Contacts of the strand formed by residues 191 - 198 (chain A) in PDB entry 1N8Z
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 191 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149A LYS 3.7 7.5 - - - +
150A VAL* 3.5 1.9 - - - -
151A ASP* 2.6 50.2 + - + +
152A ASN* 4.3 19.7 - - - +
190A LYS* 1.3 83.6 - - + +
192A TYR* 1.3 64.2 + - - +
193A ALA* 5.1 3.6 - - + +
208A SER* 4.8 10.8 - - - +
209A PHE 3.8 3.6 - - - +
210A ASN* 3.9 17.5 - - - +
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Residues in contact with TYR 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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117A ILE* 4.6 2.4 - - - +
132A VAL* 4.0 24.7 - - + -
148A TRP* 5.5 1.8 - + + -
150A VAL* 3.6 37.1 - - + +
179A LEU* 4.6 2.7 - - + -
181A LEU* 4.2 10.1 - - + +
185A ASP 4.2 0.3 + - - -
186A TYR* 2.6 59.2 + + - -
189A HIS* 3.3 27.1 - - - +
190A LYS 3.3 11.0 - - - -
191A VAL* 1.3 72.3 - - - +
193A ALA* 1.3 61.0 + - - +
208A SER* 2.8 6.0 - - - -
209A PHE* 2.7 70.4 + + + +
211A ARG* 4.3 2.2 - - + -
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Residues in contact with ALA 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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117A ILE* 5.1 0.4 - - - -
148A TRP* 3.2 16.0 - - - -
149A LYS* 2.8 56.7 + - + +
150A VAL* 4.6 0.6 - - - +
152A ASN* 6.0 1.3 - - - +
191A VAL* 5.1 4.7 - - + -
192A TYR* 1.3 75.0 - - - +
194A CYS* 1.3 61.6 + - - +
195A GLU* 6.2 0.2 - - + -
206A THR* 4.0 11.7 - - - +
207A LYS 3.2 3.6 - - - -
208A SER* 3.6 13.9 - - - +
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Residues in contact with CYS 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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115A VAL* 4.8 0.9 - - - -
117A ILE* 4.0 6.3 - - + -
134A CYS* 2.0 53.8 - - + -
146A VAL* 3.7 18.2 - - - -
147A GLN 3.7 2.9 - - - -
148A TRP* 3.8 12.8 - - + -
193A ALA* 1.3 75.4 - - - +
195A GLU* 1.3 60.0 + - - +
196A VAL* 4.2 6.6 - - - +
205A VAL 3.7 2.1 - - - +
206A THR* 3.4 2.0 - - - -
207A LYS* 2.5 47.0 + - + +
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Residues in contact with GLU 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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145A LYS 3.6 1.6 - - - +
146A VAL* 3.5 3.3 - - - -
147A GLN* 2.6 71.7 + - + +
149A LYS* 3.6 29.8 + - + +
193A ALA 4.1 0.4 - - - -
194A CYS* 1.3 72.8 - - - +
196A VAL* 1.3 61.1 + - - +
197A THR* 5.0 3.1 + - - -
204A PRO* 4.4 17.8 - - + +
205A VAL 3.5 7.4 - - - +
206A THR* 3.8 24.6 - - - +
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Residues in contact with VAL 196 (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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113A PRO* 5.6 0.7 - - + -
115A VAL* 3.8 39.5 - - + -
134A CYS* 4.6 0.2 - - - -
136A LEU* 3.2 34.8 - - + -
144A ALA* 4.4 3.6 - - + -
145A LYS 3.0 17.7 - - - +
146A VAL* 3.8 10.5 - - + -
194A CYS* 4.2 11.0 - - - -
195A GLU* 1.3 75.7 - - - +
197A THR* 1.3 67.3 + - - +
198A HIS* 4.2 1.6 - - + -
201A LEU* 4.1 10.0 - - + +
204A PRO* 3.4 2.9 - - - +
205A VAL* 2.8 38.2 + - - +
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Residues in contact with THR 197 (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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144A ALA* 3.7 2.8 - - - +
145A LYS* 3.1 65.2 + - - +
147A GLN* 5.0 0.5 + - - -
195A GLU* 4.2 5.0 + - - -
196A VAL* 1.3 75.0 - - - +
198A HIS* 1.3 69.6 + - - +
201A LEU* 6.0 0.7 - - + +
204A PRO* 3.5 37.3 - - + +
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Residues in contact with HIS 198 (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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111A ALA 3.3 15.3 - - - -
113A PRO* 3.6 25.4 - - + +
139A PHE* 3.5 15.3 - + - -
140A TYR 3.1 24.9 + - - -
141A PRO* 2.9 32.4 + - + +
143A GLU 3.6 16.8 - - - -
144A ALA* 4.1 8.3 - - + -
196A VAL* 4.2 2.2 + - + -
197A THR* 1.3 83.2 - - - +
199A GLN* 1.3 56.8 + - + +
200A GLY* 2.7 43.3 + - - -
201A LEU* 3.1 27.3 + - + +
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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