* 4.0 8.7 - - + -
156B THR* 5.5 2.0 - - + -
157B VAL* 4.0 15.5 - - + -
160B LEU* 4.5 5.8 - - + +
176B LEU 2.9 18.0 + - - +
177B GLU* 3.6 4.9 - - - +
178B HIS 3.3 0.2 - - - -
179B ALA* 1.3 73.9 - - - +
181B ASP* 1.3 58.4 + - - +
183B GLN* 3.2 5.9 + - + +
184B ILE* 2.9 52.2 + - + +
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Residues in contact with ASP 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B PHE* 4.3 16.6 - - + -
177B GLU 2.9 17.7 + - - +
178B HIS* 3.5 10.2 + - - +
180B LEU* 1.3 75.7 - - - +
182B ILE* 1.3 63.6 + - - +
184B ILE* 3.4 9.0 + - - +
185B GLY* 3.0 24.8 + - - -
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Residues in contact with ILE 182 (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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178B HIS* 3.0 40.3 + - + +
179B ALA 3.3 7.4 + - - +
181B ASP* 1.3 80.8 - - - +
183B GLN* 1.3 65.1 + - - +
185B GLY* 3.3 3.0 + - - +
186B MSE 3.1 25.7 + - + +
145D GLU* 3.8 33.0 - - + +
148D THR* 3.9 13.0 - - + -
149D ARG* 4.2 21.1 - - + +
152D LEU* 3.7 15.0 - - + -
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Residues in contact with GLN 183 (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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152B LEU 4.5 5.9 + - - -
153B LEU* 3.8 20.9 - - + -
156B THR* 3.3 28.6 + - + +
179B ALA 2.9 13.1 + - - +
180B LEU* 3.6 8.7 - - - +
182B ILE* 1.3 73.9 - - - +
184B ILE* 1.3 58.3 + - - +
186B MSE 3.1 10.3 + - - +
187B ILE* 2.8 52.7 + - + +
152D LEU* 3.5 22.5 - - + +
183D GLN* 3.0 41.8 + - - +
186D MSE 4.2 2.6 - - - +
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Residues in contact with ILE 184 (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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82B ALA* 4.2 18.2 - - + +
85B LEU* 3.8 15.7 - - + +
86B PHE* 3.5 42.6 - - + +
153B LEU* 4.1 13.5 - - + -
180B LEU* 2.9 39.9 + - + +
181B ASP* 3.8 7.9 - - - +
183B GLN* 1.3 75.2 - - - +
185B GLY* 1.3 58.8 + - - +
187B ILE* 3.2 7.2 + - - +
188B LEU* 2.9 52.5 + - + +
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Residues in contact with GLY 185 (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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181B ASP 3.0 15.3 + - - -
182B ILE* 3.3 4.0 + - - -
183B GLN 3.2 0.2 - - - -
184B ILE* 1.3 78.5 - - - +
186B MSE 1.3 58.9 + - - +
188B LEU* 3.5 6.5 + - - +
189B GLN* 3.2 30.5 + - - +
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Residues in contact with MSE 186 (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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149B ARG* 3.8 2.4 + - - -
182B ILE* 3.1 18.1 + - + +
183B GLN* 3.1 28.7 + - - +
185B GLY* 1.3 71.9 - - - +
187B ILE* 1.3 67.3 + - - +
189B GLN* 3.2 27.0 + - + +
149D ARG* 3.8 33.9 - - + +
152D LEU* 3.6 20.4 - - + -
183D GLN* 4.3 2.5 - - - +
186D MSE 3.6 53.4 - - + +
187D ILE* 3.9 16.8 - - + -
189D GLN* 6.4 0.4 - - + -
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Residues in contact with ILE 187 (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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85B LEU* 5.2 1.8 - - + -
138B LEU* 3.8 37.9 - - + -
143B THR* 3.3 10.4 - - - +
149B ARG* 2.7 51.9 + - + +
152B LEU* 4.5 2.0 - - + -
153B LEU* 4.5 16.2 - - + +
183B GLN* 2.8 38.9 + - + +
184B ILE* 3.6 9.4 - - - +
186B MSE 1.3 75.1 - - - +
188B LEU* 1.3 58.5 + - + +
189B GLN 3.3 0.2 - - - -
186D MSE 3.5 32.3 - - + -
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Residues in contact with LEU 188 (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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81B PRO* 5.1 0.4 - - + -
82B ALA* 3.6 35.9 - - + +
85B LEU* 4.1 8.1 - - + -
138B LEU* 3.9 20.6 - - + -
141B ILE* 3.5 31.2 - - + -
143B THR* 4.5 0.2 - - - +
184B ILE* 2.9 28.2 + - + +
185B GLY* 3.5 7.4 + - - +
186B MSE 3.2 0.4 - - - -
187B ILE* 1.3 76.6 - - + +
189B GLN* 1.3 59.5 + - - +
190B GLY 3.3 0.7 + - - -
191B ALA* 3.0 28.5 + - + +
193B VAL* 3.9 27.1 - - + +
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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