Contacts of the strand formed by residues 178 - 188 (chain A) in PDB entry 1R18
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 LEU 178 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A PRO* 4.2 3.6 - - - +
158A TYR 3.6 11.4 - - - +
161A ILE* 3.8 20.9 - - + +
174A LEU 3.4 10.5 + - - +
175A ILE* 3.1 23.3 + - + +
176A ASN 4.2 1.9 - - - +
177A GLN* 1.3 79.5 - - - +
179A ALA* 1.3 63.9 + - - +
182A GLY 4.2 8.3 - - - +
183A ARG 3.7 29.4 - - - +
184A LEU* 3.9 20.4 - - + -
200A TYR* 4.0 15.9 - - + +
201A ASP 5.3 0.2 - - - -
202A LYS* 2.8 39.9 + - + +
208A VAL* 6.0 0.7 - - + -
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Residues in contact with ALA 179 (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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157A PRO* 3.7 22.2 - - + +
158A TYR 3.0 22.4 + - - +
159A ASN* 4.3 15.5 - - - +
177A GLN 3.8 0.8 + - - -
178A LEU* 1.3 78.8 - - - +
180A SER* 1.3 71.9 + - - +
181A GLY 3.2 0.3 + - - -
182A GLY* 2.9 15.3 + - - +
202A LYS* 3.7 7.2 - - - +
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Residues in contact with SER 180 (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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159A ASN* 5.5 2.3 + - - -
179A ALA* 1.3 77.2 - - - +
181A GLY* 1.3 60.0 + - - +
182A GLY 3.5 0.3 + - - -
202A LYS* 4.1 9.7 - - - +
203A ASP 3.8 16.4 + - - -
204A ALA* 3.9 20.8 + - - -
206A GLY* 5.0 2.3 + - - -
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Residues in contact with GLY 181 (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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75A HIS* 3.4 19.1 + - - -
159A ASN* 6.4 0.2 - - - -
180A SER* 1.3 73.7 - - - +
182A GLY* 1.3 61.6 + - - +
202A LYS 2.7 21.8 + - - -
203A ASP* 4.1 6.6 - - - -
204A ALA 5.2 0.4 - - - -
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Residues in contact with GLY 182 (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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75A HIS* 4.2 0.2 - - - -
158A TYR 4.6 0.2 - - - -
159A ASN* 3.1 23.3 - - - -
178A LEU* 4.2 10.3 - - - +
179A ALA 2.9 16.2 + - - -
180A SER 3.2 0.6 + - - -
181A GLY* 1.3 81.5 - - - +
183A ARG* 1.3 61.7 + - - +
200A TYR 3.9 0.7 - - - +
201A ASP* 3.6 5.9 - - - +
202A LYS 3.2 23.1 + - - -
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Residues in contact with ARG 183 (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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71A TYR* 2.8 22.2 + - - +
72A LEU* 3.5 27.1 - - + +
75A HIS* 3.5 31.6 - - + +
159A ASN 3.1 7.3 + - - -
160A ALA* 3.3 5.4 - - - +
161A ILE 2.9 24.4 + - - +
178A LEU* 3.7 4.7 - - - +
182A GLY* 1.3 73.7 - - - -
184A LEU* 1.3 63.2 + - - +
185A ILE* 3.9 9.4 - - + -
199A GLN* 3.3 41.2 + - + +
200A TYR 3.4 3.8 - - - -
201A ASP* 2.8 28.7 + - - +
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Residues in contact with LEU 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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161A ILE* 3.3 31.2 - - + +
163A VAL* 3.7 18.2 - - + -
171A PRO* 4.0 12.3 - - + -
174A LEU* 4.2 14.8 - - + -
175A ILE* 3.9 31.0 - - + +
178A LEU* 3.9 16.4 - - + -
183A ARG* 1.3 76.4 - - - +
185A ILE* 1.3 67.6 + - - +
186A VAL* 4.2 9.0 - - + -
198A GLN 3.5 1.7 - - - +
199A GLN* 3.4 5.5 - - - -
200A TYR* 2.9 47.0 + - + +
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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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68A ALA* 5.5 0.9 - - - +
71A TYR* 4.1 24.2 - - + -
72A LEU* 3.6 28.7 - - + -
161A ILE 2.9 8.0 + - - +
162A HIS* 4.7 12.6 - - + -
163A VAL* 2.9 30.3 + - - +
183A ARG* 3.9 18.2 - - + -
184A LEU* 1.3 80.1 - - - +
186A VAL* 1.3 63.0 + - - +
197A MET* 3.0 38.1 - - + -
198A GLN 3.5 2.9 - - - +
199A GLN* 4.0 23.6 - - + +
213A LEU* 4.1 7.2 - - + -
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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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163A VAL* 3.7 26.0 - - + -
165A ALA 4.2 0.2 - - - +
167A ALA* 3.9 17.9 - - + -
171A PRO* 4.2 11.2 - - + -
174A LEU* 5.5 0.2 - - + -
184A LEU* 4.2 8.5 - - + -
185A ILE* 1.3 80.6 - - - +
187A PRO* 1.3 88.4 - - + +
188A VAL* 3.4 8.0 + - + +
197A MET* 3.9 3.6 - - - -
198A GLN 2.9 31.5 + - - +
200A TYR* 3.8 31.2 - - + -
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Residues in contact with PRO 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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163A VAL 3.3 20.2 - - - +
164A GLY 4.9 4.7 - - - +
165A ALA 3.6 12.8 - - - +
166A ALA* 3.4 11.3 - - + +
167A ALA 2.9 26.0 + - - -
186A VAL* 1.3 91.2 - - + +
188A VAL* 1.3 59.7 + - - +
195A GLN* 4.3 8.5 - - - +
196A TYR 3.6 7.0 - - - +
197A MET* 3.5 21.1 - - + -
216A VAL* 4.5 14.1 - - + -
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Residues in contact with VAL 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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167A ALA* 3.4 9.4 - - + +
168A PRO 4.7 0.2 - - - +
169A ASP* 3.8 27.6 - - - +
170A THR 4.3 1.6 - - - +
171A PRO* 4.7 5.4 - - + -
186A VAL* 3.7 24.0 - - + +
187A PRO* 1.3 78.7 - - - +
189A GLY* 1.3 64.5 + - - +
195A GLN* 3.3 20.5 - - - +
196A TYR* 3.0 14.2 + - - +
198A GLN* 3.1 31.6 - - + +
200A TYR* 3.9 11.0 - - - +
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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