Contacts of the strand formed by residues 187 - 194 (chain A) in PDB entry 1E1A
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 PRO 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125A ASP* 3.7 30.3 - - + +
126A TYR 4.2 1.3 - - - +
127A GLU* 3.9 25.6 - - + +
179A VAL* 4.1 5.4 - - + -
180A ARG 3.8 3.1 - - - +
181A HIS* 3.5 27.4 - - + +
185A GLY 3.5 5.4 - - - +
186A ARG* 1.3 95.9 + - + +
188A TYR* 1.3 59.5 + - - +
205A ILE* 3.8 25.3 - - + +
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Residues in contact with TYR 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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180A ARG* 3.1 43.1 + - + +
181A HIS 3.5 19.8 + - - -
182A MET* 3.4 43.0 - - + -
186A ARG* 3.8 24.7 - - - +
187A PRO* 1.3 75.8 - - - +
189A GLN* 1.3 71.3 + - + +
204A ASP* 3.5 11.9 - - - +
205A ILE* 2.9 28.8 + - - +
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Residues in contact with GLN 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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179A VAL* 3.5 3.3 - - - -
180A ARG* 2.6 80.6 + - + +
188A TYR* 1.3 95.6 - - + +
190A LEU* 1.3 64.4 + - - +
191A ILE* 3.4 22.1 + - + +
202A SER* 4.3 7.3 + - - -
203A TYR 3.3 13.0 - - - +
204A ASP* 5.3 6.3 + - - +
205A ILE* 3.6 8.0 - - - +
215A LYS* 5.1 5.3 - - - +
217A TRP* 3.7 17.8 + - - +
254A PRO 5.6 0.6 + - - -
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Residues in contact with LEU 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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131A TRP* 3.8 50.9 - - + -
155A ILE* 4.5 4.3 - - + -
177A ILE* 3.8 14.6 - - + -
178A ALA 3.5 15.3 - - - +
179A VAL* 3.9 8.1 - - + -
189A GLN* 1.3 73.6 - - - +
191A ILE* 1.3 60.4 + - - +
192A VAL* 4.0 20.9 - - + -
201A TRP 3.6 0.3 - - - +
202A SER* 3.1 8.1 - - - -
203A TYR* 3.0 49.5 + - + +
205A ILE* 3.8 13.8 - - + +
211A ILE* 4.2 12.8 - - + -
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Residues in contact with ILE 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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177A ILE* 3.3 9.0 - - - +
178A ALA* 2.8 36.7 + - + +
180A ARG* 4.5 0.4 - - - +
189A GLN* 3.4 26.5 - - + +
190A LEU* 1.3 75.9 - - - +
192A VAL* 1.3 63.1 + - - +
193A ALA 4.3 0.4 - - - -
200A LEU* 4.3 7.6 - - + -
201A TRP 3.2 5.6 - - - +
202A SER* 3.7 22.2 - - - -
217A TRP* 3.8 25.8 - - + -
231A MET* 3.9 17.0 - - + +
233A PHE* 4.2 22.2 - - + -
239A LEU* 3.7 23.8 - - + -
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Residues in contact with VAL 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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133A THR* 4.1 10.3 - - + -
155A ILE* 3.7 26.9 - - + -
171A PHE* 4.4 10.3 - - + -
174A PRO* 4.1 4.5 - - + -
176A GLY 3.7 2.5 - - - -
177A ILE* 4.0 11.0 - - + -
190A LEU* 4.0 24.9 - - + -
191A ILE* 1.3 80.4 - - - +
193A ALA* 1.3 73.1 + - - +
194A GLU 3.8 0.7 + - - -
200A LEU* 3.5 2.0 - - - -
201A TRP* 2.7 49.7 + - + +
203A TYR* 4.1 14.6 - - + -
231A MET* 4.6 1.8 - - - -
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Residues in contact with ALA 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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174A PRO* 3.2 6.2 - - - +
175A ASN 2.8 27.1 + - - -
176A GLY 2.9 28.0 + - - +
192A VAL* 1.3 76.3 - - - +
194A GLU* 1.3 57.2 + - - +
195A THR 3.8 0.7 - - - -
199A LYS 3.8 5.2 - - - -
200A LEU* 3.8 2.7 - - + -
228A ALA* 3.6 29.8 - - + +
229A ASP 3.9 1.6 - - - +
231A MET* 3.6 18.7 - - + +
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Residues in contact with GLU 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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151A LYS* 4.6 7.7 + - - -
170A ALA 4.5 1.9 - - - +
171A PHE* 3.6 18.5 - - + -
172A GLN* 2.8 45.7 + - - +
173A PHE 3.7 4.0 - - - -
192A VAL 3.8 0.6 + - - -
193A ALA* 1.3 72.5 - - - +
195A THR* 1.3 66.6 + - - +
197A THR* 2.6 45.2 + - + +
198A LYS 3.5 3.1 + - - -
199A LYS* 3.1 16.8 + - - +
201A TRP* 2.9 42.9 + - + +
228A ALA* 4.8 1.2 + - - -
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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