Contacts of the helix formed by residues 167 - 176 (chain B) in PDB entry 3F2F
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B GLY* 3.3 12.8 - - - -
142B ALA* 3.6 8.4 - - - +
165B PHE* 3.3 1.8 - - - +
166B ALA* 1.3 79.9 - - - +
168B VAL* 1.3 64.4 + - - +
169B PRO* 3.5 11.6 - - - +
170B THR* 2.9 33.0 + - - -
171B ALA* 3.1 23.7 + - - +
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Residues in contact with VAL 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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140B GLY 3.8 7.2 + - - +
142B ALA* 3.9 19.3 - - + -
167B SER* 1.3 69.4 - - - +
169B PRO* 1.3 70.7 - - + +
171B ALA* 3.2 2.9 + - - +
172B GLU* 2.8 53.0 + - - +
186B ILE* 4.0 15.0 - - + +
187B VAL* 4.7 0.7 - - - -
188B SER* 4.5 20.9 - - - +
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Residues in contact with PRO 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167B SER* 3.5 13.5 - - - +
168B VAL* 1.3 93.2 - - + +
170B THR* 1.3 63.5 + - - +
172B GLU* 3.3 14.8 + - - +
173B ASP* 3.0 27.5 + - - +
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Residues in contact with THR 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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117B CYS* 3.9 12.1 - - - -
119B ALA* 3.7 24.8 - - + +
120B THR* 3.9 21.7 - - + +
165B PHE* 4.5 1.3 - - + -
166B ALA* 4.4 6.4 - - + +
167B SER* 2.9 28.0 + - - +
169B PRO* 1.3 78.4 - - - +
171B ALA* 1.3 64.4 + - - +
173B ASP* 3.5 6.9 + - - +
174B TRP* 3.2 19.9 + - - +
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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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142B ALA* 4.2 1.1 - - + -
165B PHE* 3.5 33.4 - - + -
167B SER 3.1 16.8 + - - +
168B VAL 3.5 0.2 - - - +
170B THR* 1.3 76.0 - - - +
172B GLU* 1.3 59.5 + - - +
174B TRP* 3.2 5.6 + - - +
175B ALA* 2.8 29.5 + - - +
186B ILE* 3.4 34.3 - - + +
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Residues in contact with GLU 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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168B VAL* 2.8 44.0 + - + +
169B PRO* 3.3 14.9 + - - +
171B ALA* 1.3 72.1 - - - +
173B ASP* 1.3 63.1 + - - +
175B ALA* 3.3 5.1 + - - +
176B SER* 3.1 22.7 + - - -
186B ILE* 4.2 18.2 - - + +
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Residues in contact with ASP 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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177A LYS* 3.1 42.3 - - + +
169B PRO 3.0 13.3 + - - +
170B THR* 3.5 10.5 - - - +
172B GLU* 1.3 75.0 - - - +
174B TRP* 1.3 64.5 + - - +
176B SER* 2.7 25.8 + - - -
177B LYS 3.8 0.7 + - - -
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Residues in contact with TRP 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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177A LYS* 4.1 13.1 - - - +
178A HIS* 3.2 28.5 + + - -
118B ALA* 4.3 5.6 + - - +
119B ALA* 3.9 21.3 - - + +
144B SER* 4.0 9.4 - - - -
161B HIS* 4.3 4.9 - - - -
163B HIS* 3.8 32.5 - + - -
165B PHE* 3.5 31.4 - + + -
170B THR 3.2 10.9 + - - +
171B ALA 3.4 9.9 - - - +
173B ASP* 1.3 77.8 - - - +
175B ALA* 1.3 83.9 + - + +
177B LYS* 3.0 10.0 + - - +
178B HIS* 2.8 57.2 + + - -
181B LEU* 4.5 6.3 - - + -
184B LEU* 4.0 31.0 - - + -
186B ILE* 4.6 0.9 - - + -
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Residues in contact with ALA 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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171B ALA 2.8 19.3 + - - +
172B GLU* 3.6 10.1 - - - +
173B ASP 3.2 0.2 - - - -
174B TRP* 1.3 86.7 - - + +
176B SER* 1.3 57.1 + - - +
177B LYS 3.0 0.2 - - - -
178B HIS* 2.9 24.3 + - - +
179B GLN* 4.4 1.6 + - - -
184B LEU* 3.7 28.3 - - + +
185B ALA* 6.3 0.2 - - - -
186B ILE* 4.2 11.0 - - + -
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Residues in contact with SER 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A LYS* 4.9 1.4 + - - -
172B GLU 3.1 12.3 + - - -
173B ASP* 2.7 23.2 + - - -
174B TRP 3.2 0.2 - - - -
175B ALA* 1.3 77.3 - - - +
177B LYS* 1.3 77.1 + - - +
178B HIS 3.3 0.7 - - - -
179B GLN* 2.6 30.6 + - - +
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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