Contacts of the helix formed by residues 177 - 188 (chain B) in PDB entry 2P7I
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 ALA 177 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142B ASN* 3.8 5.2 - - - +
143B ALA* 4.1 11.4 - - + -
144B ASN* 3.8 25.6 - - - +
161B SER* 6.0 2.4 - - - -
175B THR 3.8 0.6 + - - -
176B TYR* 1.3 74.2 - - - +
178B LEU* 1.3 67.5 + - - +
179B ASP* 3.1 18.9 + - - +
180B THR* 3.1 7.2 + - + +
181B LEU* 2.9 23.0 + - - +
239B ILE* 3.2 11.9 - - - -
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Residues in contact with LEU 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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231A GLN* 3.6 47.0 + - + +
142B ASN* 4.6 1.2 + - - -
177B ALA* 1.3 74.8 - - - +
179B ASP* 1.3 63.1 + - - +
181B LEU* 4.6 1.8 - - - -
182B GLU* 3.1 26.9 + - - +
195B ARG* 4.3 6.3 - - + -
196B SER 4.3 9.2 - - - +
233B PRO* 4.1 11.2 - - + -
234B ASP* 4.1 33.6 + - + +
239B ILE* 3.3 34.3 - - + +
240B PHE 4.9 0.2 - - - +
241B LEU* 4.0 25.7 - - + +
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Residues in contact with ASP 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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231A GLN* 5.3 1.5 + - - +
144B ASN* 5.5 0.3 + - - -
177B ALA* 3.4 19.4 - - - +
178B LEU* 1.3 80.6 - - - +
180B THR* 1.3 74.8 + - - +
182B GLU* 4.2 1.8 - - - +
183B ARG* 3.1 26.7 + - - +
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Residues in contact with THR 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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161B SER* 6.3 2.5 - - - -
174B CYS* 5.1 3.3 - - - -
175B THR 4.6 1.4 + - - -
176B TYR* 3.5 13.7 - - - -
177B ALA* 3.1 25.3 + - + +
179B ASP* 1.3 90.3 + - - +
181B LEU* 1.3 64.1 + - - +
183B ARG* 3.4 36.5 + - - +
184B ASP* 3.1 27.7 + - - +
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Residues in contact with LEU 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B LEU* 3.7 29.6 - - + -
138B LEU* 3.8 21.1 - - + +
140B CYS* 3.9 20.4 - - + -
176B TYR* 3.4 14.9 - - + -
177B ALA 2.9 18.2 + - - +
178B LEU* 4.2 2.7 - - - +
180B THR* 1.3 75.0 + - - +
182B GLU* 1.3 64.3 + - - +
184B ASP* 3.3 2.8 + - - +
185B ALA* 3.1 22.0 + - - +
239B ILE* 3.9 37.2 - - + +
241B LEU* 3.9 24.2 - - + -
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Residues in contact with GLU 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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227A GLN* 3.1 14.1 - - - +
231A GLN* 4.1 8.2 + - - +
178B LEU 3.1 19.3 + - - +
179B ASP* 4.3 2.7 - - - +
181B LEU* 1.3 75.4 - - - +
183B ARG* 1.3 57.0 + - - +
185B ALA* 3.3 0.9 + - - +
186B SER* 2.8 33.6 + - - -
192B VAL* 3.9 18.4 - - + +
195B ARG* 2.8 49.9 + - - +
241B LEU* 3.6 16.2 - - + +
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Residues in contact with ARG 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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174B CYS* 5.5 4.9 - - - -
176B TYR* 4.8 2.0 - - - -
179B ASP 3.1 16.9 + - - +
180B THR* 3.4 38.3 + - - +
181B LEU 3.2 0.4 - - - -
182B GLU* 1.3 77.2 - - - +
184B ASP* 1.3 87.0 + - - +
186B SER* 3.3 5.2 + - - -
187B ARG* 2.8 72.2 + - + +
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Residues in contact with ASP 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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112B LEU* 5.0 0.4 - - + -
118B PRO* 3.6 10.9 - - - +
119B VAL* 3.9 26.7 - - + +
122B LEU* 3.8 15.1 - - + +
174B CYS* 5.6 0.2 - - - -
176B TYR* 2.7 32.6 + - + +
180B THR 3.1 14.6 + - - +
181B LEU 3.3 3.3 + - - +
183B ARG* 1.3 111.4 + - - +
185B ALA* 1.3 62.6 + - - +
187B ARG* 3.3 6.4 + - - +
188B ALA* 3.0 24.4 + - - +
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Residues in contact with ALA 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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122B LEU* 3.8 14.5 - - + +
138B LEU* 4.5 3.4 - - + -
181B LEU 3.1 16.5 + - - +
182B GLU 3.7 4.3 - - - +
184B ASP* 1.3 76.0 - - - +
186B SER* 1.3 63.1 + - - +
188B ALA* 3.2 6.9 + - - +
190B LEU* 3.2 41.1 + - + +
192B VAL* 3.9 20.9 - - + -
241B LEU* 4.2 7.6 - - + -
243B CYS* 4.4 4.0 - - - -
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Residues in contact with SER 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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182B GLU* 2.8 23.6 + - - -
183B ARG* 3.5 6.1 - - - -
185B ALA* 1.3 76.4 - - - +
187B ARG* 1.3 64.6 + - - +
189B GLY* 3.1 14.9 + - - -
190B LEU 4.2 10.2 - - - +
192B VAL* 4.9 2.8 - - - +
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Residues in contact with ARG 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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119B VAL* 3.8 24.2 - - + +
123B LYS* 6.0 0.7 - - - +
183B ARG* 2.8 60.3 + - + +
184B ASP* 3.7 11.7 + - - +
186B SER* 1.3 75.0 - - - +
188B ALA* 1.3 56.4 + - - +
189B GLY 3.2 1.1 + - - -
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Residues in contact with ALA 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B VAL* 3.6 13.9 - - + +
122B LEU* 3.3 35.7 - - + +
123B LYS* 3.5 35.0 - - - +
126B ASN* 4.0 7.6 + - - +
127B ASP* 4.8 0.7 - - - +
184B ASP 3.0 12.9 + - - +
185B ALA 3.6 6.1 - - - +
186B SER 3.1 0.6 - - - -
187B ARG* 1.3 75.8 - - - +
189B GLY* 1.3 58.8 + - - +
190B LEU* 3.7 2.5 + - + -
248B ASN* 6.0 0.9 - - - +
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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