Contacts of the strand formed by residues 186 - 192 (chain A) in PDB entry 1JQI
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 186 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A LEU* 6.1 2.9 - - + -
139A ALA 4.4 2.9 - - - +
140A GLY* 3.4 35.2 - - - +
142A ALA* 3.6 21.8 - - + -
174A PHE* 4.1 12.8 - - + -
175A ALA 3.4 18.2 - - - +
176A SER* 4.5 5.2 - - - -
182A GLN 3.9 7.9 - - - +
183A ASN* 4.3 8.9 + - - +
184A LYS 3.5 2.8 + - - -
185A GLY* 1.3 81.4 - - - +
187A SER* 1.3 67.6 + - - +
234A GLY 3.1 11.1 - - - +
236A GLY* 2.6 40.5 + - - -
237A PHE* 4.2 13.7 - - + +
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Residues in contact with SER 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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174A PHE* 3.5 2.6 - - - -
175A ALA 2.8 31.5 + - - +
177A THR* 3.0 22.2 + - - +
186A ILE* 1.3 73.3 - - - +
188A ALA* 1.3 60.3 + - - +
189A PHE* 3.5 28.1 - - - -
229A LEU* 3.9 11.8 - - - +
232A GLU 4.9 1.6 - - - -
233A PRO* 3.4 7.9 - - - +
234A GLY 3.0 18.8 + - - -
235A MET 4.9 0.2 - - - +
236A GLY* 3.8 8.3 - - - +
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Residues in contact with ALA 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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172A VAL* 4.5 2.9 - - + -
173A VAL 3.4 5.6 - - - +
174A PHE* 3.7 28.0 - - + -
187A SER* 1.3 74.4 - - - +
189A PHE* 1.3 65.2 + - - +
229A LEU* 3.6 6.4 - - - +
230A LEU* 2.9 53.7 + - + +
236A GLY* 4.0 4.0 - - - +
239A ILE* 4.2 11.4 - - + -
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Residues in contact with PHE 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 ALA* 3.6 22.9 - - + -
153A TRP* 3.5 35.0 - + + -
155A LEU* 4.8 3.4 - - + -
171A THR 3.4 1.0 - - - +
172A VAL* 3.4 5.5 - - - +
173A VAL* 2.8 52.4 + - + +
175A ALA* 4.1 11.7 - - + -
177A THR* 3.6 24.0 - - + -
187A SER* 3.5 29.8 - - - -
188A ALA* 1.3 78.2 - - - +
190A LEU* 1.3 64.1 + - - +
224A ILE* 3.9 28.3 - - + -
228A ASN 3.5 2.7 - - - -
229A LEU* 3.8 19.1 - - + -
230A LEU* 4.5 0.9 - - - +
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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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99A TYR* 4.9 1.6 - - + -
103A ILE* 3.7 30.5 - - + -
111A GLN* 4.2 26.2 - - + +
115A TRP* 3.5 52.3 - - + +
171A THR 3.6 2.9 - - - +
172A VAL* 3.8 20.4 - - + -
189A PHE* 1.3 72.4 - - - +
191A VAL* 1.3 59.4 + - - +
224A ILE* 4.2 0.9 - - - +
228A ASN* 2.7 50.7 + - + +
230A LEU* 4.6 15.9 - - + -
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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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115A TRP* 3.9 4.4 - - - -
155A LEU* 4.0 15.7 - - + -
170A ALA* 3.2 1.7 - - - +
171A THR* 2.9 46.0 + - + +
173A VAL* 3.6 28.0 - - + -
189A PHE 4.3 0.7 - - - +
190A LEU* 1.3 79.7 - - - +
192A PRO* 1.3 80.9 - - + +
195A THR* 4.0 14.8 - - + -
198A LEU* 4.4 5.4 - - + -
219A PHE* 4.4 15.9 - - + -
222A CYS* 4.5 0.9 - - - -
224A ILE* 4.2 17.5 - - + -
228A ASN* 4.6 0.2 - - - +
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Residues in contact with PRO 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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115A TRP* 3.7 24.0 - - + -
169A SER 3.8 7.4 - - - +
191A VAL* 1.3 93.2 - - + +
193A MET* 1.3 63.3 + - - +
194A PRO 3.7 5.8 - - - +
195A THR* 3.4 36.0 - - - +
224A ILE* 4.8 6.1 - - + -
225A PRO* 6.1 1.3 - - + -
228A ASN* 4.1 10.1 - - - +
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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