Contacts of the strand formed by residues 194 - 199 (chain B) 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 194 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B ASP 3.4 7.3 - - - +
186B SER* 2.9 39.6 + - - +
187B ARG 4.6 3.4 - - - -
188B THR* 3.2 33.2 - - + +
192B ARG 4.1 1.8 - - - +
193B MET* 1.3 86.6 - - - +
195B ILE* 1.3 65.9 + - - +
196B HIS* 3.2 3.3 + - - +
210B GLU* 3.3 34.8 - - + +
211B LYS 3.8 3.6 - - - -
212B ALA* 3.5 17.5 - - + -
326E ARG 4.3 3.1 - - - +
327E ASN* 3.8 32.5 - - + -
332E THR* 5.8 0.2 - - + -
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Residues in contact with ILE 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166B ILE* 3.7 35.0 - - + -
170B THR* 4.6 3.4 - - + -
172B LEU* 5.1 1.3 - - + -
180B ILE* 3.5 42.4 - - + -
184B ASP* 3.6 8.5 - - + +
185B ILE* 4.5 16.1 - - + +
193B MET* 5.0 5.2 - - + -
194B LEU* 1.3 70.2 - - - +
196B HIS* 1.3 63.0 + - - +
197B ILE* 3.8 13.7 + - + +
210B GLU* 3.2 1.4 - - - +
211B LYS* 3.0 38.4 + - + +
213B LEU* 3.8 28.9 - - + -
238B LEU* 5.5 0.2 - - + -
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Residues in contact with HIS 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B ILE* 5.7 1.2 - - - +
184B ASP* 2.9 38.7 + - + +
194B LEU 4.3 0.4 - - - +
195B ILE* 1.3 74.1 - - - +
197B ILE* 1.3 80.7 + - - +
198B GLY* 4.0 11.0 + - - -
206B THR 5.3 1.3 - - - -
207B ALA 3.8 21.1 + - - -
208B GLY* 4.2 0.6 - - - -
209B VAL 3.9 7.6 - - - -
210B GLU* 3.0 35.9 - - + +
130E ARG* 3.5 54.1 + - + +
326E ARG* 5.6 2.9 - - - -
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Residues in contact with ILE 197 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B LEU* 3.4 44.2 - - + -
176B GLU* 4.6 11.7 - - + +
180B ILE* 4.4 12.1 - - + -
195B ILE* 4.1 19.5 - - + +
196B HIS* 1.3 83.9 - - - +
198B GLY* 1.3 62.3 + - - +
199B ARG 4.0 10.3 - - - +
200B THR* 3.9 27.3 - - + +
208B GLY* 3.3 4.0 - - - -
209B VAL* 3.1 40.4 + - + +
211B LYS* 4.5 8.5 - - + -
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Residues in contact with GLY 198 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
196B HIS* 4.0 16.3 + - - -
197B ILE* 1.3 76.2 - - - +
199B ARG* 1.3 62.2 + - - +
200B THR* 4.4 1.1 + - - -
203B LEU* 4.8 3.3 - - - +
204B VAL* 4.6 0.5 - - - -
205B SER 3.1 31.9 + - - +
206B THR 6.3 0.2 - - - -
208B GLY* 4.3 7.4 - - - -
125E VAL* 4.4 7.2 - - - -
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Residues in contact with ARG 199 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B SER* 6.0 0.8 - - - -
176B GLU* 4.5 2.8 - - - +
179B ARG* 3.0 61.1 + - - +
197B ILE* 4.0 7.6 - - - +
198B GLY* 1.3 79.0 - - - +
200B THR* 1.3 76.8 + - - +
203B LEU 3.8 4.7 - - - +
204B VAL* 3.5 33.4 - - + -
124D A 4.4 14.9 + - - -
122E LYS* 3.3 29.9 - - - +
125E VAL* 3.9 11.0 + - + +
126E ASP* 3.0 40.8 + - - +
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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
------------------------------------------------------------
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