Contacts of the helix formed by residues 394 - 412 (chain A) in PDB entry 2XLR
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 ASP 394 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A PHE* 1.3 76.6 - - - +
395A ILE* 1.3 52.9 + - - +
396A PRO* 3.5 14.3 - - - +
397A ALA* 3.3 31.7 + - + +
398A THR* 2.5 36.5 + - - -
424A LEU* 4.5 17.6 + - + +
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Residues in contact with ILE 395 (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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325A TYR* 3.6 19.3 - - + +
378A GLY* 3.7 30.3 - - - +
379A ASP* 5.9 0.9 - - - +
381A ILE* 4.3 4.3 - - + -
382A GLN* 3.4 36.1 - - + +
385A ILE* 4.1 13.5 - - + -
393A PHE* 3.1 34.9 + - + +
394A ASP* 1.3 69.6 - - - +
396A PRO* 1.3 67.5 - - + +
398A THR* 2.7 9.4 + - - -
399A ASN* 2.6 50.0 + - - +
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Residues in contact with PRO 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
382A GLN* 5.4 3.4 - - - +
394A ASP* 3.5 11.2 - - - +
395A ILE* 1.3 98.4 - - + +
397A ALA* 1.3 61.5 + - - +
399A ASN* 3.4 8.4 + - - +
400A LYS* 2.7 44.1 + - - +
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Residues in contact with ALA 397 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
394A ASP* 3.3 33.4 + - + +
395A ILE 3.2 0.4 - - - -
396A PRO* 1.3 78.9 - - - +
398A THR* 1.3 55.9 + - - +
400A LYS* 3.3 8.6 + - - +
401A THR* 2.7 33.2 + - - -
424A LEU* 4.1 17.8 - - + +
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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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82A GLU 4.7 0.2 - - - +
83A CYS* 3.9 36.1 - - - +
325A TYR* 3.8 21.3 - - + -
328A ASN* 5.4 0.2 - - - +
393A PHE* 4.1 12.7 - - + -
394A ASP 2.5 24.7 + - - -
395A ILE* 2.7 13.7 + - - -
397A ALA* 1.3 70.4 - - - +
399A ASN* 1.3 67.0 + - - -
401A THR* 3.0 17.1 + - - -
402A PHE* 3.0 16.1 + - + -
424A LEU* 3.9 18.8 - - + +
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Residues in contact with ASN 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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325A TYR* 2.4 33.3 + - - -
374A TYR* 3.8 15.0 + - + +
375A THR* 3.8 34.0 + - - +
395A ILE* 2.6 33.9 + - - +
396A PRO* 3.5 11.5 - - - +
398A THR* 1.3 70.6 - - - +
400A LYS* 1.3 68.8 + - - +
402A PHE* 2.9 30.6 + - - +
403A LEU* 3.1 11.7 + - - +
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Residues in contact with LYS 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371A GLU* 5.3 9.0 - - - +
396A PRO* 2.7 43.5 + - - +
397A ALA* 3.6 11.0 - - - +
398A THR 3.2 0.4 - - - -
399A ASN* 1.3 84.3 - - - +
401A THR* 1.3 63.3 + - - +
403A LEU* 3.3 22.5 - - + +
404A GLU* 3.2 25.6 + - - +
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Residues in contact with THR 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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80A PRO* 4.2 6.6 - - + +
82A GLU* 5.0 5.4 - - + -
83A CYS* 4.0 17.5 - - - -
397A ALA 2.7 17.4 + - - -
398A THR* 3.0 9.1 + - - -
400A LYS* 1.3 74.4 - - - +
402A PHE* 1.3 63.8 + - - +
404A GLU* 3.4 14.8 + - - +
405A TRP* 3.3 20.4 + - - +
421A TYR* 3.8 34.0 - - + -
422A ARG 5.2 3.8 + - - +
424A LEU* 4.1 14.5 - - + +
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Residues in contact with PHE 402 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A GLY* 5.6 2.2 - - - -
80A PRO* 4.7 7.0 - - + -
83A CYS* 3.5 38.1 - - + -
324A TRP* 3.4 33.0 - + + -
325A TYR* 4.1 30.7 - + - -
374A TYR* 4.5 20.0 - - + -
398A THR* 3.0 21.5 + - + -
399A ASN* 2.9 17.5 + - - +
401A THR* 1.3 74.9 - - - +
403A LEU* 1.3 66.0 + - + +
405A TRP* 3.1 35.0 + + + +
406A LYS* 2.9 23.4 + - + +
501A NAP 5.1 4.9 - - - -
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Residues in contact with LEU 403 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ALA* 5.5 1.8 - - + -
371A GLU* 3.9 48.5 - - + +
374A TYR* 6.0 2.9 - - + -
399A ASN 3.1 11.6 + - - +
400A LYS* 3.3 24.2 - - + +
402A PHE* 1.3 83.2 - - + +
404A GLU* 1.3 64.5 + - - +
406A LYS* 3.1 11.6 + - + +
407A HIS* 2.9 25.9 + - - +
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Residues in contact with GLU 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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400A LYS* 3.2 11.6 + - - +
401A THR* 3.7 21.1 + - - +
402A PHE 3.2 0.8 - - - -
403A LEU* 1.3 82.0 - - + +
405A TRP* 1.3 58.9 + - - +
407A HIS* 3.4 5.2 + - - +
408A HIS* 2.8 50.1 + - - +
420A SER 4.7 2.9 - - - +
421A TYR* 3.6 28.0 - - + +
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Residues in contact with TRP 405 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASP 2.8 32.0 + - - -
79A GLY* 3.9 3.8 - - - -
80A PRO* 3.8 19.3 - - + -
102A TYR* 3.1 27.4 - + - -
212A TYR* 4.2 5.2 - + - -
324A TRP* 5.8 2.9 - + - -
401A THR 3.3 10.0 + - - +
402A PHE* 3.3 36.6 - + + +
404A GLU* 1.3 79.6 - - - +
406A LYS* 1.3 102.1 + - + +
408A HIS* 3.3 4.0 + - - +
409A LYS* 3.1 40.2 + - + +
416A PHE* 3.6 17.7 - + - -
421A TYR* 3.8 11.6 - - - +
501A NAP 3.7 28.7 - - - -
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Residues in contact with LYS 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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212A TYR* 3.4 23.3 + - - -
215A GLU* 5.9 0.4 + - - -
240A TYR* 4.9 7.4 + - - +
324A TRP* 4.7 15.7 - - + -
370A ALA* 4.9 16.4 - - + -
402A PHE* 2.9 19.8 + - + +
403A LEU* 3.6 14.1 - - + +
405A TRP* 1.3 110.1 - - + +
407A HIS* 1.3 62.2 + - - +
409A LYS* 3.0 34.8 + - + +
410A LYS* 3.1 16.4 + - - +
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Residues in contact with HIS 407 (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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403A LEU 2.9 16.7 + - - +
404A GLU* 3.7 6.3 - - - +
406A LYS* 1.3 77.0 - - - +
408A HIS* 1.3 67.6 + - - +
410A LYS* 3.1 15.0 + - + +
411A GLU* 2.9 57.1 + - + +
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Residues in contact with HIS 408 (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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102A TYR* 5.5 0.2 - - - +
404A GLU* 2.8 41.0 + - - +
405A TRP 3.5 5.6 - - - +
407A HIS* 1.3 85.8 - - - +
409A LYS* 1.3 62.2 + - - +
411A GLU* 3.6 15.2 + - - +
412A ASN 3.3 22.7 + - - +
415A THR* 5.3 0.5 + - - -
416A PHE* 3.6 11.4 + - + +
419A HIS* 2.5 53.2 + + + -
420A SER 5.2 2.0 - - - -
421A TYR* 2.7 33.4 + + - +
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Residues in contact with LYS 409 (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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78A ASP* 5.0 1.6 + - - +
212A TYR* 3.8 17.4 - - - -
215A GLU* 3.0 29.0 + - - -
240A TYR* 3.8 26.8 + - + +
405A TRP* 3.1 45.8 + - + +
406A LYS* 3.0 23.4 + - + +
408A HIS* 1.3 76.7 - - - +
410A LYS* 1.3 65.6 + - - +
412A ASN 3.3 0.6 - - - -
413A ILE* 3.2 40.3 + - + -
416A PHE* 3.6 38.2 - - + -
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Residues in contact with LYS 410 (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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238A MET 4.5 6.3 + - - -
239A GLY* 4.1 22.2 + - - -
240A TYR* 4.1 27.3 - - + +
241A LYS* 5.6 4.5 + - - +
406A LYS 3.1 12.5 + - - +
407A HIS* 3.3 17.5 - - + +
409A LYS* 1.3 76.3 - - - +
411A GLU* 1.3 66.8 + - + +
412A ASN* 4.6 0.2 - - - -
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Residues in contact with GLU 411 (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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241A LYS* 5.5 6.2 - - - +
407A HIS* 2.9 50.3 + - + +
408A HIS* 3.8 13.2 - - - +
409A LYS 3.3 0.2 - - - -
410A LYS* 1.3 80.5 - - - +
412A ASN* 1.3 66.0 + - + +
419A HIS* 4.2 18.4 + - - -
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Residues in contact with ASN 412 (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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241A LYS* 5.0 5.3 - - - +
408A HIS 3.3 7.7 + - - +
409A LYS 3.3 2.9 - - - -
410A LYS 4.6 0.2 - - - -
411A GLU* 1.3 85.0 - - + +
413A ILE* 1.3 66.5 + - - +
414A MET* 2.8 21.3 + - - +
415A THR* 3.0 49.9 + - - +
416A PHE* 3.1 12.0 + - - +
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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
------------------------------------------------------------
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