Contacts of the strand formed by residues 189 - 195 (chain A) in PDB entry 2HU4
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 TRP 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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123A SER* 3.4 47.1 - - - -
124A CYS 4.0 5.8 - - - -
125A SER* 4.1 18.1 - - - -
128A GLU* 4.7 6.0 + - + +
130A ARG* 4.0 29.5 - - + +
132A PHE* 3.6 26.5 - + - -
172A ARG* 4.0 20.0 - - - +
174A GLU* 5.7 2.5 - - - +
182A ALA* 4.7 0.2 - - + -
183A CYS* 3.6 23.1 - - - -
184A HIS* 3.3 33.5 + + + -
188A SER* 1.3 75.6 - - - +
190A LEU* 1.3 62.7 + - - +
191A THR* 4.1 8.3 - - + -
206A LYS 3.5 1.4 - - - +
207A TYR* 3.5 5.8 - - - -
208A ASN* 3.0 29.7 + - - +
209A GLY 4.9 0.8 + - - +
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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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182A ALA* 3.0 8.0 - - - +
183A CYS* 2.8 47.3 + - - +
185A ASP* 6.5 0.2 - - + -
188A SER 3.8 0.6 + - - +
189A TRP* 1.3 75.8 - - - +
191A THR* 1.3 72.8 + - - +
192A ILE* 4.3 8.7 - - + -
205A LEU* 4.5 7.6 - - + -
206A LYS 3.3 13.7 - - - +
207A TYR* 4.6 10.8 - - + -
230A CYS* 4.2 3.4 - - - -
237A CYS* 3.7 34.3 - - + -
257A MET* 4.0 24.2 - - + -
260A GLY* 4.1 20.9 - - - +
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Residues in contact with THR 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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132A PHE* 4.0 11.0 - - + -
158A LEU* 4.3 12.6 - - + -
174A GLU* 3.5 33.7 + - + +
175A SER* 4.8 2.9 - - - -
181A SER 3.7 3.4 - - - -
182A ALA* 4.0 12.1 - - + -
189A TRP* 4.1 7.2 - - + -
190A LEU* 1.3 80.2 - - - +
192A ILE* 1.3 66.4 + - - +
193A GLY 4.2 0.4 - - - -
204A VAL 3.8 0.9 + - - +
205A LEU* 3.4 4.7 - - - -
206A LYS* 3.0 54.5 + - - +
209A GLY* 5.9 0.3 - - - -
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Residues in contact with ILE 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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158A LEU* 4.1 2.9 - - - +
180A ALA* 2.9 32.2 - - - +
181A SER* 2.7 25.1 + - - +
190A LEU* 4.3 6.5 - - + -
191A THR* 1.3 78.7 - - - +
193A GLY* 1.3 60.8 + - - +
194A ILE* 4.9 1.1 - - + -
203A ALA* 4.3 4.3 - - + -
204A VAL 3.9 2.9 - - - -
205A LEU* 3.4 24.2 - - + -
225A THR* 4.5 10.1 - - + -
230A CYS* 4.7 7.6 - - - -
239A THR* 4.1 18.4 - - + +
241A MET* 3.8 27.6 - - + -
257A MET* 3.6 31.9 - - + -
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Residues in contact with GLY 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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158A LEU* 5.0 0.2 - - - -
175A SER* 4.2 13.9 + - - -
176A VAL 4.0 5.0 - - - +
177A ALA* 3.5 19.5 - - - -
179A SER 3.7 0.4 - - - -
180A ALA* 4.4 0.7 - - - -
191A THR 4.2 0.2 - - - -
192A ILE* 1.3 75.7 - - - +
194A ILE* 1.3 65.6 + - - -
195A SER* 4.0 0.3 + - - -
202A VAL 3.6 2.1 - - - +
203A ALA* 3.4 0.4 - - - -
204A VAL* 2.8 41.5 + - - +
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Residues in contact with ILE 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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177A ALA* 3.0 2.1 - - - -
178A TRP* 2.8 43.7 + - + -
179A SER* 2.9 20.5 + - - +
192A ILE* 4.9 1.1 - - + -
193A GLY* 1.3 72.1 - - - -
195A SER* 1.3 65.2 + - - +
201A ALA* 3.7 13.0 - - + -
202A VAL 3.6 9.0 - - - +
203A ALA* 3.6 18.6 - - + -
223A LEU* 3.3 36.3 - - + +
224A ARG* 3.5 25.1 - - - -
225A THR* 3.7 10.5 - - + +
241A MET* 3.8 17.0 - - + -
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Residues in contact with SER 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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153A SER 5.1 1.7 + - - -
156A ARG 5.4 0.3 + - - -
176A VAL* 3.6 28.2 - - - +
177A ALA* 4.3 1.0 - - - -
178A TRP* 3.5 15.0 - - - +
193A GLY 5.2 0.2 - - - -
194A ILE* 1.3 76.2 - - - +
196A GLY* 1.3 66.5 + - - +
201A ALA* 3.3 5.4 - - - -
202A VAL* 3.1 33.2 + - - +
204A VAL* 6.4 0.4 - - - -
99D VAL* 4.5 12.1 - - - -
456D TRP* 3.9 5.2 - - - -
458D TRP* 3.3 22.6 + - - -
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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