Contacts of the strand formed by residues 189 - 196 (chain A) in PDB entry 1I1N
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 GLN 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160A ALA* 3.2 31.3 - - + +
181A PRO* 4.9 0.2 - - + -
182A VAL 3.4 11.0 - - - +
183A GLY* 4.2 3.1 - - - -
184A PRO 3.2 22.9 + - - +
185A ALA* 4.3 2.2 - - - +
186A GLY* 4.0 11.7 - - - +
187A GLY 3.2 14.0 + - - +
188A ASN* 1.3 76.4 - - - +
190A MET* 1.3 63.6 + - - +
209A GLY* 3.5 5.5 - - - -
210A VAL* 3.0 39.0 + - + +
211A ILE* 3.5 5.7 + - - -
212A TYR* 2.7 43.6 + - - +
213A VAL 5.1 1.0 - - - -
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Residues in contact with MET 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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182A VAL* 2.8 41.7 + - - +
189A GLN* 1.3 78.8 - - - +
191A LEU* 1.3 63.9 + - - +
192A GLU* 3.4 14.3 + - + +
206A PRO* 3.6 29.4 - - + -
208A MET* 3.2 32.3 - - - +
209A GLY* 3.8 13.7 - - - +
210A VAL* 4.0 2.2 - - - -
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Residues in contact with LEU 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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63A MET* 6.0 0.7 - - + -
66A TYR* 5.8 3.1 - - + -
70A LEU* 3.9 28.0 - - + -
157A VAL 5.7 0.4 - - - +
179A ILE* 3.7 24.0 - - + -
180A LEU 3.8 17.9 - - - -
181A PRO* 3.9 8.3 - - + -
190A MET* 1.3 72.6 - - - +
192A GLU* 1.3 54.3 + - - +
206A PRO* 3.5 2.9 - - - +
207A LEU* 2.7 44.8 + - + -
208A MET* 2.9 33.8 + - + +
210A VAL* 3.6 20.3 - - + +
212A TYR* 3.8 22.4 - - + +
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Residues in contact with GLU 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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164A VAL* 4.7 0.4 - - - +
178A LEU 3.7 0.9 - - - +
179A ILE* 3.5 6.2 - - - +
180A LEU* 2.9 37.9 + - - +
182A VAL* 4.0 23.7 - - + +
190A MET* 3.9 16.7 - - + +
191A LEU* 1.3 78.8 - - - +
193A GLN* 1.3 60.9 + - - +
194A TYR* 3.4 26.3 + - + -
204A MET* 3.1 33.2 - - - +
205A LYS 3.6 3.4 - - - +
206A PRO* 3.9 17.3 - - + +
207A LEU* 4.6 2.9 - - - -
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Residues in contact with GLN 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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70A LEU* 4.1 6.8 - - - +
177A ARG* 3.2 43.6 + - + +
178A LEU 3.4 3.4 - - - -
179A ILE* 3.7 17.6 - - + +
192A GLU* 1.3 74.2 - - - +
194A TYR* 1.3 62.2 + - - +
195A ASP* 2.8 26.0 + - - +
203A LYS 3.7 0.9 - - - +
204A MET* 3.3 5.0 - - - +
205A LYS* 2.9 63.9 + - + +
207A LEU* 3.7 26.1 - - + +
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Residues in contact with TYR 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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164A VAL* 2.9 28.6 - - + +
169A ILE* 3.8 26.0 - - + -
172A LEU* 4.2 6.5 - - + +
176A GLY 4.0 0.2 - - - +
177A ARG* 3.3 5.2 - - - +
178A LEU* 2.8 57.5 + - + +
180A LEU* 3.7 31.0 - - + -
192A GLU* 3.4 17.5 + - + -
193A GLN* 1.3 77.2 - - - +
195A ASP* 1.3 62.1 + - - +
202A ILE* 3.9 15.9 - - + -
203A LYS 3.3 3.6 - - - +
204A MET* 3.3 34.8 - - + +
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Residues in contact with ASP 195 (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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74A GLN* 5.0 1.2 + - - -
172A LEU* 5.1 0.7 - - - -
175A GLY 5.4 0.3 - - - +
176A GLY 3.5 4.9 - - - +
177A ARG* 2.7 38.7 + - - +
193A GLN* 2.8 29.9 + - - +
194A TYR* 1.3 73.7 - - - +
196A LYS* 1.3 64.5 + - - +
197A LEU* 3.8 8.2 + - + -
201A SER 3.7 0.3 - - - +
202A ILE* 3.3 6.9 - - - +
203A LYS* 2.8 48.1 + - + +
205A LYS* 5.0 3.3 - - - +
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Residues in contact with LYS 196 (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 ILE 4.8 3.4 + - - +
170A ASP* 5.9 1.1 - - - +
172A LEU* 3.2 40.1 - - + +
173A LYS 3.5 16.4 - - - +
174A PRO* 4.1 13.0 - - + -
175A GLY* 2.7 33.1 + - - -
176A GLY 3.0 10.4 + - - +
194A TYR 4.3 0.2 - - - -
195A ASP* 1.3 73.0 - - - +
197A LEU* 1.3 64.9 + - - +
200A GLY* 2.8 37.7 + - - +
201A SER 3.3 2.9 - - - -
202A ILE* 3.6 21.0 - - + +
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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