Contacts of the strand formed by residues 286 - 294 (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 LYS 286 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169C GLU* 2.5 45.0 + - - +
151D PHE* 3.6 8.3 - - - -
248L ALA 4.4 0.4 - - - -
249L ARG* 3.4 5.2 - - - -
250L THR* 2.8 41.3 + - - +
251L GLU 3.5 9.8 + - - +
252L LEU* 4.0 7.0 - - + -
254L VAL* 2.9 32.6 + - - +
276L ASP* 3.4 24.9 + - - +
279L THR* 4.5 3.4 - - - -
285L MET* 1.3 81.6 - - - +
287L LYS* 1.3 63.3 + - - +
288L PHE* 3.3 14.8 - - + -
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Residues in contact with LYS 287 (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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247L THR* 3.6 26.9 - - + -
248L ALA 3.5 2.5 - - - -
249L ARG* 3.9 25.7 - - + +
276L ASP* 3.3 6.6 + - - +
277L LEU* 2.8 60.1 + - + +
279L THR* 4.8 16.2 - - + +
285L MET* 4.7 11.0 - - - -
286L LYS* 1.3 75.5 - - - +
288L PHE* 1.3 62.0 + - - +
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Residues in contact with PHE 288 (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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148D THR* 3.5 40.6 - - + -
246L CYS 3.6 0.7 - - - +
247L THR* 3.2 8.1 - - - +
248L ALA* 2.8 43.4 + - + +
250L THR* 3.5 24.2 - - + -
254L VAL* 3.3 11.0 - - + -
255L GLY* 4.6 0.2 - - - -
256L ILE* 3.4 26.2 - - + -
258L PHE* 3.9 20.9 - - + -
275L ARG 3.6 2.9 - - - +
276L ASP* 3.7 22.9 - - - -
286L LYS* 3.3 34.1 - - + -
287L LYS* 1.3 76.3 - - - +
289L LEU* 1.3 61.5 + - - +
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Residues in contact with LEU 289 (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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245L ASN* 3.8 24.0 - - + +
246L CYS 3.4 10.1 - - - +
247L THR* 3.7 15.0 - - - +
258L PHE* 4.1 3.2 - - - -
273L VAL 3.7 1.4 - - - +
274L ASN* 3.1 5.4 - - - +
275L ARG* 2.8 70.1 + - + +
277L LEU* 4.1 22.9 - - + -
287L LYS 4.2 0.2 + - - -
288L PHE* 1.3 76.0 - - - +
290L SER* 1.3 67.3 + - - +
291L THR* 3.6 19.7 - - - +
1Q NAG 4.1 20.6 - - - +
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Residues in contact with SER 290 (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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244L LEU 3.6 1.7 - - - +
245L ASN* 3.6 0.9 - - - -
246L CYS* 2.7 42.3 + - - +
258L PHE* 3.6 31.8 - - - -
260L TRP* 2.9 28.6 + - - -
272L LEU* 4.5 3.3 - - - +
274L ASN* 2.5 25.3 + - - -
289L LEU* 1.3 73.6 - - - +
291L THR* 1.3 60.7 + - - +
292L LEU 4.0 0.2 - - - -
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Residues in contact with THR 291 (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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243L VAL* 4.0 16.6 - - + -
244L LEU 3.6 2.5 - - - +
245L ASN* 2.8 25.2 + - - +
271L LYS 3.3 7.4 - - - +
272L LEU* 3.5 3.6 - - - -
273L VAL* 3.1 42.0 + - + +
274L ASN* 4.2 0.2 + - - -
275L ARG* 5.0 3.1 + - - -
289L LEU* 3.6 17.0 - - - +
290L SER* 1.3 72.7 + - - +
292L LEU* 1.3 59.3 + - - +
293L THR* 3.8 17.3 + - - +
1Q NAG 4.5 5.5 + - - -
2Q NAG 6.4 1.8 - - + -
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Residues in contact with LEU 292 (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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242L LEU* 3.6 3.7 - - + +
243L VAL* 3.4 4.7 - - - -
244L LEU* 2.9 43.6 + - + +
260L TRP* 3.8 21.5 - - + -
262L TYR* 3.3 37.2 - - + +
270L LYS* 4.3 14.1 - - + -
271L LYS 3.7 4.9 - - - +
272L LEU* 3.8 18.4 - - + -
290L SER 4.0 1.2 + - - -
291L THR* 1.3 71.9 - - - +
293L THR* 1.3 78.7 + - - +
294L ILE* 4.8 4.5 - - + -
305L TYR* 3.6 29.4 - - + -
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Residues in contact with THR 293 (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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241L LYS* 3.8 28.0 - - + -
242L LEU 3.2 8.7 - - - +
243L VAL* 4.1 8.8 - - + +
269L HIS 3.2 6.2 - - - +
270L LYS* 3.2 4.9 - - - +
271L LYS* 3.0 42.6 + - + +
291L THR* 3.9 14.7 + - - +
292L LEU* 1.3 77.7 + - - +
294L ILE* 1.3 71.6 + - - +
295L ASP* 4.4 2.9 - - + +
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Residues in contact with ILE 294 (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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240L GLU 4.1 0.9 - - - +
241L LYS* 3.4 2.9 - - - +
242L LEU* 2.9 56.8 + - + -
268L GLN 3.5 18.6 - - - +
269L HIS 3.6 3.1 - - - -
270L LYS* 3.8 23.6 - - + -
292L LEU* 4.8 4.0 - - + -
293L THR* 1.3 79.3 - - - +
295L ASP* 1.3 64.4 + - - +
296L GLY 4.1 10.8 - - - +
297L VAL* 4.1 8.5 - - + +
301L ASP* 3.8 30.1 - - + +
305L TYR* 3.5 28.3 - - + +
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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