Contacts of the helix formed by residues 167 - 179 (chain B) in PDB entry 2P2Q
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 SER 167 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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138B TYR* 4.7 0.2 - - - -
165B GLY 3.9 0.2 + - - -
166B PHE* 1.3 75.1 - - - +
168B PRO* 1.3 72.6 - - - +
169B GLU 3.4 0.5 + - - -
170B ALA 2.9 14.4 + - - -
171B VAL* 2.9 24.8 + - - +
201B ASN* 5.1 0.9 - - - +
584B GLU 3.8 7.9 - - - -
585B LYS* 2.9 30.5 + - - -
586B GLU 3.3 6.1 + - - -
587B ILE 2.8 25.1 + - - -
588B GLY* 4.2 1.3 - - - -
589B PRO* 5.9 0.4 - - - -
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Residues in contact with PRO 168 (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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167B SER* 1.3 87.4 - - - +
169B GLU* 1.3 57.0 + - - +
171B VAL* 3.3 6.4 + - + -
172B ALA* 2.9 31.9 + - - +
201B ASN* 3.4 54.0 - - + +
204B ASP* 3.8 16.4 - - + +
205B ALA* 3.4 15.6 - - - +
585B LYS* 4.7 4.9 - - + +
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Residues in contact with GLU 169 (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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167B SER* 3.2 4.4 + - - +
168B PRO* 1.3 81.0 - - - +
170B ALA* 1.3 60.7 + - - +
172B ALA* 3.5 6.0 - - - +
173B GLY* 3.3 17.8 + - - -
208B ASN* 4.5 17.4 + - - -
585B LYS* 3.8 11.4 + - + +
586B GLU* 3.4 44.5 - - - +
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Residues in contact with ALA 170 (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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166B PHE* 3.6 15.3 - - + -
167B SER* 2.9 13.2 + - - +
169B GLU* 1.3 73.4 - - - +
171B VAL* 1.3 64.5 + - - +
173B GLY* 3.5 2.0 + - - -
174B ARG* 2.8 49.2 + - - +
586B GLU 3.9 2.2 + - - -
587B ILE* 3.5 29.6 - - + +
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Residues in contact with VAL 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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138B TYR* 3.5 44.0 - - + +
162B ILE* 4.0 21.4 - - + +
166B PHE* 4.3 2.0 - - + +
167B SER 2.9 18.8 + - - +
168B PRO* 3.6 7.0 - - + +
170B ALA* 1.3 75.2 - - - +
172B ALA* 1.3 63.7 + - - +
174B ARG* 3.3 4.2 + - - +
175B ILE* 3.0 43.0 + - + +
183B VAL* 5.9 0.9 - - + -
201B ASN* 5.5 0.7 - - + -
202B VAL* 5.0 14.1 - - + -
205B ALA* 3.8 13.5 - - + -
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Residues in contact with ALA 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B PRO 2.9 17.7 + - - +
169B GLU* 3.5 9.6 - - - +
171B VAL* 1.3 75.3 - - - +
173B GLY* 1.3 52.8 + - - +
175B ILE* 3.4 4.5 + - - +
176B ILE* 2.8 41.1 + - - +
205B ALA* 3.9 20.6 - - - +
208B ASN* 3.8 26.9 - - + +
211B VAL* 4.4 7.6 - - + -
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Residues in contact with GLY 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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169B GLU 3.3 11.7 + - - -
170B ALA* 3.5 3.7 + - - -
171B VAL 3.4 0.4 - - - -
172B ALA* 1.3 78.2 - - - +
174B ARG* 1.3 57.3 + - - +
176B ILE* 3.6 9.7 + - - +
177B ASP* 2.9 29.8 + - - +
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Residues in contact with ARG 174 (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 SER* 5.5 0.9 - - - +
161B VAL 5.9 0.4 - - - -
162B ILE* 3.9 38.6 - - + +
166B PHE* 3.3 36.8 - - - -
170B ALA* 2.8 48.3 + - - +
171B VAL 3.3 7.4 + - - +
173B GLY* 1.3 73.8 - - - +
175B ILE* 1.3 59.8 + - - +
177B ASP* 3.2 4.1 + - - +
178B SER* 2.9 34.1 + - - -
180B SER* 5.2 0.2 - - - -
263B TYR* 3.5 48.6 + - + +
271B PRO* 4.0 29.3 - - - +
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Residues in contact with ILE 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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136B ALA* 4.1 21.1 - - + -
162B ILE* 4.4 3.6 - - + +
171B VAL* 3.0 40.7 + - + +
172B ALA* 3.7 5.4 - - - +
174B ARG* 1.3 74.4 - - - +
176B ILE* 1.3 57.8 + - - +
178B SER* 3.7 6.1 - - - -
179B SER* 2.9 26.7 + - - -
180B SER* 3.3 7.5 + - - -
183B VAL* 3.5 26.2 - - + -
202B VAL* 5.8 0.9 - - + -
205B ALA* 5.0 2.7 - - + -
206B LEU* 4.6 9.6 - - + -
211B VAL* 3.8 18.8 - - + -
213B SER* 3.9 7.5 + - - +
214B VAL* 3.5 25.8 - - + -
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Residues in contact with ILE 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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172B ALA 2.8 29.2 + - - +
173B GLY* 3.9 7.2 - - - +
175B ILE* 1.3 74.0 - - - +
177B ASP* 1.3 63.7 + - - +
179B SER* 3.5 11.8 + - - -
208B ASN* 4.1 11.4 - - - +
210B ASN* 3.5 44.2 - - + +
211B VAL* 3.5 24.7 - - + +
213B SER* 5.5 0.7 - - - -
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Residues in contact with ASP 177 (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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173B GLY 2.9 19.6 + - - +
174B ARG 3.2 2.4 + - - +
176B ILE* 1.3 79.2 - - - +
178B SER* 1.3 59.7 + - - +
179B SER* 3.7 1.6 + - - -
263B TYR* 2.4 40.8 + - + +
272B LYS* 5.6 1.1 - - - +
273B GLY 4.8 2.1 + - - -
478B PHE* 3.6 24.5 - - - +
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Residues in contact with SER 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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134B VAL* 3.6 34.8 - - - +
160B SER* 4.8 3.7 + - - -
174B ARG 2.9 17.4 + - - -
175B ILE* 3.5 0.9 + - - -
177B ASP* 1.3 75.6 - - - +
179B SER* 1.3 70.0 + - - +
180B SER* 2.8 22.7 + - - -
261B ILE* 5.5 2.5 - - - -
263B TYR* 3.5 17.9 - - - -
478B PHE* 3.7 17.3 - - - -
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Residues in contact with SER 179 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134B VAL* 4.6 3.0 + - - +
175B ILE 2.9 10.8 + - - -
176B ILE* 3.5 8.5 + - - +
177B ASP 3.4 3.4 + - - -
178B SER* 1.3 79.8 - - - +
180B SER* 1.3 64.2 + - - +
181B ARG* 3.2 10.0 + - - +
213B SER* 3.3 21.7 - - - -
478B PHE* 6.2 0.2 - - - -
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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