Contacts of the strand formed by residues 236 - 244 (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 PHE 236 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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208F LEU* 3.8 21.5 - - + -
228F MET* 3.5 49.1 - - + -
230F SER* 3.9 9.2 - - - -
233F ASN* 3.1 46.2 - - + -
234F ARG 3.8 10.9 + - - -
235F LYS* 1.3 77.5 - - - +
237F ARG* 1.3 65.7 + - - +
238F TYR* 3.7 26.2 - - + +
256F ASP* 3.6 25.5 + - - +
274F ALA* 4.4 4.0 - - + -
275F ARG 3.4 17.5 - - - +
276F GLU* 3.9 6.7 - - - -
277F ARG* 4.6 4.9 - - - +
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Residues in contact with ARG 237 (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* 1.3 74.6 + - - +
238F TYR* 1.3 64.4 + - - +
253F GLN* 5.9 8.3 - - - +
254F VAL 4.6 1.1 - - - +
255F ARG* 3.9 20.6 - - + +
256F ASP* 3.7 22.9 - - + +
274F ALA 3.7 0.3 - - - -
275F ARG* 2.9 48.1 + - + +
277F ARG* 3.9 27.3 + - - +
21J ASP* 3.1 27.1 + - - +
24J ILE* 4.4 9.5 - - - +
25J THR* 5.3 4.0 + - - -
28J LYS* 5.7 0.6 - - - +
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Residues in contact with TYR 238 (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* 4.6 7.4 - - + -
226F TRP* 3.6 17.2 - + + -
228F MET* 3.3 33.7 - - + +
236F PHE* 3.7 28.2 + - + +
237F ARG* 1.3 75.5 - - - +
239F GLU* 1.3 66.0 + - - +
253F GLN* 3.9 7.9 + - - -
254F VAL* 2.7 43.7 + - + +
256F ASP* 3.9 24.0 - - - +
257F ARG 3.1 29.2 - - - -
258F THR* 5.2 0.9 - - - -
272F ILE* 4.4 9.0 - - + -
273F ARG 3.3 7.6 - - - +
274F ALA* 3.9 21.1 - - + -
275F ARG* 5.8 0.4 - - - -
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Residues in contact with GLU 239 (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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238F TYR* 1.3 71.7 - - - +
240F LEU* 1.3 64.5 + - - +
251F THR* 4.0 17.8 - - + +
252F GLU 3.8 5.2 - - - +
253F GLN* 3.3 34.5 - - - +
254F VAL* 4.8 0.2 - - - -
272F ILE* 3.2 8.1 - - - +
273F ARG* 2.9 66.9 + - + +
275F ARG* 2.6 30.8 + - - +
285F TRP* 3.6 15.0 - - + -
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Residues in contact with LEU 240 (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* 4.5 2.7 - - - -
224F MET* 4.9 4.3 - - - -
226F TRP* 4.1 15.0 - - + -
239F GLU* 1.3 73.8 - - - +
241F GLN* 1.3 60.8 + - - +
242F ILE* 4.0 15.7 - - + +
250F ILE 3.7 0.5 - - - +
251F THR* 3.3 7.6 - - - +
252F GLU* 2.9 42.4 + - + +
254F VAL* 4.4 8.7 - - + -
260F PHE* 3.6 48.2 - - + -
270F VAL* 4.3 9.2 - - + -
271F GLN 3.5 4.7 - - - +
272F ILE* 3.6 39.5 - - + -
285F TRP* 4.3 1.6 - - - -
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Residues in contact with GLN 241 (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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240F LEU* 1.3 70.6 - - - +
242F ILE* 1.3 62.6 + - - +
243F GLN* 5.7 0.4 - - - -
249F VAL* 3.8 28.9 - - + +
250F ILE 3.4 2.2 - - - -
251F THR* 4.0 15.6 + - + +
269F THR 3.8 0.7 - - - +
270F VAL* 3.3 6.6 - - - +
271F GLN* 2.9 56.8 + - - +
285F TRP* 3.7 37.2 - - + +
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Residues in contact with ILE 242 (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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224F MET* 4.4 18.4 - - + -
240F LEU* 4.3 17.9 - - + +
241F GLN* 1.3 73.9 - - - +
243F GLN* 1.3 62.8 + - - +
244F LYS* 4.1 5.2 - - + +
249F VAL* 3.8 3.8 - - - +
250F ILE* 2.9 56.4 + - + +
252F GLU* 5.0 7.4 - - + -
260F PHE* 5.1 4.3 - - + -
262F LEU* 4.2 13.7 - - + -
268F TYR* 3.8 28.5 - - + -
269F THR 3.8 1.3 - - - -
270F VAL* 3.7 26.9 - - + -
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Residues in contact with GLN 243 (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 5.7 0.2 - - - -
242F ILE* 1.3 73.2 - - - +
244F LYS* 1.3 82.4 + - - +
245F ARG 3.8 10.3 + - - +
246F MET* 5.3 1.3 - - - +
247F GLN 3.0 25.5 + - - +
248F PRO 4.7 0.7 - - - +
249F VAL* 3.3 31.1 - - + +
268F TYR* 3.4 3.5 - - - -
269F THR* 2.9 56.3 + - + +
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Residues in contact with LYS 244 (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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242F ILE* 4.1 5.2 + - + -
243F GLN* 1.3 77.2 + - - +
245F ARG* 1.3 76.8 + - + +
247F GLN* 2.7 60.6 + - + +
250F ILE* 5.1 9.3 - - + +
262F LEU* 6.4 1.6 - - + -
264F ASN 3.5 15.4 + - - -
265F PRO* 3.2 26.0 + - + +
266F GLY* 5.0 2.7 - - - -
267F THR 3.5 17.9 - - - +
268F TYR* 4.2 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