Contacts of the strand formed by residues 183 - 190 (chain A) in PDB entry 3OJE
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 ILE 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A LYS* 5.3 11.4 - - + +
136A MET* 3.2 53.6 - - + +
139A GLY* 3.7 15.5 - - - -
140A GLY 3.4 0.9 - - - +
142A ILE* 3.1 35.9 - - + -
175A ALA 4.3 3.6 - - - +
178A LEU* 3.0 43.5 + - + +
179A GLY* 3.6 8.0 + - - -
181A HIS* 4.9 10.1 - - + +
182A GLY* 1.3 77.4 - - - +
184A ARG* 1.3 70.0 + - - +
185A VAL* 4.0 2.0 + - + +
242A THR* 4.3 1.4 + - - -
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Residues in contact with ARG 184 (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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7A LYS* 5.4 2.0 - - - +
140A GLY* 2.6 31.3 + - - +
141A ASN* 3.2 11.6 - - - +
142A ILE 2.7 32.7 + - - -
182A GLY 4.4 5.3 + - - +
183A ILE* 1.3 80.4 - - - +
185A VAL* 1.3 56.1 + - - +
186A ASN* 3.8 8.7 - - - +
233A LEU 2.5 26.8 + - - -
234A PHE 3.9 6.1 + - - -
235A SER 3.1 24.9 + - - -
236A ASP* 5.2 0.4 - - - +
238A ALA* 2.9 29.9 + - - +
239A ARG* 3.3 27.7 - - - +
241A VAL 3.5 9.6 + - - -
242A THR* 3.4 17.0 - - - +
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Residues in contact with VAL 185 (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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125A LEU* 5.1 6.1 - - + -
142A ILE* 3.4 22.4 - - + +
144A THR* 5.0 4.3 - - + -
171A VAL* 4.0 27.4 - - + -
174A LEU* 3.8 32.5 - - + +
175A ALA* 3.8 13.4 - - + +
178A LEU* 4.3 5.4 - - + -
183A ILE* 4.0 14.6 + - + +
184A ARG* 1.3 78.7 - - - +
186A ASN* 1.3 62.9 + - - +
242A THR* 3.4 4.8 + - - -
243A GLY* 2.5 38.8 + - - -
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Residues in contact with ASN 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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141A ASN* 2.9 28.9 - - - +
142A ILE 3.5 2.9 + - - +
143A LEU* 3.3 7.2 - - + +
144A THR* 3.0 24.9 + - - +
171A VAL* 4.6 4.9 - - - -
184A ARG* 3.8 8.5 - - - +
185A VAL* 1.3 87.7 - - - +
187A ALA* 1.3 60.2 + - - +
233A LEU* 3.9 29.7 - - + +
241A VAL 3.1 20.2 + - - +
242A THR* 3.4 4.3 - - - -
243A GLY 3.0 3.5 + - - -
244A GLU* 2.9 31.6 + - - +
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Residues in contact with ALA 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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143A LEU* 4.1 0.7 - - - -
144A THR* 3.1 19.5 - - + +
146A THR* 4.9 8.7 - - - +
167A LEU* 6.3 0.7 - - + -
171A VAL* 4.6 11.6 - - + +
186A ASN* 1.3 76.2 - - - +
188A ILE* 1.3 69.3 + - - +
189A SER 4.1 0.4 - - - -
233A LEU* 4.5 1.6 - - - +
244A GLU 3.2 8.5 + - - +
245A ASN* 3.5 23.0 - - + +
246A ILE* 3.2 24.1 + - - +
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Residues in contact with ILE 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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143A LEU* 3.8 32.1 - - + -
144A THR 3.0 9.7 + - - +
145A LEU* 3.4 15.5 - - + +
146A THR* 2.8 27.0 + - - +
187A ALA* 1.3 79.2 - - - +
189A SER* 1.3 65.6 + - - +
190A ALA* 3.1 10.9 + - + +
226A VAL* 3.5 30.7 - - + +
229A THR* 3.9 17.7 - - + -
230A ALA 4.1 4.5 - - - +
233A LEU* 4.0 7.4 - - + -
246A ILE* 3.3 5.2 - - + +
248A VAL* 3.4 27.4 - - + -
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Residues in contact with SER 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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146A THR* 3.5 19.2 + - - +
148A LEU* 5.0 2.2 - - - -
187A ALA* 5.3 0.2 - - - +
188A ILE* 1.3 71.2 - - - +
190A ALA* 1.3 59.6 + - - +
191A GLY 4.0 0.9 + - - -
245A ASN* 2.8 30.5 + - - -
246A ILE 3.0 6.7 + - - -
247A HIS* 3.1 31.4 + - - +
248A VAL 2.8 23.7 + - - -
249A ASP* 4.5 2.1 - - - +
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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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20A ILE* 5.4 1.6 - - + -
145A LEU* 4.0 19.7 - - + -
146A THR 2.7 14.1 + - - +
147A TYR* 3.3 11.0 - - + -
148A LEU* 2.5 32.4 + - - +
188A ILE* 3.1 5.3 + - + -
189A SER* 1.3 72.7 - - - +
191A GLY* 1.3 61.1 + - - +
193A ILE* 5.6 0.7 - - + -
226A VAL* 3.9 27.8 - - + -
248A VAL 3.7 4.5 - - - -
249A ASP* 4.8 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