Contacts of the strand formed by residues 282 - 291 (chain M) in PDB entry 3CX5
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 GLY 282 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221M PRO* 5.3 0.7 - - - -
245M VAL* 3.6 13.2 - - - -
246M ASN* 5.1 0.2 - - - -
247M LYS* 3.7 18.5 - - - +
250M LEU* 4.6 6.5 - - - +
278M LYS* 3.8 1.0 - - - -
279M PHE* 2.7 42.3 + - - +
280M THR 3.4 2.2 + - - -
281M ASP* 1.3 79.0 - - - +
283M GLY* 1.3 53.9 + - - -
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Residues in contact with GLY 283 (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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151M PHE* 4.1 9.0 - - - -
244M PRO* 3.7 4.2 - - - +
245M VAL* 2.9 41.6 + - - +
250M LEU* 5.7 0.7 - - - -
276M LEU* 4.7 1.1 - - - -
277M ASP 3.1 14.4 - - - -
278M LYS* 4.5 1.3 - - - -
279M PHE* 4.0 8.3 - - - -
282M GLY* 1.3 73.9 - - - -
284M LEU* 1.3 62.7 + - - +
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Residues in contact with LEU 284 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146M LEU* 4.6 3.1 - - + -
147M TYR* 3.6 57.4 - - + +
150M THR* 4.0 24.0 - - + +
151M PHE* 4.0 15.5 - - + -
242M GLY 4.3 0.9 - - - -
243M ILE 3.4 32.1 - - - +
244M PRO* 3.9 4.3 - - + -
275M LYS 3.9 0.2 - - - +
276M LEU* 3.6 4.3 - - - +
277M ASP* 2.9 38.0 + - - +
279M PHE* 4.7 1.3 - - + -
283M GLY* 1.3 74.3 - - - +
285M PHE* 1.3 60.5 + - - +
286M THR* 3.8 19.4 + - + +
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Residues in contact with PHE 285 (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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241M ILE* 4.6 6.7 - - + -
242M GLY* 3.2 6.6 - - - -
243M ILE* 2.8 64.8 + - + +
245M VAL* 4.3 0.2 - - + -
253M TYR* 3.9 36.3 - + + -
256M LEU* 3.8 21.5 - - + -
257M ALA* 4.0 20.0 - - + -
260M LEU* 3.9 24.7 - - + -
274M ALA* 4.6 1.8 - - + -
275M LYS 3.5 15.7 - - - -
276M LEU* 3.9 8.8 - - + +
284M LEU* 1.3 73.3 - - - +
286M THR* 1.3 64.2 + - - +
287M LEU* 3.9 28.5 - - + -
308M LEU* 5.6 2.5 - - + -
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Residues in contact with THR 286 (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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143M GLU* 4.9 5.4 - - + -
146M LEU* 3.6 22.0 - - + -
241M ILE 3.5 2.9 - - - -
274M ALA* 3.2 5.0 - - - +
275M LYS* 2.9 62.3 + - - +
277M ASP* 4.6 3.5 + - - +
284M LEU* 3.8 24.8 + - + +
285M PHE* 1.3 83.1 - - - +
287M LEU* 1.3 60.8 + - - +
288M PHE* 3.5 23.1 - - + -
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Residues in contact with LEU 287 (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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146M LEU* 5.0 0.2 - - - +
240M ALA* 3.2 6.8 - - - +
241M ILE* 3.1 39.1 + - + -
260M LEU* 3.5 31.0 - - + -
271M ILE* 4.1 24.5 - - + -
273M SER 3.3 8.5 - - - +
274M ALA* 4.3 5.2 - - + -
285M PHE* 3.9 17.0 - - + -
286M THR* 1.3 75.3 - - - +
288M PHE* 1.3 65.4 + - - +
289M VAL* 4.2 16.2 - - + -
301M ILE* 4.5 9.0 - - + -
304M ILE* 4.1 24.2 - - + -
308M LEU* 4.6 4.5 - - + -
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Residues in contact with PHE 288 (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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139M VAL* 3.7 38.6 - - + -
142M ALA* 4.0 8.1 - - + -
143M GLU* 3.8 32.3 - - + -
146M LEU* 4.1 2.9 - - + -
238M VAL* 4.3 5.6 - - + -
239M ALA 3.8 2.2 - - - -
240M ALA* 3.4 26.7 - - + -
271M ILE* 3.7 4.5 - - - +
272M SER* 2.8 31.6 + - - -
273M SER* 2.7 41.3 + - - +
275M LYS* 4.8 8.7 - - + -
286M THR* 3.5 36.8 - - - -
287M LEU* 1.3 75.0 - - - +
289M VAL* 1.3 57.5 + - - +
290M ARG 4.0 0.2 - - - -
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Residues in contact with VAL 289 (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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238M VAL* 3.2 6.6 - - - +
239M ALA 3.0 31.5 + - - +
270M LEU 3.7 15.7 - - - +
271M ILE* 4.6 1.8 - - - -
272M SER* 3.7 3.4 - - - +
287M LEU* 4.2 8.7 - - + -
288M PHE* 1.3 76.8 - - - +
290M ARG* 1.3 63.4 + - - +
291M ASP* 5.9 0.9 - - + -
297M VAL* 3.6 26.2 - - + +
300M ASN* 3.5 29.2 - - + +
301M ILE* 3.9 33.0 - - + +
304M ILE* 4.5 6.1 - - + -
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Residues in contact with ARG 290 (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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136M GLN 4.8 4.0 + - - -
137M CYS* 3.7 27.5 - - - +
138M PRO* 3.9 21.1 - - + +
139M VAL* 3.8 27.9 - - + +
236M ASP* 3.1 33.7 + - + +
237M SER 3.4 10.3 - - - +
238M VAL* 4.5 3.6 - - + -
272M SER* 2.6 29.0 + - - +
289M VAL* 1.3 77.8 - - - +
291M ASP* 1.3 68.8 + - - +
292M GLN* 5.1 0.2 + - - -
297M VAL* 4.4 0.4 - - - -
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Residues in contact with ASP 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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236M ASP* 4.1 4.9 - - - -
237M SER* 2.9 29.6 + - - +
289M VAL* 5.9 1.1 - - + -
290M ARG* 1.3 80.0 - - - +
292M GLN* 1.3 84.5 + - - +
293M ASP* 2.9 34.7 + - - +
296M VAL* 3.8 25.7 - - + +
297M VAL* 3.7 19.0 - - + +
300M ASN* 6.0 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