Contacts of the strand formed by residues 207 - 216 (chain A) in PDB entry 6NMY
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 THR 207 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177A ARG* 3.5 2.1 - - - +
178A LEU* 2.6 67.4 + - + +
179A GLN* 4.6 3.7 + - - +
206A SER* 1.3 74.9 - - - +
208A TYR* 1.3 59.1 + - - +
234A CYS* 4.9 5.4 - - + -
235A TRP 3.6 12.6 - - - +
236A ASP* 2.6 22.3 + - - +
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Residues in contact with TYR 208 (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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175A TYR* 4.5 8.5 - + + -
176A LYS* 3.4 26.9 - - - -
177A ARG* 3.4 23.5 - - + +
201A HIS 4.4 2.4 + - - -
202A LEU* 3.5 34.1 - - + -
203A MET* 2.9 54.7 + - - +
206A SER* 4.0 12.1 - - - -
207A THR* 1.3 76.5 - - - +
209A VAL* 1.3 61.6 + - - +
234A CYS* 3.4 2.4 - - - +
235A TRP* 2.9 59.9 + + + +
237A SER* 4.3 11.7 - - - -
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Residues in contact with VAL 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174A VAL 4.1 0.2 - - - +
175A TYR* 3.3 3.8 - - - +
176A LYS* 2.8 71.0 + - - +
177A ARG 4.7 0.4 - - - +
178A LEU* 3.6 21.5 - - + -
182A TRP* 3.7 15.9 - - + -
208A TYR* 1.3 75.2 - - - +
210A ALA* 1.3 62.8 + - - +
232A GLU* 4.6 13.5 - - + +
233A VAL 3.0 7.0 - - - +
234A CYS* 3.5 32.1 - - + -
235A TRP* 3.9 1.8 - - - -
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Residues in contact with ALA 210 (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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139A LEU* 3.9 1.3 - - + +
150A LEU* 4.5 17.9 - - + -
173A VAL* 4.7 2.9 - - + -
174A VAL 3.3 10.1 - - - +
175A TYR* 4.2 6.7 - - + -
182A TRP* 4.6 1.1 - - - -
209A VAL* 1.3 78.1 - - - +
211A ARG* 1.3 62.9 + - - +
232A GLU* 3.1 7.8 - - - -
233A VAL* 2.9 40.6 + - + +
235A TRP* 3.6 22.0 - - + -
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Residues in contact with ARG 211 (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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139A LEU* 4.0 3.8 - - - -
173A VAL* 4.6 2.2 - - - -
174A VAL* 2.9 34.6 + - + +
182A TRP* 3.5 69.9 + - + +
210A ALA* 1.3 77.2 - - - +
212A VAL* 1.3 59.7 + - - +
229A TRP* 3.5 62.7 - - + +
230A SER* 3.8 24.0 - - - +
232A GLU* 4.1 13.3 + - + -
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Residues in contact with VAL 212 (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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136A PRO* 3.7 11.0 - - + +
139A LEU* 4.0 12.3 - - + -
152A TRP* 3.9 46.9 - - + -
171A PHE* 4.1 10.3 - - + -
172A GLU 3.2 14.1 - - - +
173A VAL* 3.6 24.9 - - + -
211A ARG* 1.3 75.8 - - - +
213A ARG* 1.3 65.9 + - - +
229A TRP* 3.9 3.1 - - - -
230A SER* 3.1 41.3 + - - +
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Residues in contact with ARG 213 (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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136A PRO* 3.8 7.9 - - - -
171A PHE* 3.5 2.2 - - - -
172A GLU* 2.9 69.9 + - + +
212A VAL* 1.3 77.2 - - - +
214A THR* 1.3 64.9 + - - +
215A ARG* 5.0 1.4 - - + +
226A PRO* 3.9 31.0 - - + +
227A SER* 3.5 27.5 + - - +
228A LYS 3.6 8.5 - - - +
229A TRP* 3.5 47.4 - - + +
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Residues in contact with THR 214 (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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133A PRO* 3.2 21.4 - - + +
134A PRO 2.8 28.8 + - - +
136A PRO* 3.5 9.8 - - + +
154A VAL* 4.1 11.7 - - + -
169A LEU* 4.6 7.0 - - + -
170A GLU 3.6 6.7 - - - -
171A PHE* 3.4 30.1 - - + -
213A ARG* 1.3 75.2 - - - +
215A ARG* 1.3 64.1 + - - +
226A PRO* 3.8 1.7 - - - +
227A SER* 3.1 33.9 + - - -
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Residues in contact with ARG 215 (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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133A PRO* 4.3 11.2 - - - -
169A LEU* 3.4 5.7 - - - -
170A GLU* 2.5 80.1 + - + +
172A GLU* 3.3 38.0 + - + -
189A LEU* 3.7 13.5 - - - +
213A ARG* 5.0 1.1 - - + +
214A THR* 1.3 78.7 - - - +
216A LEU* 1.3 80.7 + - + +
217A ALA 3.3 0.3 + - - -
218A PRO* 5.4 2.0 - - - +
226A PRO* 3.9 24.4 - - + +
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Residues in contact with LEU 216 (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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131A VAL 5.7 0.9 - - - +
133A PRO* 4.4 6.2 - - + +
168A ASP 4.1 4.3 - - - -
169A LEU* 4.6 5.2 - - - -
170A GLU* 4.0 1.7 - - - +
215A ARG* 1.3 105.5 + - + +
217A ALA* 1.3 67.7 + - - +
218A PRO* 3.9 1.5 - - + +
220A SER* 5.9 0.9 - - - +
222A LEU* 3.6 30.1 - - + +
223A SER* 4.2 12.6 - - - +
224A GLY 3.5 23.6 - - - +
225A ARG 4.2 13.2 - - - +
226A PRO* 4.4 7.9 - - + -
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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