Contacts of the strand formed by residues 268 - 276 (chain F) 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 TYR 268 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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215F ALA* 4.8 2.3 - - - +
217F CYS* 4.4 4.8 - - - +
222F SER* 3.0 21.4 + - - -
224F MET* 3.6 22.6 - - + +
242F ILE* 3.8 24.7 - - + -
243F GLN 3.4 11.2 - - - +
244F LYS* 4.2 11.9 - - + -
262F LEU* 3.9 14.6 - - + -
265F PRO* 3.5 36.3 - - + +
266F GLY 4.3 0.2 - - - -
267F THR* 1.3 73.7 - - - +
269F THR* 1.3 61.1 + - - +
270F VAL* 3.9 28.3 - - + -
289F GLN 3.9 0.3 - - - +
290F ARG* 3.7 2.6 - - - +
291F PHE* 2.9 57.7 + + + +
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Residues in contact with THR 269 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241F GLN 3.8 0.9 - - - +
242F ILE* 3.8 0.9 - - - -
243F GLN* 2.9 56.9 + - + +
268F TYR* 1.3 74.8 - - - +
270F VAL* 1.3 62.9 + - - +
271F GLN* 5.6 0.2 - - - +
288F PRO* 3.8 20.6 - - - +
289F GLN 3.2 13.3 + - - -
290F ARG* 4.3 17.2 + - - +
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Residues in contact with VAL 270 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F MET* 3.7 33.4 - - + +
224F MET* 4.3 8.3 - - - -
240F LEU* 4.3 4.9 - - + -
241F GLN 3.3 4.3 - - - +
242F ILE* 3.7 23.3 - - + -
268F TYR* 3.9 23.3 - - + -
269F THR* 1.3 76.2 + - - +
271F GLN* 1.3 75.1 + - - +
287F THR 4.4 0.2 - - - +
288F PRO* 3.5 3.1 - - - +
289F GLN* 2.9 37.2 + - + +
291F PHE* 3.9 13.7 - - + -
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Residues in contact with GLN 271 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213F MET* 4.4 0.9 - - - -
240F LEU* 3.5 4.0 - - - -
241F GLN* 2.9 55.1 + - + +
269F THR* 5.6 0.2 - - - +
270F VAL* 1.3 83.1 - - - +
272F ILE* 1.3 62.1 + - - +
285F TRP* 3.6 26.8 - - + +
286F SER* 3.4 27.2 - - - +
288F PRO* 3.4 31.9 - - + +
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Residues in contact with ILE 272 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F PRO* 3.7 28.8 - - + +
213F MET* 3.9 17.9 - - + -
226F TRP* 3.3 54.1 - - + +
238F TYR* 4.4 4.9 - - + -
239F GLU 3.2 12.8 - - - +
240F LEU* 3.6 13.7 - - + -
271F GLN* 1.3 75.7 - - - +
273F ARG* 1.3 68.9 + - - +
284F ALA 4.1 0.9 - - - +
285F TRP* 3.5 3.1 - - - -
286F SER* 2.9 44.9 + - - +
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Residues in contact with ARG 273 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211F PRO* 4.5 2.5 - - - -
238F TYR* 3.3 7.1 - - - +
239F GLU* 2.9 70.9 + - + +
272F ILE* 1.3 78.0 - - - +
274F ALA* 1.3 68.3 + - - +
275F ARG* 3.7 8.3 - - - +
282F LEU* 3.4 24.5 - - - +
283F SER* 3.2 32.8 - - - +
284F ALA 4.3 1.8 - - - +
285F TRP* 3.2 52.5 - - + +
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Residues in contact with ALA 274 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F LEU* 5.1 0.9 - - + -
211F PRO* 4.2 3.1 - - + +
228F MET* 3.8 32.8 - - + -
236F PHE* 4.4 5.4 - - + -
237F ARG 3.8 3.1 - - - -
238F TYR* 3.9 19.5 - - + -
273F ARG* 1.3 79.8 - - - +
275F ARG* 1.3 61.5 + - - +
281F PHE 3.8 0.8 - - - +
282F LEU* 3.4 4.9 - - - +
283F SER* 3.0 38.5 + - - +
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Residues in contact with ARG 275 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236F PHE* 3.4 5.4 - - - -
237F ARG* 2.9 51.2 + - + +
239F GLU* 2.6 31.9 + - - +
253F GLN* 3.7 15.0 - - - +
273F ARG* 3.7 5.5 - - - +
274F ALA* 1.3 75.1 - - - +
276F GLU* 1.3 74.5 + - - +
280F GLU* 3.8 37.3 + - - -
281F PHE 3.2 4.7 - - - +
282F LEU* 3.3 32.8 - - + +
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Residues in contact with GLU 276 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208F LEU* 4.3 3.8 - - + -
233F ASN* 3.8 21.1 - - + +
235F LYS 4.2 5.1 - - - +
236F PHE* 3.9 9.4 - - + -
275F ARG* 1.3 76.8 - - - +
277F ARG* 1.3 77.1 + - - +
278F VAL* 2.9 13.7 + - - +
279F TYR* 2.5 38.1 + - - +
280F GLU* 3.1 20.1 + - - +
281F PHE* 2.7 37.8 + - + +
116J LYS* 2.5 42.2 + - - +
119J GLU* 4.1 3.5 - - - +
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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