Contacts of the strand formed by residues 185 - 191 (chain A) in PDB entry 3CJR
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 PHE 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A LYS* 3.6 22.4 - - + +
124A VAL 3.8 15.3 - - - -
125A LEU* 3.7 35.0 - - + -
144A LYS 5.4 1.6 - - - -
146A LEU* 3.7 32.3 - - + -
179A ALA* 3.5 23.3 - - + -
180A LEU* 5.4 0.7 - - - -
182A PHE* 3.9 10.8 - - + -
183A GLY* 3.5 19.5 - - - -
184A PRO* 1.3 74.6 - - - +
186A ASP* 1.3 63.2 + - - +
187A LEU 4.0 11.0 - - - +
207A ALA* 2.9 23.4 + - + +
208A LEU* 3.2 12.8 - - + +
209A VAL* 2.9 25.3 + - - +
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Residues in contact with ASP 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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121A GLY 4.4 1.6 - - - +
122A ASP* 3.6 31.3 - - - +
123A LYS* 2.9 38.5 + - - +
185A PHE* 1.3 73.4 - - - +
187A LEU* 1.3 60.0 + - - +
208A LEU* 4.1 1.6 - - - -
209A VAL* 3.6 23.4 - - - +
212A GLY* 3.4 4.3 - - - -
213A ARG* 3.1 26.3 + - - +
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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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114A LEU* 3.8 15.9 - - + -
117A HIS* 3.8 31.9 - - + +
118A LEU* 4.0 31.9 - - + +
122A ASP* 4.7 2.7 - - - +
123A LYS 3.1 7.0 + - - +
124A VAL* 3.3 10.6 - - + +
125A LEU 2.9 25.6 + - - -
185A PHE* 3.4 2.6 - - - +
186A ASP* 1.3 82.5 - - + +
188A LEU* 1.3 76.5 + - - +
189A VAL 4.0 2.0 - - - +
208A LEU* 3.9 4.3 - - - -
213A ARG* 3.3 20.9 - - + +
215A LEU* 3.8 19.5 - - + -
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Residues in contact with LEU 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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125A LEU* 3.4 39.0 - - + +
127A LEU* 3.9 22.4 - - + -
176A LEU* 4.7 2.0 - - + -
187A LEU* 1.3 78.1 - - - +
189A VAL* 1.3 61.7 + - - +
190A ALA* 4.5 1.3 - - + +
204A TYR* 3.4 47.6 - - + +
207A ALA* 5.8 3.1 - - + -
208A LEU* 3.6 15.4 - - + +
213A ARG 2.9 10.0 + - - +
214A ALA* 3.4 14.8 - - + -
215A LEU* 2.6 33.1 + - - -
216A LEU* 4.1 5.8 - - + -
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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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110A ALA* 4.0 17.0 - - + -
114A LEU* 4.2 30.3 - - + -
124A VAL* 4.3 7.9 - - + -
125A LEU 2.8 16.7 + - - +
126A ASP* 3.3 23.7 - - + +
127A LEU 2.9 24.9 + - - -
134A LEU* 3.8 26.5 - - + +
187A LEU* 4.0 2.4 - - + +
188A LEU* 1.3 74.4 - - - +
190A ALA* 1.3 64.4 + - - +
215A LEU* 3.4 17.7 - - + +
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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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127A LEU* 3.8 24.0 - - + +
188A LEU* 4.5 4.7 - - + -
189A VAL* 1.3 76.4 - - - +
191A ASN* 1.3 60.1 + - - +
192A LEU* 3.5 3.8 - - + -
197A HIS* 3.2 25.2 - - + -
204A TYR* 4.0 11.0 - - - +
215A LEU 2.9 9.8 + - - -
216A LEU* 3.6 8.9 - - + -
217A THR* 2.9 26.8 + - - -
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Residues in contact with ASN 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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99A PHE* 3.8 6.0 - - - -
106A THR* 3.0 26.2 + - - -
107A THR* 3.6 6.9 + - - +
126A ASP* 5.3 0.4 + - - -
127A LEU 4.1 4.6 + - - -
128A GLY 4.7 0.7 - - - +
134A LEU* 4.4 8.3 - - + +
189A VAL 4.2 0.4 - - - -
190A ALA* 1.3 69.8 - - - +
192A LEU* 1.3 66.2 + - - +
217A THR* 3.5 17.5 - - + -
218A GLY* 3.2 24.4 + - - -
255A SFG 2.8 66.1 + - + +
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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