Contacts of the strand formed by residues 199 - 205 (chain A) in PDB entry 3NYN
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 GLU 199 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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191A VAL* 3.7 32.4 - - + +
193A GLY 3.6 7.4 - - - +
194A LYS* 4.8 1.3 - - + +
198A GLY* 1.3 77.5 - - - -
200A VAL* 1.3 65.0 - - - +
201A CYS* 4.1 2.0 - - + +
216A LYS* 2.9 53.4 + - + +
218A GLU* 5.2 10.7 + - - +
482A GLN* 5.1 8.5 + - - -
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Residues in contact with VAL 200 (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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191A VAL* 4.4 0.4 - - - -
192A LEU* 2.6 34.8 + - + +
193A GLY 3.1 8.7 + - - +
195A GLY* 4.6 15.9 - - - +
198A GLY 4.7 0.2 - - - +
199A GLU* 1.3 81.9 - - - +
201A CYS* 1.3 55.3 + - - +
213A ALA* 4.9 7.9 - - + -
214A CYS 3.5 9.9 - - - +
215A LYS* 3.8 27.8 - - + -
329A ASP* 6.0 0.2 - - - +
577A SGV 3.5 56.5 - - + +
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Residues in contact with CYS 201 (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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188A GLN* 3.3 28.5 - - - -
189A TYR 3.5 11.9 - - - +
190A ARG 3.3 17.0 - - - +
191A VAL* 3.6 14.4 - - + +
192A LEU* 3.7 6.1 - - - +
199A GLU* 4.1 1.8 - - + -
200A VAL* 1.3 73.7 - - - +
202A ALA* 1.3 69.6 + - - +
213A ALA* 3.6 0.6 - - - -
214A CYS* 2.7 41.9 + - - -
216A LYS* 4.1 14.4 - - - -
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Residues in contact with ALA 202 (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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12A LEU* 3.8 29.8 - - + -
189A TYR* 3.1 32.5 + - + -
190A ARG 3.4 5.6 + - - +
192A LEU* 3.2 21.1 - - + +
201A CYS* 1.3 82.9 - - - +
203A CYS* 1.3 61.7 + - - +
211A MET* 5.9 0.9 - - + -
212A TYR 3.7 7.2 - - - +
265A LEU* 4.4 11.9 - - + -
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Residues in contact with CYS 203 (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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186A PHE* 4.6 12.8 - - + -
187A ARG 3.1 15.7 - - - +
188A GLN* 4.0 17.0 - - - +
189A TYR* 3.8 4.2 - - - -
202A ALA* 1.3 78.1 - - - +
204A GLN* 1.3 62.6 + - - +
211A MET* 3.0 11.8 - - - +
212A TYR* 2.8 60.8 + - - +
213A ALA 4.2 0.4 - - - -
214A CYS* 3.9 20.6 - - + -
262A VAL* 4.3 8.1 - - - -
265A LEU* 5.4 0.2 - - - +
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Residues in contact with GLN 204 (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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15A ALA* 4.3 12.4 + - - +
19A GLY* 5.3 1.7 - - - -
25A GLY* 3.6 21.3 - - - -
186A PHE* 3.0 8.9 - - - -
187A ARG* 2.7 63.6 + - + +
189A TYR* 2.7 31.1 + - + -
203A CYS* 1.3 72.7 - - - +
205A VAL* 1.3 65.7 + - - +
206A ARG 3.3 0.2 + - - -
209A GLY* 3.0 31.6 + - - +
210A LYS 3.4 4.3 - - - +
211A MET* 3.1 26.8 - - + +
212A TYR* 5.8 0.2 - - - -
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Residues in contact with VAL 205 (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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185A THR* 3.8 17.3 - - + +
186A PHE* 4.0 15.7 - - + -
204A GLN* 1.3 71.6 - - - +
206A ARG* 1.3 59.8 + - - +
207A ALA* 3.9 6.3 - - + +
208A THR* 3.4 32.5 - - + +
209A GLY* 2.7 33.1 + - - -
210A LYS 3.0 6.9 + - - +
212A TYR* 3.7 27.6 - - + -
251A TYR* 4.0 11.4 - - - +
514A GLU* 3.4 18.8 - - - +
515A MET* 5.8 0.4 - - + -
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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