Contacts of the strand formed by residues 189 - 195 (chain A) in PDB entry 3NT2
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 TYR 189 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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178A ILE* 2.5 49.2 + - + -
181A LEU* 3.6 7.4 - - - +
182A HIS* 3.2 38.9 + + + -
188A ASP* 1.3 82.2 - - - +
190A GLU* 1.3 59.7 + - - +
215A ILE* 3.3 29.4 - - + -
216A GLU 3.8 3.4 - - - -
217A THR* 4.1 11.7 - - + +
218A LYS* 4.6 6.1 + - - +
223A ILE* 3.7 23.3 - - + -
307A ILE* 4.5 8.3 - - + +
311A THR* 3.4 22.9 - - + +
327A VAL* 3.9 32.8 - - + +
329A LEU* 5.1 5.6 - - + +
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Residues in contact with GLU 190 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189A TYR* 1.3 76.0 - - - +
191A SER* 1.3 64.9 + - - +
216A GLU* 2.9 16.6 + - + +
217A THR 3.9 12.2 - - - +
218A LYS* 3.2 40.3 + - + +
326A LYS* 3.0 37.1 - - + +
327A VAL* 2.9 27.9 + - - -
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Residues in contact with SER 191 (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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190A GLU* 1.3 83.5 - - - +
192A VAL* 1.3 72.8 + - - +
214A VAL 4.5 0.2 - - - -
215A ILE* 3.3 4.2 - - - +
216A GLU* 3.2 41.8 + - - +
324A LYS* 3.3 33.1 - - - -
325A GLU 3.2 15.0 - - - -
326A LYS* 4.8 2.2 - - - -
327A VAL* 4.3 2.6 - - - +
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Residues in contact with VAL 192 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A SER* 1.3 80.8 - - - +
193A GLN* 1.3 62.4 + - - +
194A VAL* 6.0 0.2 - - + -
213A VAL* 4.9 2.7 - - + -
214A VAL 3.2 7.0 - - - +
215A ILE* 3.6 29.4 - - + -
311A THR* 4.4 3.6 - - + -
314A ALA* 3.5 41.7 - - + +
315A CYS* 3.9 19.1 - - - +
318A ALA* 4.0 4.8 - - + +
323A GLN 3.8 0.7 - - - +
324A LYS* 3.6 3.5 - - - +
325A GLU* 3.0 34.1 + - + +
327A VAL* 4.0 14.4 - - + -
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Residues in contact with GLN 193 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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192A VAL* 1.3 77.4 - - - +
194A VAL* 1.3 72.4 + - - +
195A ILE* 3.8 22.9 - - + +
212A ILE 3.6 0.9 - - - +
213A VAL* 3.4 3.7 - - - +
214A VAL* 2.8 48.9 + - + +
318A ALA* 4.2 1.6 - - - -
322A GLY 5.1 6.6 + - - +
323A GLN 4.0 17.7 - - - +
324A LYS* 4.4 19.9 - - + +
193B GLN* 3.5 36.1 + - - -
195B ILE* 5.0 4.7 - - - +
324B LYS* 6.1 1.2 - - - +
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Residues in contact with VAL 194 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170A VAL* 5.4 0.2 - - + -
193A GLN* 1.3 84.1 + - - +
195A ILE* 1.3 68.0 + - - +
196A TYR* 3.8 36.0 + - + +
211A GLN* 4.0 17.0 - - + +
212A ILE 3.4 7.6 - - - +
213A VAL* 4.3 18.4 - - + -
315A CYS* 3.9 16.6 - - + +
318A ALA* 3.9 31.7 + - + +
319A GLN* 3.9 6.5 - - + +
322A GLY* 4.7 13.5 - - - +
323A GLN 4.6 1.2 + - - -
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Residues in contact with ILE 195 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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193A GLN* 3.8 27.1 - - + +
194A VAL* 1.3 80.2 - - - +
196A TYR* 1.3 64.7 + - - +
197A PRO* 3.3 5.5 - - - +
211A GLN* 4.1 0.3 - - - -
212A ILE* 2.9 47.5 + - + +
214A VAL* 4.4 18.6 - - + -
193B GLN* 5.0 3.8 - - - +
195B ILE* 6.4 0.7 - - + -
214B VAL* 4.0 27.4 - - + -
216B GLU* 4.6 18.8 - - + +
222B VAL* 4.2 25.4 - - + -
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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