Contacts of the strand formed by residues 186 - 196 (chain B) in PDB entry 1AF6
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 186 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B GLN* 4.4 16.6 - - + -
179B MET 3.4 7.4 - - - +
180B GLU* 4.2 22.7 - - + +
181B ILE* 5.3 0.7 - - - -
184B GLY 4.4 1.3 - - - -
185B GLY* 1.3 79.5 - - - +
187B LEU* 1.3 60.3 + - - +
218B GLU 3.8 0.3 - - - +
219B HIS* 3.3 8.1 - - - -
220B THR* 2.7 59.4 + - - +
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Residues in contact with LEU 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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176B LEU 4.1 0.9 - - - +
177B ALA* 3.9 1.4 - - - -
178B GLN 3.4 6.3 + - - -
179B MET* 3.1 44.2 + - + +
181B ILE* 4.1 27.6 - - + -
186B THR* 1.3 75.7 - - - +
188B GLU* 1.3 67.5 + - - +
189B LEU* 3.9 30.3 - - + -
217B ALA* 4.9 4.5 - - + -
218B GLU 3.4 22.2 - - - +
219B HIS* 4.4 12.1 - - + +
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B GLN* 4.2 8.0 - - - +
110B HIS* 3.1 26.5 + - - -
120B TRP* 3.8 23.9 - - + -
175B ARG* 3.8 21.8 - - - +
176B LEU 3.3 11.7 - - - +
177B ALA* 3.6 22.6 - - + +
178B GLN 5.0 0.4 - - - +
187B LEU* 1.3 75.9 - - - +
189B LEU* 1.3 74.6 + - - +
216B THR* 4.0 0.7 - - - +
217B ALA* 3.5 1.0 - - - -
218B GLU* 2.8 43.7 + - + +
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Residues in contact with LEU 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174B VAL 4.1 0.2 - - - +
175B ARG* 3.3 3.1 - - - +
176B LEU* 2.8 45.7 + - + +
179B MET* 4.8 14.8 - - + -
187B LEU* 3.9 27.4 - - + -
188B GLU* 1.3 89.3 - - - +
190B GLY* 1.3 59.2 + - - +
191B VAL* 6.5 0.2 - - + -
216B THR 3.4 4.0 - - - +
217B ALA* 4.0 19.7 - - + -
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Residues in contact with GLY 190 (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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120B TRP* 3.7 24.0 - - - -
174B VAL 3.3 9.9 - - - -
189B LEU* 1.3 75.8 - - - +
191B VAL* 1.3 66.2 + - - +
192B ASP* 5.4 0.2 - - - -
214B LEU 4.5 0.4 - - - -
215B PHE* 3.5 3.6 - - - +
216B THR* 2.8 37.3 + - - +
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Residues in contact with VAL 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B PHE 3.7 1.0 - - - +
173B ASP* 3.6 2.8 - - - -
174B VAL* 3.0 40.1 + - + +
189B LEU 6.0 0.2 - - - -
190B GLY* 1.3 78.7 - - - +
192B ASP* 1.3 67.9 + - - +
193B TYR 4.8 0.2 - - - +
213B TRP* 3.7 34.1 - - + -
214B LEU 3.5 2.7 - - - -
215B PHE* 3.9 21.1 - - + -
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Residues in contact with ASP 192 (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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120B TRP* 3.0 31.1 + - - -
122B ILE* 4.0 6.5 - - - +
171B VAL* 3.6 12.9 - - + +
172B PHE 3.4 2.2 - - - +
173B ASP* 2.5 39.1 - - - +
190B GLY 5.4 0.2 - - - -
191B VAL* 1.3 80.0 - - - +
193B TYR* 1.3 59.3 + - - +
194B GLY 4.1 0.4 - - - -
213B TRP* 3.2 8.8 - - - +
214B LEU* 2.7 50.0 + - + +
216B THR* 5.0 0.3 + - - -
239B MET* 3.7 20.8 - - + +
245B GLY 4.7 0.4 - - - -
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Residues in contact with TYR 193 (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* 3.4 3.3 - - - -
172B PHE* 2.8 59.3 + + + +
191B VAL* 4.8 1.0 - - + +
192B ASP* 1.3 74.0 - - - +
194B GLY* 1.3 58.5 + - - +
195B ARG* 3.9 35.3 + - + +
211B ASP* 2.5 41.1 + - + +
212B GLY 3.3 17.9 - - - -
213B TRP* 3.5 45.1 - + + -
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Residues in contact with GLY 194 (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 ASP 3.1 11.7 - - - -
171B VAL* 4.1 6.1 - - - -
192B ASP 4.1 0.8 - - - -
193B TYR* 1.3 77.3 - - - +
195B ARG* 1.3 61.4 + - - -
211B ASP* 3.2 4.5 - - - +
212B GLY 2.9 34.9 + - - +
238B SER* 3.6 0.9 + - - -
239B MET* 4.1 5.4 - - - -
247B SER* 3.8 18.2 - - - -
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Residues in contact with ARG 195 (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 ASN* 3.8 7.0 - - - -
170B ASP* 3.0 37.1 + - + +
172B PHE* 4.6 15.3 - - + -
193B TYR* 3.9 30.7 + - + +
194B GLY* 1.3 74.2 - - - +
196B ALA* 1.3 81.3 + - - +
197B ASN* 3.5 13.8 + - + +
198B LEU 5.5 1.8 - - - +
210B LYS* 3.3 12.4 - - + +
211B ASP* 3.6 16.6 + - + +
247B SER* 3.7 2.5 + - - -
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Residues in contact with ALA 196 (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 THR* 3.9 17.7 - - - +
168B ALA 3.5 6.3 - - - -
169B ASN* 3.5 14.2 - - - +
195B ARG* 1.3 93.4 + - - +
197B ASN* 1.3 57.5 + - - +
198B LEU* 3.9 6.5 + - + +
204B LEU* 4.0 25.4 - - + -
210B LYS* 2.7 23.0 + - + +
249B GLY* 4.2 6.7 - - - -
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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