Contacts of the strand formed by residues 189 - 195 (chain A) in PDB entry 2HT8
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* 3.2 44.4 - - - -
124A CYS 3.9 7.2 - - - -
125A SER* 3.7 17.8 - - - -
128A GLU* 4.5 4.2 + - + +
130A ARG* 3.5 24.7 - - + +
132A PHE* 3.3 29.2 - + - -
172A ARG* 3.8 25.9 - - - +
174A GLU* 5.5 4.9 - - - +
183A CYS* 3.6 8.1 - - - -
184A HIS* 3.1 47.2 + + - -
188A LYS* 1.3 74.1 - - - +
190A MET* 1.3 62.8 + - - +
191A THR* 4.0 8.2 + - + +
206A HIS 3.7 1.2 - - - +
207A TYR* 3.5 4.6 - - - -
208A GLY* 3.2 24.7 + - - +
209A GLY 4.8 0.9 + - - -
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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 ALA* 3.3 3.3 - - - +
183A CYS* 2.8 74.2 + - - +
185A ASP* 6.3 0.2 - - - -
188A LYS 3.8 1.2 + - - +
189A TRP* 1.3 75.0 - - - +
191A THR* 1.3 71.9 + - - +
192A VAL* 4.3 6.7 - - + -
205A ILE* 4.1 14.8 - - + -
206A HIS 3.3 11.2 - - - +
207A TYR* 4.1 15.0 - - + -
230A CYS* 3.6 6.7 - - - -
237A CYS* 3.6 20.0 - - + -
239A TRP* 3.5 40.6 - - + -
257A ALA* 4.3 9.6 - - - -
259A GLN 6.2 0.2 - - - -
260A GLY* 4.9 5.2 - - - -
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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* 4.5 2.0 - - + -
158A LEU* 4.1 14.1 - - + -
174A GLU* 3.5 38.3 + - - +
175A ALA* 4.5 1.3 - - - +
181A THR 3.6 4.9 - - - -
182A ALA* 3.9 14.4 - - + -
189A TRP* 4.9 8.0 + - + +
190A MET* 1.3 81.5 - - - +
192A VAL* 1.3 64.7 + - - +
193A GLY 4.2 0.7 - - - -
204A VAL 4.4 0.2 - - - -
205A ILE* 3.1 4.2 - - - +
206A HIS* 2.6 60.0 + - - +
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Residues in contact with VAL 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* 5.3 0.4 - - - -
175A ALA* 5.1 0.2 - - - -
179A SER 4.1 0.3 - - - +
180A ALA* 3.2 6.7 - - - +
181A THR* 3.0 48.2 + - + -
190A MET* 4.3 13.7 - - + -
191A THR* 1.3 81.5 - - - +
193A GLY* 1.3 60.9 + - - +
194A VAL* 4.9 1.8 - - + -
203A ALA* 4.0 19.1 - - + -
204A VAL 3.3 4.5 - - - +
205A ILE* 3.4 38.6 - - + -
225A THR* 4.6 3.0 - - + +
239A TRP* 4.2 20.6 - - + +
241A MET* 4.7 3.8 - - + -
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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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175A ALA* 4.2 11.8 - - - +
176A VAL 3.7 9.2 - - - +
177A ALA* 3.3 22.2 - - - -
179A SER 3.8 0.7 - - - -
180A ALA* 4.2 1.8 - - - -
192A VAL* 1.3 74.3 - - - +
194A VAL* 1.3 63.3 + - - -
195A THR* 4.0 0.3 + - - +
202A VAL 3.6 1.6 - - - +
204A VAL* 2.8 41.0 + - - +
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Residues in contact with VAL 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* 3.2 1.3 - - - -
178A TRP* 2.9 45.9 + - + -
179A SER* 2.8 19.0 + - - +
192A VAL* 4.9 1.3 - - + -
193A GLY* 1.3 72.9 - - - -
195A THR* 1.3 64.8 + - - +
201A ALA* 3.9 7.6 - - + -
202A VAL 3.2 13.0 - - - +
203A ALA* 3.4 24.5 - - + -
223A LEU* 2.6 35.4 - - + +
224A ARG* 4.9 0.4 - - - -
225A THR* 4.4 11.7 - - + -
241A MET* 4.1 12.1 - - + -
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Residues in contact with THR 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 4.6 4.3 + - - -
154A PRO* 5.0 5.0 - - - +
156A ARG 5.1 0.9 + - - -
176A VAL* 3.5 40.9 - - + +
177A ALA* 4.2 2.3 - - - -
178A TRP* 3.3 20.6 + - - +
193A GLY 4.9 1.6 - - - +
194A VAL* 1.3 76.2 - - - +
196A GLY* 1.3 70.5 + - - +
201A ALA* 3.2 4.7 - - - +
202A VAL* 3.0 41.3 + - + +
204A VAL* 5.5 4.0 - - + -
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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