Contacts of the strand formed by residues 285 - 294 (chain M) in PDB entry 2X1W
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 MET 285 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224M TYR* 3.9 28.9 - - + -
249M ARG* 3.9 42.2 - - + +
250M THR 3.2 7.6 - - - +
252M LEU* 3.8 10.2 - - - +
279M THR* 3.7 29.3 + - + +
283M SER* 3.0 12.4 - - - +
284M GLU* 1.3 87.2 - - + +
286M LYS* 1.3 69.4 + - - +
287M LYS* 5.1 9.4 - - + +
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Residues in contact with LYS 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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151A PHE* 4.8 4.9 - - - -
169B GLU* 3.2 36.3 + - - +
248M ALA 3.8 0.3 - - - +
249M ARG* 3.4 5.2 - - - +
250M THR* 2.7 39.9 + - - +
251M GLU 3.7 11.4 - - - +
252M LEU* 3.9 12.1 - - + -
254M VAL* 3.0 31.7 + - - +
276M ASP* 4.5 9.4 + - - +
277M LEU 5.5 0.2 - - - -
279M THR* 4.4 3.1 - - - -
285M MET* 1.3 81.8 - - - +
287M LYS* 1.3 61.4 + - - +
288M PHE* 3.5 20.7 - - + -
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Residues in contact with LYS 287 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
247M THR* 3.8 16.8 - - + -
248M ALA 3.5 1.3 - - - -
249M ARG* 3.6 32.9 - - + +
276M ASP* 3.9 4.7 + - - +
277M LEU* 2.9 67.7 + - + +
278M LYS 4.6 10.5 - - - -
279M THR* 4.2 12.2 - - + +
285M MET* 5.1 7.6 - - + +
286M LYS* 1.3 76.1 - - - +
288M PHE* 1.3 66.5 + - - +
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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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148A THR* 3.3 42.6 - - + -
246M CYS 3.6 0.5 - - - +
247M THR* 3.2 7.4 - - - +
248M ALA* 2.8 47.3 + - + +
250M THR* 3.6 22.0 - - + -
254M VAL* 3.3 22.4 - - + -
256M ILE* 3.4 28.5 - - + -
258M PHE* 3.7 20.0 - - + -
275M ARG 3.9 1.8 - - - +
276M ASP* 3.3 23.8 - - - -
277M LEU* 4.7 2.0 - - - -
286M LYS* 3.5 24.2 - - + -
287M LYS* 1.3 77.6 - - - +
289M LEU* 1.3 60.7 + - - +
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Residues in contact with LEU 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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245M ASN* 3.9 20.9 - - + +
246M CYS 3.4 19.1 - - - +
247M THR* 3.5 17.0 - - - +
258M PHE* 4.1 3.7 - - - -
273M VAL 4.0 1.4 - - - +
274M ASN* 3.4 3.8 - - - +
275M ARG* 2.9 62.7 + - + +
277M LEU* 3.9 24.5 - - + -
287M LYS 4.3 0.2 + - - -
288M PHE* 1.3 74.9 - - - +
290M SER* 1.3 64.0 + - - +
291M THR* 3.7 17.7 - - - +
1R NAG 3.8 24.9 - - - +
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Residues in contact with SER 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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244M LEU 3.6 1.4 - - - +
245M ASN 3.6 0.3 - - - -
246M CYS* 2.7 43.2 + - - +
258M PHE* 3.5 34.3 - - - +
260M TRP* 3.2 24.4 + - - -
272M LEU* 4.3 2.8 - - - +
273M VAL 3.7 4.0 - - - -
274M ASN* 2.9 20.2 + - - -
289M LEU* 1.3 74.3 - - - +
291M THR* 1.3 60.5 + - - +
292M LEU 4.1 0.2 - - - -
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Residues in contact with THR 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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243M VAL* 4.0 12.8 - - + -
244M LEU 3.3 3.8 - - - +
245M ASN* 2.8 24.6 + - - +
271M LYS 3.4 6.4 - - - +
272M LEU* 3.5 3.6 - - - -
273M VAL* 3.1 40.6 + - + +
289M LEU* 3.7 15.9 - - - +
290M SER* 1.3 73.1 + - - +
292M LEU* 1.3 65.0 + - - +
293M THR* 3.9 17.2 + - - +
1R NAG 4.4 3.6 - - - -
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Residues in contact with LEU 292 (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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242M LEU* 3.8 3.4 - - + +
243M VAL* 3.5 2.3 - - - -
244M LEU* 2.7 42.5 + - + +
260M TRP* 3.9 34.9 - - + -
262M TYR* 4.5 11.2 - - + -
270M LYS* 3.9 26.2 - - + -
271M LYS 3.5 9.0 - - - +
272M LEU* 3.8 17.0 - - + -
290M SER 4.0 1.0 + - - -
291M THR* 1.3 73.6 - - - +
293M THR* 1.3 71.6 + - - +
294M ILE* 4.9 4.7 - - + -
305M TYR* 3.4 39.0 - - + -
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Residues in contact with THR 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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241M LYS* 3.5 30.7 - - - +
242M LEU 3.3 9.4 - - - +
243M VAL* 4.4 6.2 - - + +
269M HIS 3.6 1.9 - - - +
270M LYS* 3.5 2.8 - - - -
271M LYS* 2.8 61.2 + - + +
273M VAL* 6.0 1.0 - - - +
291M THR* 3.9 14.9 + - - +
292M LEU* 1.3 78.3 + - - +
294M ILE* 1.3 71.0 + - - +
295M ASP* 4.1 4.0 + - + +
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Residues in contact with ILE 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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240M GLU 4.3 0.3 - - - +
241M LYS* 3.5 2.1 - - - +
242M LEU* 3.0 46.9 + - + +
269M HIS* 3.7 33.2 - - + +
270M LYS* 3.6 35.7 - - + +
292M LEU* 4.9 4.5 - - + -
293M THR* 1.3 76.8 - - - +
295M ASP* 1.3 60.3 + - - +
296M GLY 3.1 6.9 + - - +
297M VAL* 3.5 24.2 - - + -
301M ASP* 3.9 7.2 - - + +
305M TYR* 3.4 30.7 - - + +
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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