Contacts of the strand formed by residues 182 - 192 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A TYR* 3.3 6.9 - - - -
179A LEU 2.6 27.7 + - - +
180A GLN* 2.8 27.6 + - - +
181A ASP* 1.3 77.9 - - - +
183A LYS* 1.3 63.2 + - - +
221A GLN* 3.3 20.8 + - - +
222A GLY* 3.0 25.6 - - - +
223A TRP 2.3 29.9 + - - -
224A ILE* 3.2 42.7 - - + +
228A GLU* 3.5 10.7 + - - +
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Residues in contact with LYS 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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118A ARG* 4.2 1.4 - - - +
121A ARG* 3.8 20.4 - - - +
123A TRP* 4.1 17.0 - - - -
176A ASP* 3.3 30.2 + - - +
177A LEU 3.5 5.4 - - - +
178A TYR* 3.6 23.7 - - + +
182A ARG* 1.3 71.0 - - - +
184A LEU* 1.4 58.7 + - - +
185A ALA 4.0 10.3 - - - +
186A GLY* 4.1 4.5 - - - -
208A ASN* 3.7 3.2 + - - +
222A GLY 2.9 12.1 + - - +
223A TRP* 3.3 38.6 - - + +
224A ILE* 2.9 22.3 + - - +
500A BTN 2.6 30.6 + - - -
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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 LEU* 4.3 15.3 - - + -
169A VAL* 3.4 34.1 - - + -
177A LEU* 2.7 20.3 + - + +
179A LEU* 4.4 12.8 - - + -
182A ARG 3.3 0.8 + - - -
183A LYS* 1.4 72.2 - - - +
185A ALA* 1.3 56.8 + - - +
207A ILE* 4.7 6.3 - - + -
208A ASN* 3.0 57.9 + - - +
224A ILE* 3.6 21.5 - - + +
225A THR 3.8 2.9 - - - +
226A LEU* 3.7 30.3 - - + +
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Residues in contact with ALA 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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123A TRP* 4.8 1.6 - - - -
157A MET* 5.5 3.1 - - - -
176A ASP* 3.6 7.8 - - - +
177A LEU* 3.0 55.6 + - + +
183A LYS* 4.0 7.7 - - - +
184A LEU* 1.3 78.1 - - + +
186A GLY* 1.4 58.6 + - - +
187A ILE* 5.5 1.8 - - + -
205A ALA* 6.2 0.4 - - + -
206A GLY 2.8 15.9 - - - +
207A ILE* 3.9 15.5 - - + -
208A ASN* 4.9 0.9 - - - +
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Residues in contact with GLY 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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123A TRP* 4.1 8.0 - - - -
176A ASP* 3.6 10.5 - - - -
183A LYS* 4.1 0.7 - - - -
185A ALA* 1.4 73.3 - - - +
187A ILE* 1.3 64.7 + - - +
205A ALA* 3.4 1.6 - - - -
206A GLY 2.6 36.8 + - - -
500A BTN 3.4 25.7 - - - +
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Residues in contact with ILE 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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118A ARG* 3.5 8.7 - - - -
150A SER* 5.0 3.4 - - - +
153A ILE* 4.2 13.7 - - + -
154A GLY* 3.9 31.2 - - - +
157A MET* 4.8 6.7 - - - -
174A PRO 5.5 0.2 - - - +
175A ASN* 3.0 62.7 + - - +
176A ASP* 4.2 9.2 - - - +
177A LEU* 5.0 3.8 - - + +
185A ALA* 5.3 2.7 - - + -
186A GLY* 1.3 79.1 - - - +
188A LEU* 1.3 65.6 + - - +
189A VAL* 3.8 16.6 - - + -
203A ILE* 4.4 7.6 - - + -
204A GLY 3.2 10.1 - - - +
205A ALA* 4.7 7.2 - - + -
500A BTN 3.4 4.8 - - - +
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Residues in contact with LEU 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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91A ASN* 3.2 10.3 + - - +
116A ARG* 3.1 51.1 - - + +
117A GLY 3.8 6.5 - - - +
118A ARG* 4.0 27.8 - - + +
187A ILE* 1.3 74.7 - - - +
189A VAL* 1.3 63.3 - - - +
190A GLU* 3.7 26.0 - - + +
203A ILE 3.7 0.2 - - - -
204A GLY 2.6 37.5 + - - +
500A BTN 3.7 23.1 - - + +
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Residues in contact with VAL 189 (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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118A ARG* 5.5 1.0 - - - +
146A ALA* 5.7 5.6 - - + -
149A LEU* 3.8 15.5 - - + -
150A SER* 3.8 22.4 - - - +
175A ASN* 4.0 8.1 - - - +
187A ILE* 3.8 14.5 + - + -
188A LEU* 1.3 82.8 - - - +
190A GLU* 1.3 69.5 + - - +
191A LEU* 4.3 4.8 + - + +
201A ILE* 3.6 27.8 - - + -
202A VAL 3.5 2.5 - - - +
203A ILE* 3.7 19.3 - - + +
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Residues in contact with GLU 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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91A ASN* 2.4 38.0 + - - +
95A LEU* 3.8 25.9 - - + +
116A ARG* 3.4 26.3 + - - -
188A LEU* 3.7 17.4 - - + +
189A VAL* 1.3 82.7 - - - +
191A LEU* 1.3 62.8 + - - +
200A GLN 3.8 1.2 - - - +
201A ILE* 3.6 2.6 - - - +
202A VAL* 2.7 40.3 + - + +
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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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95A LEU* 6.2 1.1 - - - -
143A PRO* 4.1 34.5 - - + +
146A ALA* 5.1 15.7 - - + -
189A VAL* 5.7 5.2 - - + +
190A GLU* 1.3 77.6 - - - +
192A THR* 1.4 73.8 + - - +
193A GLY 4.6 0.9 - - - +
199A ALA* 4.6 2.7 - - + -
200A GLN 3.6 7.0 - - - +
201A ILE* 4.6 13.2 - - + -
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Residues in contact with THR 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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95A LEU* 4.8 13.3 - - - +
98A ILE* 5.1 6.7 - - - +
191A LEU* 1.4 76.3 + - - +
193A GLY* 1.3 67.1 + - - +
199A ALA* 3.2 6.1 - - - +
200A GLN* 2.8 44.6 + - - +
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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