Contacts of the strand formed by residues 290 - 299 (chain M) in PDB entry 6CM9
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 ARG 290 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114H ASP* 2.5 44.6 + - - +
117H ARG* 3.0 41.5 - - - +
284M GLU* 5.0 4.0 + - - -
285M LYS* 3.9 1.0 - - - -
286M HIS* 3.2 46.5 + - + +
289M SER* 1.3 82.4 - - - +
291M ILE* 1.3 67.2 + - - +
292M GLU* 3.2 24.2 + - - +
357M ARG* 5.7 1.6 - - - +
359M HIS* 4.0 12.0 + - + +
360M PHE 3.3 19.1 - - - +
361M GLY* 4.0 5.8 - - - -
362M LEU* 3.7 7.8 - - - +
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Residues in contact with ILE 291 (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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283M ILE* 3.7 30.1 - - + -
284M GLU 4.1 3.4 - - - -
285M LYS* 3.9 18.8 - - + -
290M ARG* 1.3 79.5 - - - +
292M GLU* 1.3 76.5 + - - +
293M TYR* 3.4 27.6 - - + +
317M PRO* 3.7 27.6 - - + -
320M ALA* 5.2 0.2 - - + -
358M ALA 4.7 0.2 - - - -
359M HIS* 3.5 1.0 - - - -
360M PHE* 3.2 57.7 + - + +
361M GLY 4.6 2.7 - - - +
362M LEU* 4.8 2.9 - - + -
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Residues in contact with GLU 292 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282M VAL 3.4 1.0 - - - +
283M ILE* 3.3 4.0 - - - -
284M GLU* 3.2 60.5 + - + +
290M ARG* 3.2 31.6 + - - -
291M ILE* 1.3 85.5 + - - +
293M TYR* 1.3 73.5 + - - +
294M MET* 4.0 13.0 - - - +
357M ARG* 3.4 26.2 + - - +
358M ALA 3.6 7.9 - - - +
359M HIS* 3.1 23.8 - - + -
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Residues in contact with TYR 293 (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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281M SER* 6.4 1.1 - - - -
282M VAL 3.6 12.1 - - - -
283M ILE* 3.5 24.8 - - + +
291M ILE* 3.4 18.5 - - + +
292M GLU* 1.3 85.2 - - - +
294M MET* 1.3 59.4 + - - +
295M VAL* 2.9 24.7 + - + +
314M ILE* 4.5 13.5 - - + -
315M PRO 3.4 9.0 + - - -
316M VAL* 3.3 29.2 - - + -
317M PRO* 3.3 26.9 - - - +
341M ILE* 3.7 11.2 - - + -
356M MET 2.9 11.6 - - - +
357M ARG* 3.3 7.7 - - - -
358M ALA* 3.3 35.9 + - + -
360M PHE* 3.9 11.0 - + - -
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Residues in contact with MET 294 (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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280M GLU* 3.5 16.5 - - - +
282M VAL* 3.7 38.2 + - + +
284M GLU* 3.3 33.4 - - + +
292M GLU* 4.0 13.7 - - - -
293M TYR* 1.3 68.0 - - - +
295M VAL* 1.3 60.0 + - - +
296M LYS* 3.8 1.9 + - - -
355M LEU* 4.4 13.2 - - + +
356M MET 3.5 5.2 - - - -
357M ARG* 3.7 39.3 - - + +
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Residues in contact with VAL 295 (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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279M ILE* 3.7 29.8 - - + -
280M GLU 3.4 6.7 - - - +
281M SER* 4.1 12.1 - - - +
293M TYR* 2.9 18.9 + - + +
294M MET* 1.3 71.8 - - - +
296M LYS* 1.3 63.5 + - - +
312M ILE* 5.2 0.4 - - + -
314M ILE* 3.7 19.3 - - + -
343M TRP* 4.3 12.4 - - + -
355M LEU* 3.5 1.2 - - - +
356M MET* 2.9 60.0 + - + +
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Residues in contact with LYS 296 (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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278M TRP 3.4 2.6 - - - +
279M ILE* 3.5 3.3 - - - -
280M GLU* 3.0 60.3 + - + +
294M MET 3.8 1.8 + - - -
295M VAL* 1.3 76.2 - - - +
297M ALA* 1.3 60.4 - - - +
298M LYS* 3.9 16.4 + - - +
353M GLU* 3.3 29.9 + - + +
354M TYR 3.7 6.5 - - - +
355M LEU* 3.7 25.1 - - + -
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Residues in contact with ALA 297 (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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277M ILE* 4.8 2.0 - - + -
278M TRP 3.3 6.5 - - - -
279M ILE* 3.8 7.2 - - + -
296M LYS* 1.3 73.7 - - - +
298M LYS* 1.3 60.6 + - - +
312M ILE* 3.7 30.3 - - + -
343M TRP* 3.9 11.9 - - + -
348M PHE* 3.1 28.8 - - + -
353M GLU* 3.7 1.9 - - - -
354M TYR 3.1 23.9 + - - +
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Residues in contact with LYS 298 (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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277M ILE* 3.9 0.6 - - - -
278M TRP* 3.1 59.5 + - + +
280M GLU* 4.1 17.8 - - - +
296M LYS* 3.9 12.1 - - - +
297M ALA* 1.3 74.3 - - - +
299M SER* 1.3 60.0 + - - +
300M GLN* 3.4 26.3 + - - +
348M PHE* 4.9 1.1 - - - -
352M LYS 3.6 7.0 - - - +
353M GLU* 4.1 29.4 - - + +
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Residues in contact with SER 299 (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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276M LEU 3.8 4.7 - - - -
277M ILE* 4.8 1.1 - - - -
297M ALA 3.8 1.0 + - - -
298M LYS* 1.3 69.1 - - - +
300M GLN* 1.3 63.1 + - - +
301M PHE* 3.2 18.2 - - - -
348M PHE* 3.5 26.0 - - - -
349M PRO 2.9 14.1 + - - -
351M GLY* 2.5 48.4 + - - -
352M LYS 3.0 13.1 + - - -
64N GLU 5.0 0.9 + - - +
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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