Contacts of the strand formed by residues 242 - 250 (chain L) 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 LEU 242 (chain L).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234L ILE* 4.2 22.9 - - + -
236L LEU* 3.8 24.9 - - + -
240L GLU 3.9 1.4 + - - -
241L LYS* 1.3 72.7 - - - +
243L VAL* 1.3 76.6 + - - +
244L LEU* 4.7 9.9 - - + +
292L LEU* 5.0 4.5 - - + +
293L THR* 3.2 7.3 - - - +
294L ILE* 2.9 62.5 + - + +
297L VAL* 3.8 10.7 - - + +
305L TYR* 4.0 26.5 - - + +
322L VAL* 4.6 14.1 - - + -
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Residues in contact with VAL 243 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229L SER 4.2 0.3 - - - +
230L PRO* 3.6 18.9 - - - +
241L LYS* 3.9 24.6 + - + +
242L LEU* 1.3 84.4 - - - +
244L LEU* 1.3 63.6 + - - +
245L ASN* 4.2 2.2 - - - +
291L THR* 4.0 21.5 - - + -
292L LEU 3.4 2.5 - - - -
293L THR* 4.1 10.8 - - + +
1Q NAG 4.0 32.3 - - + +
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Residues in contact with LEU 244 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228L LEU* 4.3 9.6 - - + -
229L SER 3.7 9.6 - - - +
230L PRO* 3.5 24.9 - - + +
234L ILE* 3.9 18.6 - - + -
242L LEU* 4.7 10.1 - - + -
243L VAL* 1.3 75.9 - - - +
245L ASN* 1.3 62.7 + - - +
246L CYS 3.9 0.2 + - - -
260L TRP* 4.0 20.1 - - + -
290L SER 3.6 1.4 - - - +
291L THR* 3.6 1.2 - - - -
292L LEU* 2.9 44.1 + - + +
305L TYR* 3.9 36.1 - - + -
320L THR* 4.2 13.5 - - + -
322L VAL* 4.9 3.8 - - + -
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Residues in contact with ASN 245 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227L VAL 3.5 1.2 - - - +
228L LEU* 3.2 9.1 - - - +
229L SER* 2.8 44.4 + - - +
243L VAL* 4.2 0.9 - - - +
244L LEU* 1.3 72.1 - - - +
246L CYS* 1.3 60.5 + - - +
247L THR* 4.0 4.4 + - - +
289L LEU* 3.8 12.5 - - + +
290L SER 3.6 2.7 - - - -
291L THR* 2.8 30.9 + - - +
1Q NAG 1.4 68.0 + - - +
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Residues in contact with CYS 246 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226L VAL* 3.7 23.1 - - - -
227L VAL 3.5 3.8 - - - -
228L LEU* 3.9 4.5 - - + -
244L LEU 3.9 0.4 + - - -
245L ASN* 1.3 72.5 - - - +
247L THR* 1.3 61.3 + - - +
258L PHE* 3.7 9.5 - - - -
260L TRP* 3.5 17.0 - - + -
288L PHE 3.6 1.0 - - - +
289L LEU* 3.4 3.9 - - - -
290L SER* 2.7 41.5 + - - +
307L CYS* 2.0 51.4 - - + -
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Residues in contact with THR 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225L ASP 3.7 1.2 - - - +
226L VAL* 3.3 3.6 - - - +
227L VAL* 2.8 41.6 + - - +
229L SER* 6.1 0.7 - - - -
245L ASN* 4.8 4.2 - - - +
246L CYS* 1.3 78.9 + - - +
248L ALA* 1.3 64.8 + - - +
249L ARG* 4.2 9.6 - - + -
277L LEU* 5.1 5.4 - - + +
287L LYS* 3.6 34.1 - - + -
288L PHE 3.2 6.1 - - - +
289L LEU* 3.7 13.9 - - - +
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Residues in contact with ALA 248 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223L ILE* 4.8 1.3 - - + -
225L ASP 3.5 4.5 - - - +
226L VAL* 4.2 7.4 - - + +
246L CYS 4.1 0.2 + - - -
247L THR* 1.3 74.1 - - - +
249L ARG* 1.3 63.3 + - - +
250L THR* 4.4 10.3 - - + -
256L ILE* 4.8 3.1 - - + -
258L PHE* 4.2 12.5 - - + -
287L LYS* 3.5 2.6 - - - -
288L PHE* 2.8 44.8 + - + +
309L ALA* 3.9 28.3 - - + -
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Residues in contact with ARG 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223L ILE* 3.6 1.7 - - - +
224L TYR* 2.8 30.3 + - + +
225L ASP* 3.0 45.9 + - - +
227L VAL* 5.7 1.4 - - - +
247L THR* 4.2 7.6 - - + -
248L ALA* 1.3 72.1 - - - +
250L THR* 1.3 64.6 + - - +
285L MET* 3.6 43.0 - - + +
286L LYS 3.4 3.8 - - - +
287L LYS* 3.9 26.9 - - + +
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Residues in contact with THR 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222L ARG 3.2 15.7 - - - +
223L ILE* 4.0 11.4 - - + -
224L TYR* 3.4 11.6 - - - -
248L ALA 4.2 2.7 - - - +
249L ARG* 1.3 80.8 - - - +
251L GLU* 1.3 69.6 + - - +
254L VAL* 3.3 30.0 - - + +
256L ILE* 3.8 20.2 - - + -
285L MET* 3.2 8.1 - - - -
286L LYS* 2.8 39.9 + - - +
288L PHE* 3.5 7.1 - - + -
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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