Contacts of the strand formed by residues 186 - 196 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A GLN* 4.5 16.2 - - + -
179A MET 3.4 6.3 - - - +
180A GLU* 4.1 23.3 - - + +
181A ILE* 5.4 0.7 - - - -
184A GLY 5.7 0.9 - - - -
185A GLY* 1.3 79.7 - - - +
187A LEU* 1.3 60.8 + - - +
218A GLU 3.8 0.4 - - - +
219A HIS* 3.3 9.2 - - - -
220A THR* 2.7 59.4 + - - +
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Residues in contact with LEU 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176A LEU 4.1 1.2 - - - +
177A ALA* 3.8 1.7 - - - -
178A GLN 3.4 7.1 + - - -
179A MET* 3.0 45.3 + - + +
181A ILE* 4.2 26.0 - - + -
186A THR* 1.3 75.8 - - - +
188A GLU* 1.3 66.4 + - - +
189A LEU* 3.8 30.5 - - + -
217A ALA* 4.9 4.3 - - + -
218A GLU 3.4 22.7 - - - +
219A HIS* 4.3 13.9 - - + +
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Residues in contact with GLU 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A GLN* 4.2 8.3 - - - +
110A HIS* 3.1 26.3 + - - -
120A TRP* 3.8 22.2 - - + -
175A ARG* 3.9 21.5 - - - +
176A LEU 3.3 10.5 - - - +
177A ALA* 3.6 22.5 - - + +
178A GLN 5.0 0.4 - - - +
187A LEU* 1.3 76.7 - - - +
189A LEU* 1.3 74.8 + - - +
216A THR* 4.0 0.5 - - - +
217A ALA* 3.5 0.7 - - - -
218A GLU* 2.8 44.6 + - + +
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Residues in contact with LEU 189 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174A VAL 4.1 0.2 - - - +
175A ARG* 3.3 3.1 - - - +
176A LEU* 2.8 45.0 + - + +
179A MET* 4.9 15.0 - - + -
187A LEU* 3.8 28.7 - - + -
188A GLU* 1.3 89.6 - - - +
190A GLY* 1.3 59.8 + - - +
216A THR 3.4 3.6 - - - +
217A ALA* 4.0 19.3 - - + -
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Residues in contact with GLY 190 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TRP* 3.7 24.7 - - - -
174A VAL 3.3 10.1 - - - -
189A LEU* 1.3 76.2 - - - +
191A VAL* 1.3 66.2 + - - +
192A ASP* 5.4 0.2 - - - -
214A LEU 4.6 0.7 - - - -
215A PHE* 3.5 3.8 - - - +
216A THR* 2.8 35.8 + - - +
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Residues in contact with VAL 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TRP* 4.9 0.2 - - - -
172A PHE 3.6 1.7 - - - +
173A ASP* 3.6 2.8 - - - -
174A VAL* 3.0 41.5 + - + +
189A LEU* 6.5 0.2 - - + -
190A GLY* 1.3 79.4 - - - +
192A ASP* 1.3 67.3 + - - +
193A TYR* 5.6 0.2 - - + -
213A TRP* 3.7 34.1 - - + -
214A LEU 3.6 3.4 - - - -
215A PHE* 3.9 20.9 - - + -
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Residues in contact with ASP 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A TRP* 3.0 29.5 + - - -
122A ILE* 4.0 6.9 - - - +
171A VAL* 3.6 12.6 - - + +
172A PHE 3.4 1.8 - - - +
173A ASP* 2.4 40.0 - - - +
190A GLY 5.4 0.3 - - - -
191A VAL* 1.3 78.2 - - - +
193A TYR* 1.3 60.5 + - - +
194A GLY 4.1 0.4 - - - -
213A TRP* 3.2 9.0 - - - +
214A LEU* 2.8 50.1 + - + +
216A THR* 5.0 0.5 + - - -
239A MET* 3.6 20.8 - - + +
245A GLY 4.6 0.4 - - - -
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Residues in contact with TYR 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171A VAL* 3.4 2.3 - - - -
172A PHE* 2.8 60.6 + + + +
191A VAL* 4.8 0.6 - - - +
192A ASP* 1.3 73.8 - - - +
194A GLY* 1.3 57.9 + - - +
195A ARG* 3.9 34.2 + - + +
211A ASP* 2.5 42.6 + - + +
212A GLY 3.3 16.8 - - - -
213A TRP* 3.6 46.2 - + + -
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Residues in contact with GLY 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170A ASP 3.1 11.9 - - - -
171A VAL* 4.0 6.3 - - - -
192A ASP 4.1 1.2 - - - -
193A TYR* 1.3 76.2 - - - +
195A ARG* 1.3 60.8 + - - -
211A ASP* 3.2 4.2 - - - +
212A GLY 2.9 35.0 + - - +
238A SER* 3.5 1.2 + - - -
239A MET* 4.1 5.6 - - - -
247A SER* 3.7 18.6 - - - -
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Residues in contact with ARG 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A ASN* 3.8 6.1 - - - -
170A ASP* 3.0 37.7 + - + +
172A PHE* 4.6 15.3 - - + -
193A TYR* 3.9 30.7 + - + +
194A GLY* 1.3 74.9 - - - +
196A ALA* 1.3 79.2 + - - +
197A ASN* 3.5 14.4 + - - +
198A LEU 5.5 1.0 - - - +
210A LYS* 3.3 10.8 - - + +
211A ASP* 3.5 17.1 + - + +
247A SER* 3.7 2.1 + - - -
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Residues in contact with ALA 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A THR* 3.9 17.3 - - - +
168A ALA 3.6 6.3 - - - -
169A ASN* 3.6 13.6 - - - +
195A ARG* 1.3 93.3 + - - +
197A ASN* 1.3 58.6 + - - +
198A LEU* 3.9 6.4 + - + +
204A LEU* 4.0 25.6 - - + -
210A LYS* 2.7 23.3 + - + +
249A GLY* 4.1 7.4 - - - -
250A SER 4.6 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