Contacts of the strand formed by residues 182 - 188 (chain A) in PDB entry 1Z6T
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 VAL 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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113A VAL* 4.3 10.8 + - + +
114A LEU* 3.5 26.7 - - + -
117A GLY* 3.1 17.8 + - - -
119A VAL* 3.7 17.9 - - + -
168A VAL* 4.1 17.0 - - + -
174A LEU* 3.6 26.5 - - + -
178A PHE* 4.8 1.8 - - + -
181A GLY* 1.3 80.3 - - - +
183A HIS* 1.3 69.5 + - - +
239A LEU* 3.1 18.2 - - + +
241A ILE* 4.5 9.6 - - + -
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Residues in contact with HIS 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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116A GLU* 4.5 7.2 + - - +
117A GLY* 3.6 16.4 + - - +
180A GLY 4.6 9.6 - - - -
181A GLY* 5.5 0.4 - - - -
182A VAL* 1.3 83.7 + - - +
184A TRP* 1.3 62.0 + - - +
185A VAL 3.9 0.2 + - - -
202A LEU* 4.8 4.0 - - + -
205A ARG* 4.6 18.1 + - + +
206A LEU* 3.5 25.2 - - + +
231A MET* 5.5 0.8 - - - +
235A HIS* 3.5 38.9 - + + +
238A SER* 5.0 4.2 + - - -
239A LEU 2.9 9.1 + - - -
240A LEU* 3.6 23.2 - - + +
241A ILE* 2.8 27.5 + - - +
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Residues in contact with TRP 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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117A GLY 2.9 9.6 + - - +
118A GLY 3.4 27.4 - - - +
119A VAL* 3.8 15.2 - - + +
120A PRO* 3.4 35.1 - - + +
161A SER* 3.5 28.9 - - - -
164A ALA* 4.1 6.3 - - + -
165A ALA* 3.9 18.4 - - + -
183A HIS* 1.3 72.9 - - - +
185A VAL* 1.3 62.6 + - - +
186A SER* 3.9 13.0 + - - +
205A ARG* 2.6 31.0 + - - -
241A ILE* 3.5 38.1 - - + -
243A ASP* 3.8 37.0 + - + +
263A THR* 6.0 0.4 - - + -
394A LYS* 4.5 7.0 - - - +
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Residues in contact with VAL 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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183A HIS 4.3 6.1 - - - +
184A TRP* 1.3 78.9 - - - +
186A SER* 1.3 63.0 + - - +
187A VAL* 3.6 14.6 + - + +
198A LYS* 5.0 13.7 - - + +
202A LEU* 3.8 42.2 - - + -
205A ARG* 4.0 6.7 - - - +
240A LEU* 4.3 5.2 - - + -
241A ILE 2.6 12.2 + - - +
242A LEU* 3.5 27.8 - - + -
243A ASP* 2.7 33.1 + - - +
254A PHE* 4.7 5.6 - - + -
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Residues in contact with SER 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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184A TRP* 3.9 9.5 + - - -
185A VAL* 1.3 74.3 - - - +
187A VAL* 1.3 60.8 + - - +
198A LYS* 2.9 36.5 + - - +
205A ARG* 5.2 0.2 - - - +
243A ASP* 4.2 16.0 + - - -
392A ASP* 4.4 15.8 + - - -
394A LYS* 4.1 30.6 + - - -
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Residues in contact with VAL 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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185A VAL* 3.8 25.6 - - + +
186A SER* 1.3 76.6 + - - +
188A GLY* 1.3 66.2 + - - +
190A GLN* 2.8 40.1 + - + +
195A LEU* 4.6 8.1 - - + -
198A LYS* 3.9 5.4 - - + +
242A LEU* 4.2 20.2 - - + -
243A ASP 3.0 15.5 + - - +
244A ASP 3.9 5.6 - - - +
245A VAL* 4.6 7.9 - - + -
246A TRP 5.7 0.2 - - - +
250A VAL* 4.0 24.7 - - + -
254A PHE* 4.7 7.4 - - + -
392A ASP* 3.6 8.9 - - - +
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Residues in contact with GLY 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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187A VAL* 1.3 88.3 - - - +
189A LYS* 1.3 65.7 + - - -
190A GLN* 3.3 3.8 + - - +
243A ASP 3.4 3.0 + - - -
244A ASP* 2.9 36.9 + - - +
246A TRP* 3.6 6.8 + - - +
250A VAL* 5.7 1.6 - - - +
392A ASP* 3.2 21.1 + - - -
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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