Contacts of the strand formed by residues 321 - 326 (chain A) in PDB entry 1XB2
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 ASN 321 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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276A THR* 5.3 3.3 - - - -
277A GLY* 3.4 13.9 + - - +
278A THR* 3.0 23.9 + - + +
308A MSE 3.4 17.9 - - - +
309A PHE* 5.6 2.8 - - - -
319A GLY 3.7 2.6 + - - +
320A ASP* 1.3 71.9 - - - +
322A LEU* 1.3 65.3 + - - +
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Residues in contact with LEU 322 (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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260A LEU* 4.2 9.8 - - + +
275A VAL 3.9 0.5 - - - +
276A THR* 3.2 7.0 - - - -
277A GLY 2.8 39.7 + - - +
279A LEU* 4.2 19.1 - - + +
284A LEU* 3.9 19.3 - - + -
306A ILE* 3.6 14.6 - - + -
307A GLU 3.5 12.1 - - - +
308A MSE 3.7 11.9 - - + +
316A ALA* 3.6 28.3 - - + -
320A ASP* 3.1 21.5 - - + +
321A ASN* 1.3 77.8 + - - +
323A GLY* 1.3 65.4 + - - +
324A ALA* 4.9 3.1 - - + +
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Residues in contact with GLY 323 (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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266A TYR* 5.2 1.8 - - - -
274A VAL* 3.8 15.7 - - - -
275A VAL 3.5 6.1 - - - -
276A THR* 4.3 6.5 - - - -
305A GLY 3.8 0.3 - - - +
306A ILE* 3.6 5.2 - - - +
307A GLU* 2.8 42.0 + - - +
322A LEU* 1.3 77.6 - - - +
324A ALA* 1.3 59.2 + - - -
325A LEU 4.0 0.2 + - - -
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Residues in contact with ALA 324 (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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260A LEU* 4.5 5.4 - - + -
274A VAL* 3.2 4.9 - - - +
275A VAL* 2.8 52.2 + - + +
284A LEU* 4.6 7.2 - - + -
303A VAL* 4.5 10.8 - - + -
305A GLY 3.6 4.9 - - - +
306A ILE* 4.9 0.4 - - - +
322A LEU* 4.2 2.6 - - + -
323A GLY* 1.3 74.4 - - - -
325A LEU* 1.3 62.0 + - - +
326A VAL* 3.5 2.9 + - + +
340A MSE 4.0 23.1 - - + -
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Residues in contact with LEU 325 (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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268A ILE* 5.3 1.1 - - + -
271A ARG* 3.8 50.9 - - + +
272A GLY* 3.6 21.8 - - - +
273A THR 3.2 17.7 - - - +
274A VAL* 3.8 14.8 - - + +
303A VAL* 3.5 5.8 - - - -
304A THR* 2.9 49.3 + - - +
305A GLY* 2.7 25.1 + - - +
307A GLU* 5.9 2.0 - - - +
323A GLY 4.0 0.8 + - - -
324A ALA* 1.3 70.5 - - - +
326A VAL* 1.3 61.7 + - - +
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Residues in contact with VAL 326 (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 ARG 5.3 0.5 - - - +
272A GLY* 5.0 1.7 - - - -
273A THR* 2.8 28.5 + - - +
275A VAL* 4.2 12.6 - - + -
290A CYS* 4.9 1.8 - - - -
292A PHE* 3.7 24.0 - - + -
301A THR* 3.2 30.5 - - + -
302A VAL 3.8 3.8 - - - +
303A VAL* 4.9 1.1 - - + +
304A THR* 4.4 2.4 + - - -
324A ALA* 3.9 11.0 - - + +
325A LEU* 1.3 80.8 - - - +
327A ARG* 1.3 66.2 + - - +
328A GLY 3.8 1.2 + - - -
329A LEU* 3.5 28.7 + - + +
334A LEU* 4.6 3.8 - - + -
340A MSE 4.7 6.5 - - - -
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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