Contacts of the helix formed by residues 165 - 177 (chain B) in PDB entry 2FQ6
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 ASP 165 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134B PRO 4.6 2.4 + - - -
135B LEU* 5.8 1.3 - - - +
137B GLY* 4.6 10.7 - - - -
163B VAL 3.9 0.2 + - - -
164B HIS* 1.3 71.8 - - - +
166B VAL* 1.3 59.9 + - - +
167B PRO* 3.6 1.2 - - - +
168B ALA* 3.3 30.0 + - + +
169B ILE* 3.0 27.5 + - - +
299B PHE* 3.4 45.0 - - + -
302B ARG* 2.8 25.7 + - - +
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Residues in contact with VAL 166 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 4.0 15.7 - - + -
155B SER* 4.8 3.1 - - - +
164B HIS* 3.2 25.0 + - + +
165B ASP* 1.3 72.0 - - - +
167B PRO* 1.4 65.2 - - + +
169B ILE* 3.1 5.8 + - - -
170B VAL* 2.8 46.5 + - + +
184B ILE* 4.6 6.5 - - + -
194B PHE* 3.8 25.6 - - + -
199B PHE* 4.0 16.6 - - + -
201B ILE* 3.8 22.4 - - + -
303B ASP* 4.6 1.3 + - - +
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Residues in contact with PRO 167 (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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165B ASP* 3.6 4.0 - - - +
166B VAL* 1.4 90.2 - - + +
168B ALA* 1.3 56.0 + - - +
170B VAL* 4.1 4.1 - - + +
171B ALA* 3.1 30.8 + - - +
199B PHE* 3.8 26.9 - - + +
302B ARG* 3.5 21.3 - - - +
303B ASP* 3.4 18.2 - - - +
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Residues in contact with ALA 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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137B GLY* 4.2 0.7 - - - -
138B ALA* 3.9 30.1 - - + +
165B ASP* 3.3 30.9 + - + +
166B VAL 3.2 0.8 - - - -
167B PRO* 1.3 76.4 - - - +
169B ILE* 1.3 65.5 + - - +
171B ALA* 4.0 4.4 - - - +
172B ALA* 3.1 24.6 + - - +
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Residues in contact with ILE 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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132B PHE* 4.3 14.8 - - + -
134B PRO 4.4 6.3 - - - +
136B ILE* 4.7 1.6 - - + -
137B GLY* 3.7 28.7 - - - +
140B ILE* 3.7 23.1 - - + +
151B VAL* 4.8 1.1 - - + -
153B LEU* 4.0 22.7 - - + -
164B HIS* 4.0 33.9 - - + +
165B ASP 3.0 21.1 + - - +
166B VAL* 3.1 5.1 + - - +
168B ALA* 1.3 76.4 - - - +
170B VAL* 1.3 64.1 + - + +
172B ALA* 3.1 3.3 + - - +
173B VAL* 3.0 30.0 + - + +
182B ILE* 5.8 1.1 - - + -
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 5.0 2.9 - - + -
166B VAL* 2.8 34.3 + - + +
167B PRO* 4.1 3.1 - - + +
169B ILE* 1.3 73.4 - - - +
171B ALA* 1.3 64.3 + - - +
172B ALA 3.2 0.2 + - - -
173B VAL* 3.2 2.3 + - - +
174B ARG* 2.9 37.6 + - + +
182B ILE* 4.0 24.5 - - + -
199B PHE 3.6 26.5 - - - +
200B GLY* 4.1 13.7 - - - +
201B ILE* 4.2 12.6 - - + -
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Residues in contact with ALA 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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167B PRO 3.1 20.1 + - - +
168B ALA* 4.0 4.9 - - - +
170B VAL* 1.3 77.8 - - - +
172B ALA* 1.3 61.4 + - - +
174B ARG* 4.0 5.5 - - - +
175B SER* 3.1 24.4 + - - -
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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
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138B ALA* 3.5 22.4 - - + +
140B ILE* 3.4 23.6 - - + -
141B VAL* 3.7 10.2 - - + +
168B ALA 3.1 19.9 + - - +
169B ILE 3.1 0.4 + - - +
171B ALA* 1.3 73.3 - - - +
173B VAL* 1.3 65.8 + - - +
175B SER* 2.7 24.2 + - - -
176B VAL* 3.5 11.8 - - - +
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Residues in contact with VAL 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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140B ILE* 4.1 17.5 - - + -
144B LEU* 4.0 15.9 - - + +
151B VAL* 3.9 33.0 - - + -
169B ILE* 3.0 22.6 + - + +
170B VAL 3.7 3.4 - - - +
172B ALA* 1.3 76.3 - - - +
174B ARG* 1.3 57.9 - - - +
176B VAL* 3.1 2.3 + - - +
177B VAL* 2.8 34.6 + - + +
180B ALA* 3.9 25.1 - - + -
182B ILE* 3.7 24.2 - - + -
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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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170B VAL* 2.9 29.2 + - + +
171B ALA* 4.0 5.8 - - - +
173B VAL* 1.3 76.6 - - - +
175B SER* 1.3 60.3 + - - +
176B VAL 3.3 0.7 + - - -
177B VAL 4.4 1.4 + - - -
178B PRO* 2.7 63.4 + - + +
180B ALA* 2.9 23.0 + - - +
182B ILE* 3.7 19.4 - - - +
200B GLY 3.2 23.6 + - - -
202B ASP* 2.7 31.7 + - - -
228B ARG* 3.9 3.9 - - - +
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Residues in contact with SER 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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141B VAL* 4.3 3.6 - - - +
171B ALA 3.1 14.6 + - - -
172B ALA* 2.7 21.7 + - - -
173B VAL 3.1 0.4 - - - -
174B ARG* 1.3 75.1 - - - +
176B VAL* 1.3 67.4 + - - +
178B PRO* 4.7 1.6 - - - +
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Residues in contact with VAL 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B VAL* 3.6 22.0 - - + +
144B LEU* 3.6 25.6 - - + -
145B GLN 6.4 0.4 - - - -
172B ALA 3.5 7.9 - - - +
173B VAL 3.1 1.0 + - - -
175B SER* 1.3 94.7 - - - +
177B VAL* 1.3 68.4 + - + +
178B PRO* 3.5 9.8 - - - +
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Residues in contact with VAL 177 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144B LEU* 4.5 14.6 - - + -
145B GLN 3.9 20.9 - - - +
146B PRO* 5.2 7.4 - - + +
148B THR* 3.4 24.0 - - - +
173B VAL* 2.8 21.4 + - + +
174B ARG* 4.4 0.2 + - - -
176B VAL* 1.3 89.1 - - + +
178B PRO* 1.4 67.4 - - - +
179B ASP* 3.1 21.5 - - - +
180B ALA* 3.0 27.4 + - + +
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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