Contacts of the helix formed by residues 173 - 184 (chain B) in PDB entry 3BFT
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 THR 173 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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59B GLY 5.3 7.9 - - - +
138B LEU* 3.6 10.1 - - - -
171B VAL* 3.4 7.0 - - - +
172B ARG* 1.3 90.6 - - + +
174B THR* 1.3 64.7 + - - +
175B ALA* 3.7 9.0 + - - +
176B GLU* 3.1 32.1 + - - +
177B GLY 3.2 9.2 + - - -
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Residues in contact with THR 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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13B GLU* 2.9 39.6 + - - +
61B TYR* 5.2 0.5 - - - -
138B LEU* 3.8 7.6 - - - +
173B THR* 1.3 72.9 - - - +
175B ALA* 1.3 59.4 + - - +
177B GLY* 3.0 4.5 + - - -
178B VAL* 2.9 33.8 + - + +
190B TYR* 4.0 11.9 + - + -
192B LEU* 4.1 26.7 - - + -
196B MET* 4.4 10.5 - - + -
200B ILE* 5.4 5.4 - - + -
1440B S2P 4.0 15.0 + - - -
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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
----------------------------------------------------------
13B GLU* 4.8 1.4 + - - +
173B THR* 3.3 8.8 + - - +
174B THR* 1.3 78.5 - - - +
176B GLU* 1.3 58.6 + - - +
178B VAL* 3.7 8.7 - - - +
179B ALA* 2.8 32.2 + - - +
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Residues in contact with GLU 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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170B PHE 4.7 1.6 - - - +
171B VAL* 3.6 16.8 - - + +
172B ARG* 2.8 64.6 + - - +
173B THR* 3.1 21.8 + - - +
175B ALA* 1.3 79.4 - - - +
177B GLY* 1.3 58.7 + - - +
179B ALA* 3.4 5.9 + - - +
180B ARG* 2.9 28.4 + - - +
183B LYS* 5.4 0.5 + - - -
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Residues in contact with GLY 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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171B VAL* 3.8 23.9 - - - +
173B THR 3.2 4.6 + - - -
174B THR 3.0 7.3 + - - -
176B GLU* 1.3 78.0 - - - +
178B VAL* 1.3 64.5 + - - +
180B ARG* 3.1 5.2 + - - +
181B VAL* 3.0 26.0 + - - +
188B TYR* 4.0 2.2 - - - -
190B TYR* 4.0 18.6 - - - -
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Residues in contact with VAL 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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114B MET* 3.7 33.7 - - + -
174B THR* 2.9 30.4 + - + +
175B ALA* 3.8 7.4 - - - +
177B GLY* 1.3 75.0 - - - +
179B ALA* 1.3 64.1 + - - +
181B VAL* 3.1 4.3 + - - +
182B ARG* 3.0 54.7 + - + +
190B TYR* 4.4 0.9 - - + -
192B LEU* 4.9 2.0 - - + -
200B ILE* 3.9 29.8 - - + -
208B THR* 4.7 0.7 - - + -
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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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175B ALA 2.8 19.4 + - - +
176B GLU* 3.7 6.3 - - - +
178B VAL* 1.3 77.9 - - - +
180B ARG* 1.3 62.8 + - - +
182B ARG* 3.4 10.3 + - - +
183B LYS* 3.1 32.2 + - - +
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Residues in contact with ARG 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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134B ALA* 5.6 1.8 - - - +
167B PRO* 5.0 7.5 + - - +
168B SER 2.8 29.5 + - - -
169B VAL* 3.9 7.2 + - - +
170B PHE 3.8 16.0 + - - -
171B VAL* 4.2 9.8 - - + +
176B GLU* 2.9 19.2 + - + +
177B GLY* 3.5 6.5 - - - +
178B VAL 3.1 0.4 - - - -
179B ALA* 1.3 78.5 - - - +
181B VAL* 1.3 59.5 + - - +
183B LYS* 3.5 21.1 + - - +
184B SER* 2.5 38.8 + - - +
188B TYR* 3.2 52.6 + - + -
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Residues in contact with VAL 181 (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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114B MET* 4.0 13.7 - - - +
115B ILE 3.7 7.4 - - - +
116B LYS* 3.4 44.1 - - + +
177B GLY 3.0 20.4 + - - +
178B VAL 3.1 6.0 + - - +
180B ARG* 1.3 78.5 - - - +
182B ARG* 1.3 62.6 + - - +
184B SER* 3.3 11.3 + - - -
185B LYS 4.3 0.5 + - - -
186B GLY 4.5 1.0 + - - -
188B TYR* 3.8 26.2 - - + +
190B TYR* 3.5 28.7 - - + +
208B THR* 4.5 8.7 - - + -
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Residues in contact with ARG 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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116B LYS* 3.4 26.3 - - - +
178B VAL* 3.0 35.1 + - - +
179B ALA* 3.7 8.9 - - - +
180B ARG 3.3 0.2 - - - -
181B VAL* 1.3 78.4 - - - +
183B LYS* 1.3 58.1 + - - +
185B LYS 4.4 0.7 + - - -
200B ILE* 3.6 24.9 + - - +
203B ARG* 3.9 13.1 + - - +
204B LYS 3.8 16.0 + - - -
205B PRO* 3.8 18.2 - - - +
206B CYS 4.8 0.4 - - - +
207B ASP* 2.9 38.4 + - - +
208B THR* 3.8 13.2 + - + +
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Residues in contact with LYS 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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176B GLU 5.4 0.4 + - - -
179B ALA* 3.1 17.0 + - - +
180B ARG* 3.6 32.7 - - - +
182B ARG* 1.3 74.0 - - - +
184B SER* 1.3 61.1 + - - +
185B LYS* 3.3 18.9 + - - +
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Residues in contact with SER 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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180B ARG* 2.5 31.0 + - - +
181B VAL 3.3 5.6 + - - -
183B LYS* 1.3 79.3 - - - +
185B LYS* 1.3 73.1 + - - +
186B GLY 3.0 0.4 - - - -
187B LYS* 2.9 23.5 + - - +
188B TYR* 3.3 33.2 - - - +
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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