Contacts of the strand formed by residues 397 - 406 (chain A) in PDB entry 2XAR
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 GLN 397 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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275A PHE 2.6 27.7 + - - -
276A ILE* 3.8 1.7 - - - +
277A GLN* 2.9 58.3 + - - +
377A SER* 5.5 7.8 - - - +
390A VAL 3.9 0.3 - - - +
391A SER* 3.7 0.9 - - - -
392A LEU* 2.7 36.1 + - - +
395A THR* 2.6 27.1 + - - +
396A ASN* 1.3 81.0 - - - +
398A THR* 1.3 61.0 + - - +
399A PHE* 3.5 24.2 + - + -
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Residues in contact with THR 398 (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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377A SER* 3.7 5.9 + - - -
378A ARG* 2.8 63.5 + - + +
389A TYR* 3.7 28.7 - - + -
390A VAL 3.5 5.4 - - - +
391A SER* 3.6 14.5 + - - +
397A GLN* 1.3 74.9 + - - +
399A PHE* 1.3 58.4 + - - +
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Residues in contact with PHE 399 (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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275A PHE* 3.2 58.6 - + - -
276A ILE* 4.5 4.9 - - + -
290A LEU* 3.6 33.4 - - + -
375A PHE* 4.3 9.2 - - + -
376A GLN 3.5 5.6 - - - +
377A SER* 3.9 24.5 - - - -
389A TYR* 3.2 6.1 - - - +
390A VAL* 2.8 38.6 + - - +
392A LEU* 3.7 23.1 - - + -
397A GLN* 3.5 34.8 - - + -
398A THR* 1.3 75.7 - - - +
400A ASP* 1.3 62.5 + - - +
401A TYR* 3.9 1.4 + - - -
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Residues in contact with ASP 400 (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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152A PHE* 4.0 21.3 - - + -
374A SER 3.7 0.3 - - - +
375A PHE* 3.4 5.0 - - - +
376A GLN* 2.9 39.7 + - + +
378A ARG* 2.8 57.8 + - - +
379A ASN* 3.9 5.4 + - - +
382A ASP* 3.9 12.8 - - - +
386A SER* 3.6 10.8 - - - -
388A ASP 3.4 11.4 - - - +
389A TYR* 3.5 1.6 - - - +
399A PHE* 1.3 72.9 - - - +
401A TYR* 1.3 59.5 + - - +
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Residues in contact with TYR 401 (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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152A PHE* 4.1 2.4 - - - -
294A ALA* 4.0 12.3 - - + -
297A GLY* 4.1 2.5 - - - -
298A SER* 3.3 42.9 + - - -
373A ILE* 4.0 14.1 - - + -
374A SER 3.1 11.0 - - - +
375A PHE* 3.9 19.3 - - + -
386A SER* 4.7 3.8 + - - -
388A ASP* 3.5 39.7 + - + +
389A TYR* 3.5 35.2 - - - -
390A VAL* 3.9 20.6 - - + -
399A PHE 4.6 0.2 - - - -
400A ASP* 1.3 75.6 - - - +
402A LYS* 1.3 76.7 + - - +
403A VAL* 4.1 10.3 - - + -
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Residues in contact with LYS 402 (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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101A HIS* 5.7 1.3 - - - -
152A PHE* 3.5 41.7 + - + +
153A SER* 3.4 34.1 - - - +
372A MET 3.4 1.3 - - - +
373A ILE* 3.1 8.7 - - - +
374A SER* 3.0 38.1 + - - +
386A SER* 6.1 2.0 - - - +
388A ASP* 5.8 0.7 - - - -
401A TYR* 1.3 82.6 - - - +
403A VAL* 1.3 63.1 + - - +
404A HIS* 4.1 19.5 - - - +
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Residues in contact with VAL 403 (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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101A HIS* 2.6 56.2 + - + +
294A ALA 6.4 0.2 - - - -
295A VAL* 6.3 0.4 - - - -
298A SER* 4.3 11.2 - - - +
300A VAL* 3.8 26.7 - - + -
371A ILE* 3.6 16.4 - - + -
372A MET 3.3 1.3 - - - -
373A ILE* 3.6 31.4 - - + -
388A ASP* 5.9 0.7 - - - +
401A TYR* 4.1 18.2 - - + -
402A LYS* 1.3 74.0 - - - +
404A HIS* 1.3 71.4 + - - +
405A PHE* 6.0 0.4 - - + -
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Residues in contact with HIS 404 (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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100A LYS 3.9 18.8 - - - -
101A HIS* 2.9 20.1 + - - +
102A VAL* 4.3 2.5 + - - -
103A ASP* 4.7 6.1 + - + -
149A HIS* 3.1 44.1 + + + +
152A PHE 5.6 2.7 + - - -
370A SER 3.7 0.2 - - - +
371A ILE* 3.4 6.1 - - - -
372A MET* 2.8 43.5 + - + +
374A SER* 4.8 4.9 - - - -
402A LYS* 4.1 28.6 - - + +
403A VAL* 1.3 89.6 + - - +
405A PHE* 1.3 68.0 + - - +
406A ILE* 3.8 2.6 + - + -
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Residues in contact with PHE 405 (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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97A LEU* 3.3 33.2 - - + -
101A HIS* 2.8 26.0 + + + +
102A VAL* 3.8 22.6 - - + +
103A ASP 5.0 4.3 + - - +
300A VAL* 3.7 44.2 - - + -
301A LEU* 5.9 0.2 - - + -
303A ARG* 6.0 0.2 - - + -
304A LEU* 3.8 32.3 - - + -
369A CYS* 4.1 17.5 - - - -
370A SER 3.5 1.8 - - - +
371A ILE* 4.3 18.2 - - + -
403A VAL* 6.0 0.4 - - + -
404A HIS* 1.3 75.1 - - - +
406A ILE* 1.3 64.2 + - - +
408A LEU* 3.9 28.1 - - + +
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Residues in contact with ILE 406 (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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146A LEU* 6.4 1.8 - - + -
149A HIS* 5.1 12.8 - - + +
166A GLU* 3.7 35.2 - - + +
369A CYS* 3.2 6.6 - - - +
370A SER* 2.8 42.9 + - - +
372A MET* 4.1 21.3 - - + -
404A HIS* 4.6 9.4 - - + +
405A PHE* 1.3 78.7 - - - +
407A ASP* 1.3 85.4 + - - +
408A LEU* 3.3 3.9 + - - +
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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