Contacts of the strand formed by residues 183 - 190 (chain A) in PDB entry 1RC7
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 LYS 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174A SER 3.7 0.7 - - - +
175A VAL* 3.2 5.8 - - - -
176A GLU* 2.7 76.4 + - + +
177A GLY* 5.3 0.9 - - - -
181A LYS 5.1 1.6 - - - +
182A LYS* 1.3 72.9 - - - +
184A PHE* 1.3 65.0 + - - +
185A ILE* 4.0 13.7 + - + +
198A GLU* 2.6 53.1 + - + +
199A GLY 3.7 5.8 - - - +
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Residues in contact with PHE 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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172A LEU* 4.0 11.4 - - + -
174A SER 3.7 0.9 - - - -
175A VAL* 3.5 35.0 - - + -
182A LYS* 4.0 21.3 - - + -
183A LYS* 1.3 74.1 - - - +
185A ILE* 1.3 62.5 + - - +
198A GLU* 2.9 7.3 - - - +
199A GLY 2.8 36.9 + - - +
200A LYS 3.8 7.0 - - - -
201A SER* 3.4 27.4 - - - +
202A LYS* 4.0 24.0 - - + +
205A ALA* 3.6 15.6 - - + +
16C G 3.4 36.8 - - - -
17C C 3.7 11.9 - - - -
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Residues in contact with ILE 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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172A LEU* 3.2 7.4 - - - +
173A ILE* 2.9 38.8 + - + -
174A SER* 3.0 32.8 + - - +
176A GLU* 3.6 18.6 - - - +
183A LYS* 4.0 24.5 - - + +
184A PHE* 1.3 77.6 - - - +
186A VAL* 1.3 63.1 + - - +
196A LEU* 4.1 25.4 - - + -
197A GLY 3.4 8.7 - - - +
198A GLU* 4.3 2.9 - - + -
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Residues in contact with VAL 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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170A TYR* 4.3 4.9 - - + -
171A ARG 3.4 16.8 - - - +
172A LEU* 3.7 22.2 - - + -
173A ILE* 4.3 0.4 - - - -
184A PHE* 5.0 0.4 - - + -
185A ILE* 1.3 81.5 - - - +
187A GLU* 1.3 72.3 + - - +
196A LEU* 3.3 6.9 - - - -
197A GLY 2.8 34.1 + - - +
202A LYS* 4.4 8.7 - - + +
205A ALA* 3.7 23.8 - - + -
206A GLU* 3.9 32.5 - - + +
209A ALA* 3.5 5.0 - - + +
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Residues in contact with GLU 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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169A GLU 3.4 1.7 - - - +
170A TYR* 3.1 6.6 - - - -
171A ARG* 2.8 72.5 + - + +
173A ILE* 3.9 11.8 - - + +
186A VAL* 1.3 76.9 - - - +
188A ALA* 1.3 67.8 + - - +
189A LYS* 3.9 15.8 - - - +
194A ARG* 3.0 35.9 + - + +
195A THR 3.2 15.9 - - - +
196A LEU* 3.6 16.1 - - + +
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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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156A LEU* 4.6 1.8 - - + -
168A PRO* 5.6 0.2 - - + -
169A GLU 3.2 4.7 - - - -
170A TYR* 3.8 20.0 - - + -
187A GLU* 1.3 75.2 - - - +
189A LYS* 1.3 60.1 + - - +
194A ARG* 3.5 4.7 - - - -
195A THR* 2.9 36.2 + - - +
209A ALA* 3.7 25.2 - - + +
210A ALA* 4.2 1.6 - - - +
213A LEU* 3.6 18.5 - - + +
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Residues in contact with LYS 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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168A PRO* 3.2 7.2 - - - +
169A GLU* 2.6 68.7 + - + +
171A ARG* 5.0 8.5 - - - +
187A GLU* 3.9 18.1 + - - +
188A ALA* 1.3 74.8 - - - +
190A ILE* 1.3 65.5 + - - +
191A LYS 3.6 18.6 - - - +
193A TYR 3.5 12.8 - - - +
194A ARG* 3.3 37.9 - - + +
213A LEU* 4.0 3.5 - - - +
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Residues in contact with ILE 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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160A THR* 3.6 27.4 - - + -
164A TRP* 3.5 27.8 - - + -
166A GLU* 4.4 15.7 - - + +
167A ARG 4.1 19.3 - - - +
168A PRO* 4.2 2.5 - - + -
189A LYS* 1.3 76.2 - - - +
191A LYS* 1.3 77.1 + - + +
193A TYR* 2.9 36.7 + - + +
213A LEU* 4.0 14.1 - - + -
217A LEU* 3.9 15.7 - - + -
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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