Contacts of the strand formed by residues 193 - 200 (chain F) in PDB entry 1NZB
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 MET 193 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F ILE* 5.2 0.4 - - + -
185F ILE* 3.4 44.4 - - + -
186F SER 3.5 7.2 - - - +
187F ARG* 4.2 23.5 - - - +
191F GLY 3.9 3.0 + - - -
192F ARG* 1.3 76.4 - - - +
194F LEU* 1.3 62.7 + - - +
195F ILE* 4.3 6.5 - - + -
212F ALA* 3.6 1.0 - - - +
213F LEU* 3.2 43.8 + - + -
218F THR* 3.9 28.9 + - - +
221F VAL* 3.1 42.4 - - + -
222F GLU* 4.8 1.6 - - - -
225F ILE* 4.7 6.7 - - - -
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Residues in contact with LEU 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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326A ARG 5.1 3.1 - - - +
327A ASN* 3.5 31.0 - - + -
332A THR* 5.1 1.1 - - + -
184F ASP 3.4 4.3 - - - +
185F ILE* 3.7 1.6 - - - -
186F SER* 2.9 46.9 + - - +
187F ARG 4.3 0.9 - - - -
188F THR* 3.4 35.9 - - + +
192F ARG 4.1 0.9 - - - +
193F MET* 1.3 73.1 - - - +
195F ILE* 1.3 65.0 + - - +
196F HIS 3.7 0.5 + - - -
210F GLU* 4.3 24.5 - - + +
211F LYS 3.5 3.1 - - - +
212F ALA* 3.3 35.7 - - + +
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Residues in contact with ILE 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F ILE* 3.5 36.6 - - + -
170F THR* 5.0 2.5 - - + -
172F LEU* 5.2 1.1 - - + -
180F ILE* 3.4 44.6 - - + -
184F ASP 3.7 4.9 - - - +
185F ILE* 4.7 6.3 - - + -
193F MET* 4.7 11.4 - - + -
194F LEU* 1.3 74.0 - - - +
196F HIS* 1.3 63.9 + - - +
197F ILE* 3.5 16.4 + - + +
210F GLU* 3.7 1.9 - - - +
211F LYS* 2.8 39.8 + - + +
213F LEU* 4.0 26.7 - - + -
238F LEU* 5.3 0.2 - - + -
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Residues in contact with HIS 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A ARG* 3.2 55.6 + - + +
326A ARG* 4.9 1.6 - - - -
180F ILE* 5.6 0.7 - - - +
184F ASP* 3.0 42.5 + - + +
195F ILE* 1.3 72.3 - - - +
197F ILE* 1.3 80.5 + - - +
198F GLY* 3.8 9.5 + - - -
206F THR 5.2 0.4 - - - -
207F ALA 3.4 23.3 + - - -
208F GLY* 4.4 1.1 - - - -
209F VAL 3.8 7.4 - - - -
210F GLU* 3.1 37.4 + - + +
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Residues in contact with ILE 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F LEU* 3.6 39.7 - - + -
176F GLU* 4.1 14.4 - - + +
180F ILE* 4.5 8.7 - - + -
195F ILE* 3.5 35.7 - - + +
196F HIS* 1.3 77.4 - - - +
198F GLY* 1.3 68.7 + - - +
199F ARG 4.7 1.8 - - - +
200F THR* 3.7 26.8 - - + +
208F GLY* 3.5 3.5 - - - -
209F VAL* 3.0 38.4 + - + +
211F LYS* 4.2 11.4 - - + -
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Residues in contact with GLY 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125A VAL* 4.2 14.3 - - - +
196F HIS* 3.8 14.3 + - - -
197F ILE* 1.3 78.1 - - - +
199F ARG* 1.3 61.7 + - - +
200F THR* 3.9 3.1 + - - +
203F LEU* 4.1 8.5 - - - +
205F SER 4.3 10.2 + - - +
208F GLY* 4.2 11.8 - - - -
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Residues in contact with ARG 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A LYS* 3.6 31.4 - - - +
125A VAL* 3.7 20.5 + - + +
126A ASP* 2.9 37.8 + - - +
38F SER* 6.0 1.8 - - - +
176F GLU* 3.9 5.4 - - - +
179F ARG* 3.2 60.1 + - - +
197F ILE* 4.7 1.6 - - - +
198F GLY* 1.3 73.1 - - - +
200F THR* 1.3 73.9 + - - +
203F LEU 3.4 11.2 - - - +
204F VAL* 3.6 23.3 - - + -
124H A 4.6 13.8 + - - -
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Residues in contact with THR 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172F LEU* 5.1 1.8 - - + -
173F ARG* 4.0 5.2 - - - -
176F GLU* 3.6 22.7 - - - +
179F ARG* 5.2 2.5 - - - -
197F ILE* 3.7 28.9 - - + -
198F GLY 3.9 3.8 + - - +
199F ARG* 1.3 87.5 - - - +
201F LYS* 1.3 66.4 + - - +
202F THR* 3.8 3.5 + - - -
203F LEU* 2.9 34.1 + - + +
209F VAL* 5.4 8.1 - - + -
124H A 4.1 5.8 + - - -
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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