Contacts of the strand formed by residues 185 - 191 (chain A) in PDB entry 3OEY
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 ARG 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141A GLY* 4.0 16.0 + - - -
142A GLY 2.9 12.8 + - - +
143A SER* 3.6 16.1 + - - +
144A ILE* 2.8 29.4 + - - +
179A ALA* 4.6 0.2 - - - -
183A GLY 5.5 1.8 - - - +
184A VAL* 1.3 82.2 - - - +
186A SER* 1.3 57.9 + - - +
187A ASN* 3.9 6.0 - - - +
245A LEU* 3.1 30.1 + - - +
246A LEU 4.5 0.6 + - - -
247A SER 2.9 26.0 + - - -
248A ASP* 4.8 2.8 + - - +
250A LEU* 2.9 39.2 + - - +
251A PRO* 3.6 21.1 - - - +
253A THR 3.4 25.7 + - - +
254A THR* 3.4 11.4 - - + +
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Residues in contact with SER 186 (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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127A TYR* 2.8 22.6 + - - -
144A ILE* 3.3 8.5 - - - -
172A ASN* 2.7 22.1 + - - +
175A VAL* 3.5 14.0 - - - +
176A ALA* 3.8 23.3 - - - -
179A ALA* 4.6 2.0 - - - -
185A ARG* 1.3 75.4 - - - +
187A ASN* 1.3 60.6 + - - +
254A THR* 2.9 7.1 + - - -
255A GLY* 2.6 34.8 + - - -
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Residues in contact with ASN 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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127A TYR* 3.4 2.8 + - - -
143A SER* 5.3 2.0 + - - -
144A ILE 2.9 9.3 + - - +
145A VAL* 3.2 8.0 - - + -
146A GLY 3.0 21.8 + - - -
172A ASN* 3.7 3.4 - - - -
185A ARG* 3.9 11.5 - - - +
186A SER* 1.3 78.8 + - - +
188A LEU* 1.3 65.5 + - - +
245A LEU* 3.8 36.9 - - + +
253A THR* 2.9 26.6 + - - +
254A THR* 3.4 5.3 - - - +
256A ASP* 3.0 42.9 + - - +
258A ILE* 5.4 1.1 - - + -
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Residues in contact with LEU 188 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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127A TYR* 4.2 10.8 - - + -
146A GLY* 3.2 29.4 - - - +
148A ASP* 3.9 17.3 - - + +
168A LEU* 4.0 22.7 - - + -
169A GLU* 3.7 42.2 - - + -
172A ASN* 3.7 23.8 - - + +
187A ASN* 1.3 78.1 - - - +
189A VAL* 1.3 66.1 + - - +
190A ALA 3.9 0.4 - - - -
245A LEU* 4.2 2.5 - - - +
256A ASP 2.9 10.0 + - - +
257A ILE* 3.4 7.3 - - + -
258A ILE* 2.8 27.0 + - - +
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Residues in contact with VAL 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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145A VAL* 4.0 4.9 - - + -
146A GLY 2.9 8.5 + - - -
147A MET* 3.5 26.5 - - + +
148A ASP* 2.8 25.9 + - - +
188A LEU* 1.3 71.6 - - - +
190A ALA* 1.3 63.0 + - - +
191A ALA 3.4 1.4 + - - +
238A VAL* 4.8 4.5 - - + +
241A THR* 4.0 17.7 - - + -
242A VAL* 3.9 22.2 - - + -
245A LEU* 3.4 28.3 - - + -
258A ILE 3.3 10.1 - - - +
260A ALA* 4.0 24.0 - - + -
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Residues in contact with ALA 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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148A ASP* 3.3 21.5 - - + +
150A ASP* 4.3 11.2 - - + +
188A LEU 3.9 1.8 - - - -
189A VAL* 1.3 69.0 - - - +
191A ALA* 1.3 62.3 + - - +
257A ILE* 3.7 15.4 - - + +
258A ILE 2.9 8.8 + - - +
259A TYR* 3.5 32.3 - - + +
260A ALA 2.9 26.0 + - - +
261A ASP* 4.3 2.8 - - - +
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Residues in contact with ALA 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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21A ILE* 5.0 3.6 - - + -
147A MET* 3.9 20.2 - - + -
148A ASP 3.0 7.7 + - - +
149A PHE* 3.2 23.0 - - - -
150A ASP 5.0 0.7 + - - -
189A VAL* 3.4 1.4 + - + -
190A ALA* 1.3 73.9 - - - +
192A GLY* 1.3 72.4 + - - +
194A ILE* 5.1 0.2 - - + -
222A TRP* 4.4 2.8 - - - -
238A VAL* 4.0 22.2 - - + -
260A ALA* 3.3 6.7 - - - +
261A ASP* 4.6 2.5 - - - -
4345A NAD 3.9 13.7 - - + -
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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