Contacts of the strand formed by residues 171 - 178 (chain D) in PDB entry 1XV2
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 GLY 171 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158D PHE 3.5 1.2 - - - +
159D PHE* 3.3 28.5 - - - -
160D THR 2.9 33.4 + - - -
169D SER 3.2 6.5 - - - +
170D ALA* 1.3 75.1 - - - +
172D PHE* 1.3 61.4 + - - -
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Residues in contact with PHE 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96D PHE* 3.5 70.0 - + + -
99D ILE* 3.5 41.7 - - + -
100D LYS* 3.9 14.1 - - + -
103D MSE 5.5 0.7 - - - -
112D VAL* 4.3 18.6 - - + -
158D PHE 3.6 6.7 - - - -
159D PHE* 3.8 36.6 - + + -
169D SER* 4.9 5.7 + - - -
170D ALA 4.0 1.1 + - - +
171D GLY* 1.3 71.7 - - - -
173D HIS* 1.3 60.0 + - - +
174D ILE* 3.8 7.6 - - + +
234D GLU* 3.6 16.8 - - - +
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Residues in contact with HIS 173 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 4.9 10.9 - - + +
36D ILE* 3.4 28.5 - - + +
73D TYR* 4.6 23.1 + + - -
157D GLY* 3.2 2.9 - - - -
158D PHE* 3.0 34.9 + - + +
160D THR* 6.0 1.6 - - - +
169D SER* 4.4 25.6 + - - +
172D PHE* 1.3 73.6 - - - +
174D ILE* 1.3 62.4 + - - +
175D HIS* 3.4 5.5 + + - -
186D HIS* 3.4 17.2 + + - -
234D GLU* 4.7 4.7 - - - -
804D ZN 2.2 35.8 - - - -
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Residues in contact with ILE 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ILE* 4.9 0.4 - - - -
92D GLN* 5.0 1.3 - - - +
96D PHE* 3.6 34.1 - - + -
112D VAL* 4.0 14.4 - - + -
114D ILE* 5.9 0.9 - - + -
155D ILE* 3.5 25.6 - - + -
156D VAL 3.3 4.0 - - - +
157D GLY* 3.5 17.0 - - - +
158D PHE 4.4 0.4 - - - +
172D PHE* 3.8 17.0 - - + +
173D HIS* 1.3 85.4 - - - +
175D HIS* 1.3 66.7 + - - +
186D HIS* 3.9 3.8 + - - -
187D VAL* 2.8 61.5 + - + +
190D PHE* 5.1 2.2 - - + -
234D GLU* 5.1 3.4 - - - +
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Residues in contact with HIS 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36D ILE* 3.4 25.1 - - + +
37D ALA 3.6 14.4 - - - -
45D GLU* 3.2 22.0 + - + +
46D VAL 2.9 27.4 + - - -
47D ILE* 3.9 16.0 - - + +
155D ILE* 3.3 6.6 - - - +
156D VAL* 2.8 33.5 + - - +
173D HIS* 3.4 3.4 + + - -
174D ILE* 1.3 87.7 - - - +
176D PHE* 1.3 61.2 - - - +
185D GLY 3.1 10.8 - - - +
186D HIS* 3.5 9.4 - - - -
187D VAL* 4.2 2.2 - - - +
804D ZN 2.3 34.4 - - - -
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Residues in contact with PHE 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ILE* 3.7 9.7 - - - +
118D PHE* 3.8 15.5 - + - -
121D MSE 3.5 47.6 - - + -
151D ILE* 4.1 9.9 - - + -
152D ARG 4.2 0.7 - - - -
153D GLY* 3.7 11.2 - - - -
154D ALA 3.4 36.1 - - - -
155D ILE* 3.8 13.7 - - + -
175D HIS* 1.3 74.9 - - - +
177D ALA* 1.3 61.3 + - - +
178D ASP* 3.5 37.0 - - + -
183D TYR* 3.9 16.8 - + - -
184D GLY* 3.1 11.8 - - - -
185D GLY 2.8 29.1 + - - +
187D VAL* 4.9 2.0 - - + -
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Residues in contact with ALA 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47D ILE* 4.2 12.8 - - + +
49D LEU* 4.0 22.6 - - + +
54D TYR* 4.8 3.4 - - + -
62D PHE* 3.9 20.0 - - + -
153D GLY* 3.5 0.2 - - - -
154D ALA 3.0 28.5 + - - -
176D PHE* 1.3 81.4 - - - +
178D ASP* 1.3 63.1 + - - +
181D ARG* 3.8 9.3 + - - +
183D TYR 3.6 6.7 - - - -
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Residues in contact with ASP 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148D ARG* 4.5 3.3 + - - -
151D ILE* 3.8 24.2 - - + +
152D ARG 3.4 15.0 - - - +
176D PHE* 3.5 6.8 - - + -
177D ALA* 1.3 73.3 - - - +
179D ASP* 1.3 54.9 + - - +
180D GLU* 3.0 26.5 - - + +
181D ARG* 2.7 55.3 + - - -
182D ALA 2.9 10.6 + - - -
183D TYR* 3.1 30.5 + - - +
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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