Contacts of the strand formed by residues 203 - 212 (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 LEU 203 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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198F GLY 4.1 5.6 - - - +
199F ARG* 3.4 2.9 - - - +
200F THR* 2.9 43.1 + - + +
201F LYS 3.6 2.6 + - - -
202F THR* 1.3 82.9 - - - +
204F VAL* 1.3 63.3 + - - +
205F SER* 4.0 19.7 - - - +
208F GLY* 4.4 20.0 - - - +
209F VAL* 5.4 4.9 - - + +
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Residues in contact with VAL 204 (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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121A ARG* 3.0 37.9 + - - +
122A LYS* 4.0 22.0 - - + -
125A VAL* 3.6 24.0 - - + -
199F ARG* 3.6 31.6 - - + -
203F LEU* 1.3 77.7 - - - +
205F SER* 1.3 60.2 + - - +
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Residues in contact with SER 205 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A ARG* 5.1 5.6 - - - +
125A VAL* 3.5 27.4 - - - +
129A GLU 4.7 1.6 - - - +
198F GLY* 4.3 9.8 + - - +
203F LEU* 4.0 15.3 - - - +
204F VAL* 1.3 78.1 - - - +
206F THR* 1.3 64.3 + - - +
207F ALA* 3.5 14.7 + - - +
208F GLY 3.6 13.7 + - - -
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Residues in contact with THR 206 (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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85A VAL* 4.3 16.6 - - + -
86A LYS* 5.3 9.7 - - + +
121A ARG* 6.6 0.2 - - + -
125A VAL* 5.1 4.0 - - + -
129A GLU* 3.2 44.6 - - + +
130A ARG* 3.3 11.1 - - - +
131A ALA* 2.8 40.4 + - - +
114D A 5.5 2.4 + - - +
196F HIS* 5.2 0.4 - - - -
205F SER* 1.3 74.9 - - - +
207F ALA* 1.3 62.6 + - - +
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Residues in contact with ALA 207 (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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131A ALA* 4.7 8.5 - - + -
323A ASN* 5.0 14.3 + - - +
326A ARG* 3.8 7.9 + - - +
196F HIS* 3.4 15.9 + - - -
205F SER* 3.3 8.1 + - - +
206F THR* 1.3 82.5 + - - +
208F GLY* 1.3 72.5 + - - +
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Residues in contact with GLY 208 (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* 3.2 16.5 + - - -
196F HIS* 4.4 4.3 - - - -
197F ILE 3.5 13.7 - - - -
198F GLY* 4.2 11.0 - - - -
203F LEU* 4.4 14.7 - - - +
205F SER* 3.6 9.8 + - - -
206F THR 3.8 0.6 - - - -
207F ALA* 1.3 90.7 - - - +
209F VAL* 1.3 61.3 + - - -
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Residues in contact with VAL 209 (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* 4.0 9.9 - - - +
196F HIS* 3.8 3.2 - - - -
197F ILE* 3.0 42.7 + - + +
200F THR* 5.4 7.4 - - + -
203F LEU* 5.9 5.4 - - + -
208F GLY* 1.3 76.0 - - - +
210F GLU* 1.3 85.0 + - - +
211F LYS* 4.0 21.3 + - - +
311F GLN* 5.9 4.5 - - - +
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Residues in contact with GLU 210 (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* 3.3 12.6 + - - -
326A ARG* 3.5 46.4 + - + +
327A ASN* 5.8 1.6 - - + +
186F SER* 5.3 2.9 + - - -
194F LEU* 4.3 28.6 - - + +
195F ILE 3.7 2.5 - - - +
196F HIS* 3.1 48.7 + - - +
209F VAL* 1.3 87.3 - - - +
211F LYS* 1.3 61.0 + - - +
212F ALA* 4.0 2.1 + - - +
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Residues in contact with LYS 211 (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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170F THR* 3.2 50.5 - - + +
171F LEU 5.6 0.2 - - - -
172F LEU* 4.3 12.6 - - + +
194F LEU* 3.5 2.1 - - - -
195F ILE* 2.8 48.2 + - + +
197F ILE* 4.2 19.5 - - + -
209F VAL* 4.0 22.0 + - + +
210F GLU* 1.3 73.7 - - - +
212F ALA* 1.3 63.0 + - - +
213F LEU* 4.0 1.4 + - - +
311F GLN 4.1 10.5 + - - -
312F ALA* 3.4 19.0 + - - +
313F GLY 5.0 1.7 - - - -
314F GLY* 4.7 7.9 - - - +
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Residues in contact with ALA 212 (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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332A THR* 3.7 40.9 + - + +
336A VAL* 3.5 12.9 - - + +
169F ASN* 3.9 9.7 + - - +
170F THR* 4.8 1.6 - - - +
188F THR* 5.2 0.2 - - + -
192F ARG* 5.6 0.4 - - + -
193F MET 3.6 2.5 - - - +
194F LEU* 3.3 26.2 - - + -
210F GLU 4.0 2.6 + - - +
211F LYS* 1.3 75.6 - - - +
213F LEU* 1.3 68.5 + - - +
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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