Contacts of the strand formed by residues 267 - 276 (chain M) 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 267 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244M LYS* 3.5 17.8 - - - +
245M ARG* 4.0 16.5 + - - +
265M PRO 3.5 0.8 + - - -
266M GLY* 1.3 72.0 - - - +
268M TYR* 1.3 59.5 + - - +
290M ARG* 4.8 13.8 + - - +
291M PHE 3.3 5.8 - - - -
292M GLU* 3.8 30.5 - - + +
294M ASP* 3.4 23.8 - - - +
295M GLN* 5.7 0.2 - - - +
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Residues in contact with TYR 268 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215M ALA* 4.7 2.6 - - - +
217M CYS* 4.3 4.9 - - - +
222M SER* 3.3 20.8 + - - -
224M MET* 3.6 28.9 - - + +
242M ILE* 3.8 24.7 - - + -
243M GLN 3.4 12.3 - - - +
244M LYS* 4.1 12.3 - - + -
262M LEU* 4.2 6.1 - - + -
265M PRO* 3.6 35.9 - - + +
267M THR* 1.3 73.3 - - - +
269M THR* 1.3 62.5 + - - +
270M VAL* 3.9 28.5 - - + -
289M GLN 3.9 0.3 - - - +
290M ARG* 3.7 3.9 - - - +
291M PHE* 2.9 57.2 + + + +
293M CYS* 4.5 0.2 - - - -
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Residues in contact with THR 269 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241M GLN 3.8 0.9 - - - +
242M ILE* 3.8 1.0 - - - -
243M GLN* 2.9 59.2 + - + +
268M TYR* 1.3 75.0 - - - +
270M VAL* 1.3 63.8 + - - +
288M PRO* 3.7 19.1 - - + +
289M GLN 3.2 16.6 + - - -
290M ARG* 3.9 18.8 + - - +
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Residues in contact with VAL 270 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213M MET* 3.6 35.9 - - + +
224M MET* 4.5 0.9 - - - -
240M LEU* 4.5 4.3 - - + -
241M GLN 3.2 10.5 - - - +
242M ILE* 3.6 18.8 - - + -
268M TYR* 3.9 23.3 - - + -
269M THR* 1.3 74.5 + - - +
271M GLN* 1.3 75.4 + - - +
286M SER* 4.7 0.2 + - - -
287M THR 4.3 0.2 - - - +
288M PRO* 3.5 2.7 - - - +
289M GLN* 2.9 42.3 + - + +
291M PHE* 3.9 12.3 - - + -
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Residues in contact with GLN 271 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213M MET* 5.5 0.2 - - - -
240M LEU* 3.6 3.8 - - - -
241M GLN* 2.9 50.9 + - + +
269M THR 6.0 0.2 - - - -
270M VAL* 1.3 82.4 - - - +
272M ILE* 1.3 63.8 + - - +
285M TRP* 3.7 29.0 + - + +
286M SER* 3.3 27.3 + - - +
287M THR* 5.1 0.2 - - - +
288M PRO* 3.6 30.7 - - + +
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Residues in contact with ILE 272 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211M PRO* 3.7 24.2 - - + +
213M MET* 3.8 22.0 - - + -
226M TRP* 3.3 52.7 - - + +
238M TYR* 4.4 4.9 - - + -
239M GLU 3.1 12.6 - - - +
240M LEU* 3.7 13.2 - - + -
271M GLN* 1.3 77.0 - - - +
273M ARG* 1.3 69.4 + - - +
284M ALA 4.0 1.2 - - - +
285M TRP* 3.5 3.4 - - - -
286M SER* 2.9 44.3 + - - +
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Residues in contact with ARG 273 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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211M PRO* 4.5 2.7 - - - -
238M TYR* 3.2 7.8 - - - +
239M GLU* 2.9 70.9 + - + -
272M ILE* 1.3 77.8 - - - +
274M ALA* 1.3 67.5 + - - +
275M ARG* 3.9 6.1 - - - +
282M LEU* 3.4 26.6 - - + +
283M SER* 3.2 32.8 - - - +
284M ALA 4.2 2.2 - - - +
285M TRP* 3.3 49.6 - - + +
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Residues in contact with ALA 274 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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208M LEU* 4.5 1.5 - - + +
211M PRO* 4.3 4.0 - - + +
228M MET* 3.9 31.0 - - + -
236M PHE* 4.4 5.2 - - + -
237M ARG 3.8 3.6 - - - -
238M TYR* 3.8 20.4 - - + -
273M ARG* 1.3 80.7 - - - +
275M ARG* 1.3 60.7 + - - +
281M PHE 3.7 0.5 - - - +
282M LEU* 3.5 3.7 - - - +
283M SER* 2.9 38.0 + - - +
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Residues in contact with ARG 275 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236M PHE* 3.5 5.5 - - - -
237M ARG* 2.9 59.1 + - + +
238M TYR 5.2 0.2 + - - -
239M GLU* 2.3 34.6 + - - +
253M GLN* 3.5 26.1 - - - +
273M ARG* 3.9 8.7 - - - +
274M ALA* 1.3 74.6 - - - +
276M GLU* 1.3 69.3 + - - +
280M GLU* 3.8 46.0 + - - +
281M PHE 3.2 4.9 - - - +
282M LEU* 4.3 18.5 - - + +
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Residues in contact with GLU 276 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I LYS* 2.4 39.6 + - - +
119I GLU* 5.6 0.3 - - - +
208M LEU* 4.2 4.4 - - + +
233M ASN* 3.9 17.3 - - + +
235M LYS* 3.9 8.8 + - - +
236M PHE* 4.0 10.5 - - + -
237M ARG* 5.9 0.2 + - - -
275M ARG* 1.3 75.5 - - - +
277M ARG* 1.3 79.2 + - - +
278M VAL* 2.9 9.7 + - - +
279M TYR* 2.6 37.9 + - - +
280M GLU* 3.0 20.8 + - - +
281M PHE* 2.6 44.2 + - + +
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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