Contacts of the strand formed by residues 270 - 277 (chain O) 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 270 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262O TYR* 3.4 54.0 + - + +
263O PRO* 3.4 25.7 + - - +
269O HIS* 1.3 83.7 - - - +
271O LYS* 1.3 60.9 + - - +
272O LEU* 3.8 3.1 + - - +
292O LEU* 3.8 9.8 - - + +
293O THR 3.3 4.7 - - - +
294O ILE* 3.2 27.4 - - + -
301O ASP* 3.3 27.8 + - - +
305O TYR* 3.6 15.4 + - + -
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Residues in contact with LYS 271 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269O HIS 4.8 6.5 - - - +
270O LYS* 1.3 73.8 - - - +
272O LEU* 1.3 61.2 + - - +
273O VAL* 5.0 8.8 - - + +
291O THR 3.5 2.6 - - - +
292O LEU* 3.3 4.0 - - - +
293O THR* 2.8 52.1 + - + +
295O ASP* 5.6 13.6 + - - +
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Residues in contact with LEU 272 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258O PHE 6.1 0.4 - - - +
260O TRP* 3.3 60.3 - - + +
262O TYR* 4.3 15.3 - - + +
270O LYS 3.8 3.0 + - - +
271O LYS* 1.3 74.3 - - - +
273O VAL* 1.3 66.6 + - - +
274O ASN* 4.3 9.1 - - - +
290O SER* 4.6 1.1 - - - +
291O THR 3.7 0.7 - - - -
292O LEU* 3.5 31.4 - - + +
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Residues in contact with VAL 273 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271O LYS* 5.0 10.1 - - + -
272O LEU* 1.3 82.1 - - - +
274O ASN* 1.3 72.0 + - - +
275O ARG* 4.2 22.4 + - - +
289O LEU* 3.9 1.4 - - - +
290O SER* 3.5 0.3 - - - -
291O THR* 2.8 46.4 + - + +
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Residues in contact with ASN 274 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258O PHE* 4.0 32.4 + - + +
260O TRP* 5.5 0.2 - - - -
272O LEU* 4.6 6.0 - - - +
273O VAL* 1.3 88.0 + - - +
275O ARG* 1.3 67.1 + - - +
289O LEU 3.4 4.9 - - - +
290O SER* 2.6 28.0 + - - -
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Residues in contact with ARG 275 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258O PHE* 5.6 0.6 - - - -
273O VAL* 4.2 21.6 + - - +
274O ASN* 1.3 80.0 + - - +
276O ASP* 1.3 74.8 + - - +
277O LEU* 4.0 13.2 - - + +
288O PHE* 3.8 2.1 - - - -
289O LEU* 2.9 50.0 + - + +
291O THR* 5.4 6.5 + - - -
1U NAG 4.1 24.4 - - - -
2U NAG 5.0 9.7 + - - +
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Residues in contact with ASP 276 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148C THR* 3.3 50.1 + - + +
275O ARG* 1.3 80.1 - - - +
277O LEU* 1.3 102.4 + - - +
278O LYS* 5.5 2.9 - - - +
286O LYS* 4.1 10.2 + - - +
287O LYS 3.7 1.8 - - - +
288O PHE* 3.1 40.2 - - + -
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Residues in contact with LEU 277 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247O THR* 5.8 1.1 - - + -
275O ARG* 4.0 25.8 - - + +
276O ASP* 1.3 109.4 + - - +
278O LYS* 1.3 61.0 + - - +
279O THR 4.4 0.2 + - - -
286O LYS* 4.8 7.6 - - - +
287O LYS* 2.9 56.2 + - + +
289O LEU* 4.4 20.0 - - + -
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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