Contacts of the strand formed by residues 182 - 192 (chain B) in PDB entry 1HXD
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 ARG 182 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178B TYR* 3.0 8.4 - - - -
179B LEU 2.6 40.9 + - - +
180B GLN* 3.5 15.0 + - + +
181B ASP* 1.3 80.9 - - + +
183B LYS* 1.4 61.0 + - - +
221B GLN* 2.9 33.8 - - - +
222B GLY* 3.6 21.3 - - - +
223B TRP 2.3 30.4 + - - -
224B ILE* 3.1 39.0 - - + +
228B GLU* 4.0 11.7 + - - +
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Residues in contact with LYS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ARG* 3.0 31.2 - - - +
123B TRP* 4.0 0.4 - - - -
176B ASP* 3.3 33.0 + - - +
177B LEU 3.5 3.1 - - - -
178B TYR* 3.9 23.2 - - + +
182B ARG* 1.4 68.6 - - - +
184B LEU* 1.3 60.4 - - - +
185B ALA 3.9 8.3 - - - +
186B GLY* 3.7 11.7 - - - +
222B GLY 3.0 15.4 + - - +
223B TRP* 3.4 47.7 - - + +
224B ILE* 3.1 22.5 + - - +
501B BTN 2.6 27.1 + - - -
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Residues in contact with LEU 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161B LEU* 4.2 20.9 - - + -
169B VAL* 4.3 13.2 - - + -
177B LEU* 2.7 20.0 + - + +
179B LEU* 4.3 22.0 - - + -
182B ARG 3.4 0.4 + - - -
183B LYS* 1.3 73.7 - - - +
185B ALA* 1.3 58.3 + - + +
207B ILE* 5.3 2.9 - - + -
208B ASN* 3.1 64.4 + - - +
224B ILE* 3.7 23.3 - - + +
225B THR 3.9 2.5 - - - -
226B LEU* 3.8 35.7 - - + +
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Residues in contact with ALA 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B TRP* 4.7 0.2 - - - -
157B MET* 4.2 7.4 - - + -
176B ASP* 3.1 10.8 - - - +
177B LEU* 2.8 49.9 + - + -
183B LYS* 3.7 7.1 - - - -
184B LEU* 1.3 82.4 - - + +
186B GLY* 1.3 57.9 + - - +
187B ILE* 4.3 0.4 - - - -
206B GLY 3.1 17.3 - - - +
207B ILE* 3.9 19.5 - - + -
208B ASN* 4.9 1.6 - - - +
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Residues in contact with GLY 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B TRP* 3.9 6.6 - - - -
176B ASP* 3.7 5.6 - - - -
183B LYS* 3.7 2.7 - - - -
185B ALA* 1.3 74.2 - - - +
187B ILE* 1.4 58.9 + - - -
205B ALA* 3.6 1.4 - - - +
206B GLY 2.9 33.4 + - - +
501B BTN 3.0 37.5 - - - +
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Residues in contact with ILE 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ARG* 2.3 30.7 + - - +
150B SER 4.1 6.5 - - - +
153B ILE* 4.0 20.9 - - + -
154B GLY* 3.6 36.3 - - - +
157B MET* 4.1 20.0 - - + -
174B PRO 5.0 0.4 - - - +
175B ASN* 3.0 45.7 + - - +
176B ASP* 4.6 5.4 - - - +
177B LEU* 4.9 2.0 - - + -
185B ALA 5.1 0.4 - - - +
186B GLY* 1.4 74.9 - - - +
188B LEU* 1.3 59.7 + - - +
189B VAL* 4.2 16.2 - - + -
203B ILE* 5.0 1.8 - - + -
204B GLY 3.4 9.9 - - - +
205B ALA* 5.1 1.3 - - + -
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Residues in contact with LEU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASN* 3.6 10.6 + - - +
116B ARG* 3.6 31.4 - - - +
117B GLY 3.9 2.9 - - - +
118B ARG* 3.7 40.4 - - + +
187B ILE* 1.3 74.1 - - - +
189B VAL* 1.3 61.6 + - - +
190B GLU* 3.6 34.5 - - + +
204B GLY 2.8 30.6 + - - +
501B BTN 3.5 25.5 - - + +
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Residues in contact with VAL 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ARG* 5.5 1.4 - - - +
146B ALA* 5.8 4.5 - - - +
149B LEU* 5.2 7.2 - - + -
150B SER* 4.4 25.6 - - - +
153B ILE* 4.8 1.6 - - + -
175B ASN* 4.7 3.5 + - - +
187B ILE* 3.9 20.2 + - + -
188B LEU* 1.3 78.0 - - - +
190B GLU* 1.4 67.9 + - - +
191B LEU* 4.4 15.4 + - + +
201B ILE* 3.4 26.9 - - + -
202B VAL 3.6 2.5 - - - +
203B ILE* 4.1 18.8 - - + -
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASN* 2.3 37.6 + - - +
95B LEU* 3.9 29.8 - - + +
116B ARG* 3.5 23.2 + - - -
188B LEU* 3.6 18.6 - - + +
189B VAL* 1.4 78.7 - - - +
191B LEU* 1.3 63.4 + - - +
200B GLN 3.5 0.9 - - - +
201B ILE* 3.3 3.5 - - - +
202B VAL* 2.7 45.4 + - + +
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Residues in contact with LEU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 6.1 2.2 - - - -
146B ALA* 4.6 20.9 - - + -
147B ILE* 5.8 2.9 - - + -
189B VAL* 4.7 15.7 - - + +
190B GLU* 1.3 80.1 - - - +
192B THR* 1.3 64.7 + - - +
193B GLY 5.6 0.2 - - - +
199B ALA* 5.8 4.0 - - + -
200B GLN 3.4 6.5 - - - +
201B ILE* 4.8 12.6 - - + -
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Residues in contact with THR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95B LEU* 5.8 9.4 - - + -
98B ILE* 5.6 7.0 - - + -
191B LEU* 1.3 78.8 - - - +
193B GLY* 1.3 63.0 + - - +
199B ALA* 3.5 4.2 - - - +
200B GLN* 3.1 52.0 + - + +
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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