Contacts of the strand formed by residues 270 - 274 (chain A) in PDB entry 1WXR
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 270 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A VAL* 3.9 22.2 - - + -
261A THR 4.5 0.7 - - - +
262A PHE* 3.8 41.4 - - + +
269A ALA* 1.3 70.7 - - - +
271A GLU* 1.3 62.5 + - - +
272A TRP 3.5 1.0 + - - -
283A LEU* 4.2 13.0 - - + +
284A THR 3.5 3.4 - - - -
285A GLN* 3.5 31.6 - - + +
290A TYR* 4.1 25.8 - - + -
314A GLN 2.8 15.9 + - - +
315A ILE* 3.3 12.9 - - + +
316A ASN 2.9 22.2 + - - -
334A TYR* 4.0 9.0 - - + +
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Residues in contact with GLU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269A ALA* 3.5 21.6 + - - +
270A LEU* 1.3 69.9 - - - +
272A TRP* 1.3 59.5 - - - +
273A SER* 3.8 1.6 + - - -
282A ALA 3.4 2.9 - - - +
283A LEU* 3.3 2.4 - - - -
284A THR* 2.7 42.9 + - - +
316A ASN* 2.6 45.7 + - - +
318A LYS* 3.6 23.3 - - + +
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Residues in contact with TRP 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270A LEU 3.5 0.6 + - - -
271A GLU* 1.3 69.2 - - - +
273A SER* 1.3 75.7 + - - +
274A PHE* 4.8 0.2 - - - +
282A ALA 3.3 2.7 - - - -
283A LEU* 3.5 33.1 - - + +
292A MET* 3.6 19.3 - - + -
306A LEU* 3.7 14.6 - - + -
308A PHE* 4.6 8.7 - + - -
315A ILE* 3.6 24.5 - - + -
316A ASN 2.8 15.3 + - - +
317A LEU* 3.7 20.8 - - + +
318A LYS* 3.0 25.9 + - - +
319A ASP 3.9 3.1 + - - +
321A VAL* 3.9 22.5 - - + +
323A GLN* 3.2 27.8 - - - -
328A LEU* 4.0 20.2 - - + -
336A VAL* 5.6 0.9 - - + -
344A TRP* 3.6 20.0 - + - -
359A TRP* 5.3 3.4 - + - -
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Residues in contact with SER 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271A GLU 3.8 1.7 + - - -
272A TRP* 1.3 79.5 - - - +
274A PHE* 1.3 63.4 + - - +
281A GLY* 3.0 3.2 - - - -
282A ALA* 2.7 48.8 + - - +
318A LYS* 4.7 17.0 - - - -
319A ASP* 3.4 14.8 - - - -
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Residues in contact with PHE 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A TRP* 4.8 0.7 - - - +
273A SER* 1.3 76.4 - - - +
275A ASN* 1.3 58.9 + - - +
276A SER* 3.6 28.2 + - - -
279A GLY* 3.6 37.0 - - - -
280A ALA 3.6 11.7 - - - -
292A MET* 3.6 23.1 - - + -
294A GLY* 3.8 12.6 - - - -
295A GLN 4.0 8.1 - - - -
319A ASP* 3.0 28.4 + - + +
320A SER 3.4 20.0 - - - +
321A VAL* 3.8 23.3 - - + -
322A SER* 3.4 35.9 - - - -
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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