Contacts of the strand formed by residues 207 - 216 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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177C ARG* 3.5 3.2 - - - +
178C LEU* 2.7 65.4 + - + +
179C GLN* 4.4 4.6 + - - +
206C SER* 1.3 73.2 - - - +
208C TYR* 1.3 58.7 + - - +
234C CYS* 4.8 6.7 - - + -
235C TRP 3.6 13.5 - - - +
236C ASP* 2.4 22.7 + - - +
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Residues in contact with TYR 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175C TYR* 4.4 8.3 - + - -
176C LYS* 3.4 25.6 - - - -
177C ARG* 3.5 24.5 - - + +
201C HIS 4.4 2.9 + - - -
202C LEU* 3.5 41.4 - - + -
203C MET* 3.0 53.2 + - - +
206C SER* 3.8 12.1 - - - -
207C THR* 1.3 76.2 - - - +
209C VAL* 1.3 61.0 + - - +
234C CYS* 3.4 1.4 - - - +
235C TRP* 2.9 62.2 + + + -
237C SER* 4.4 6.7 - - - -
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Residues in contact with VAL 209 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
174C VAL 4.0 0.2 - - - +
175C TYR* 3.2 4.3 - - - +
176C LYS* 2.8 59.1 + - - +
177C ARG 4.8 0.4 - - - +
178C LEU* 3.6 22.9 - - + -
182C TRP* 3.6 27.7 - - + -
207C THR 4.2 0.2 + - - -
208C TYR* 1.3 76.5 - - - +
210C ALA* 1.3 62.3 + - - +
232C GLU* 4.7 13.7 - - + +
233C VAL 3.1 6.1 - - - +
234C CYS* 3.5 31.9 - - + -
235C TRP* 3.9 0.4 - - - -
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Residues in contact with ALA 210 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C LEU* 3.8 2.0 - - + +
150C LEU* 4.5 12.8 - - + -
173C VAL* 4.6 9.2 - - + -
174C VAL 3.3 9.6 - - - +
175C TYR* 4.2 6.5 - - + -
182C TRP* 4.5 0.9 - - - -
209C VAL* 1.3 78.1 - - - +
211C ARG* 1.3 60.9 + - - +
212C VAL* 5.9 0.2 - - + -
232C GLU* 3.1 7.1 - - - -
233C VAL* 2.9 41.3 + - + +
235C TRP* 3.6 21.8 - - + -
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Residues in contact with ARG 211 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139C LEU* 4.1 2.2 - - - -
173C VAL* 3.6 0.2 - - - -
174C VAL* 2.9 33.0 + - + +
182C TRP* 3.5 68.6 - - + +
210C ALA* 1.3 76.4 - - - +
212C VAL* 1.3 62.6 + - - +
229C TRP* 3.4 63.2 - - + +
230C SER* 3.8 23.1 - - - +
232C GLU* 4.2 11.9 + - + -
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Residues in contact with VAL 212 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C PRO* 3.7 27.0 - - + +
139C LEU* 4.4 10.8 - - + -
150C LEU* 5.3 1.8 - - + -
152C TRP* 4.0 37.2 - - + -
171C PHE* 5.2 1.1 - - + -
172C GLU 3.2 8.7 - - - +
173C VAL* 3.6 34.1 - - + -
210C ALA* 5.9 0.2 - - + -
211C ARG* 1.3 77.7 - - - +
213C ARG* 1.3 63.5 + - - +
229C TRP* 3.6 3.3 - - - -
230C SER* 2.9 43.8 + - - +
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Residues in contact with ARG 213 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C PRO* 3.9 9.6 - - - -
171C PHE* 3.4 5.1 - - - +
172C GLU* 2.9 69.8 + - + +
212C VAL* 1.3 76.2 - - - +
214C THR* 1.3 65.4 + - - +
215C ARG* 4.6 6.0 - - + +
226C PRO* 3.8 30.8 - - - +
227C SER* 3.5 27.4 + - - +
228C LYS 3.6 8.1 - - - +
229C TRP* 3.5 45.0 - - + +
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Residues in contact with THR 214 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C PRO* 3.2 19.0 - - + +
134C PRO 2.7 29.0 + - - +
136C PRO* 3.6 8.2 - - + +
154C VAL* 4.4 9.4 - - + -
169C LEU* 4.9 8.1 - - + -
170C GLU 3.6 6.1 - - - -
171C PHE* 3.3 32.1 - - + -
213C ARG* 1.3 73.3 - - - +
215C ARG* 1.3 63.6 + - - +
226C PRO* 3.6 2.1 - - - +
227C SER* 2.9 40.5 + - - -
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Residues in contact with ARG 215 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C PRO* 4.3 7.6 - - - -
169C LEU* 3.4 5.5 - - - +
170C GLU* 2.9 67.1 + - + +
172C GLU* 3.1 41.9 + - + +
189C LEU* 4.5 12.9 - - - +
213C ARG* 4.6 6.5 - - + +
214C THR* 1.3 78.0 - - - +
216C LEU* 1.3 65.1 + - - +
217C ALA 3.3 0.2 + - - -
226C PRO* 3.8 31.8 - - + +
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Residues in contact with LEU 216 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C VAL* 3.8 31.6 - - + +
133C PRO* 3.9 15.9 - - + +
168C ASP 3.8 3.6 - - - +
169C LEU* 3.9 11.4 - - + -
170C GLU* 4.4 1.7 - - - +
215C ARG* 1.3 82.8 + - - +
217C ALA* 1.3 66.6 + - - +
218C PRO* 3.7 2.4 - - - +
220C SER* 5.1 2.2 - - - +
222C LEU* 3.5 36.1 - - + +
223C SER* 3.4 35.4 - - - +
224C GLY 3.6 9.2 - - - +
225C ARG 4.6 3.6 + - - +
226C PRO* 5.3 0.2 - - - +
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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