Contacts of the strand formed by residues 223 - 229 (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 ILE 223 (chain M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221M TYR 3.3 11.5 + - - +
222M ARG* 1.3 74.0 - - - +
224M TYR* 1.3 67.0 + - - +
225M ASP 4.0 12.6 - - - +
226M VAL* 4.1 11.2 - - + -
248M ALA* 5.0 1.8 - - + -
249M ARG 3.8 10.1 - - - +
250M THR* 4.0 14.8 - - + -
256M ILE* 3.6 20.6 - - + -
309M ALA* 3.3 27.4 - - + +
311M SER* 3.9 5.2 - - - +
314M MET* 3.3 34.1 - - - +
316M LYS* 3.2 36.8 - - + +
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Residues in contact with TYR 224 (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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222M ARG* 3.9 26.8 + - + -
223M ILE* 1.3 76.7 - - - +
225M ASP* 1.3 68.1 + - - +
249M ARG* 2.7 27.3 + - + +
250M THR 3.7 22.4 - - - -
251M GLU* 3.6 22.1 + - + +
284M GLU* 4.8 5.6 + - - +
285M MET* 3.9 27.4 - - + -
316M LYS* 3.4 16.0 + - - -
1S NAG 5.7 0.2 - - - -
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Residues in contact with ASP 225 (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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223M ILE* 4.0 2.2 - - - +
224M TYR* 1.3 79.4 - - - +
226M VAL* 1.3 66.4 + - - +
227M VAL* 3.8 21.7 - - + +
247M THR 3.8 1.2 - - - +
248M ALA* 3.4 3.1 - - - -
249M ARG* 2.6 72.7 + - - +
316M LYS* 4.4 3.4 - - - -
1S NAG 4.1 17.7 - - - +
2S NAG 5.4 6.3 - - - +
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Residues in contact with VAL 226 (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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223M ILE* 4.1 5.4 - - + -
225M ASP* 1.3 79.8 - - - +
227M VAL* 1.3 56.7 + - - +
246M CYS* 3.5 27.1 - - - -
247M THR 3.4 4.3 - - - +
248M ALA* 4.1 4.3 - - + -
307M CYS* 3.9 17.7 - - - +
309M ALA* 3.6 20.0 - - + -
316M LYS* 3.5 36.7 - - + +
317M LYS* 4.2 2.7 - - - -
318M ASN* 2.6 40.6 + - + +
1S NAG 3.6 8.5 + - - +
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Residues in contact with VAL 227 (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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225M ASP* 3.8 27.6 - - + +
226M VAL* 1.3 82.6 - - - +
228M LEU* 1.3 74.9 + - - +
229M SER* 4.0 3.2 + - - -
231M SER* 5.9 1.1 - - - -
245M ASN 3.6 0.5 - - - +
246M CYS* 3.6 3.4 - - - -
247M THR* 2.9 41.9 + - + +
318M ASN* 3.9 2.2 - - - +
1S NAG 4.6 21.8 - - - +
2S NAG 5.8 1.1 - - - -
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Residues in contact with LEU 228 (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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227M VAL* 1.3 82.3 - - - +
229M SER* 1.3 61.2 + - - +
230M PRO 3.6 11.0 - - - +
231M SER* 3.2 27.0 - - - -
244M LEU* 4.0 9.0 - - + -
245M ASN 3.3 14.4 - - - +
246M CYS* 4.0 9.9 - - + -
260M TRP* 3.8 26.5 - - + -
305M TYR 4.0 5.2 - - - +
307M CYS* 4.0 6.7 - - + +
318M ASN* 3.9 17.4 - - + +
319M SER* 3.4 44.9 - - - +
320M THR* 3.7 14.6 - - + +
1S NAG 4.9 2.5 + - - +
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Residues in contact with SER 229 (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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227M VAL* 4.0 3.5 + - - -
228M LEU* 1.3 74.3 - - - +
230M PRO* 1.3 67.3 - - - +
244M LEU* 4.2 0.9 - - - -
245M ASN* 2.9 42.8 + - - +
1R NAG 3.0 24.0 + - - +
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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