Contacts of the helix formed by residues 387 - 400 (chain A) in PDB entry 1XR2
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 GLU 387 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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386A LYS* 1.3 77.4 - - - +
388A TYR* 1.3 68.3 + - - +
389A THR* 3.7 25.5 + - - +
390A GLU* 3.1 14.5 + - + +
391A ARG* 3.0 18.2 + - - +
1202A SO4 3.8 12.6 - - - +
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Residues in contact with TYR 388 (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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387A GLU* 1.3 71.6 - - - +
389A THR* 1.3 61.4 + - + +
391A ARG* 2.9 11.0 + - - +
392A ASP* 2.6 62.5 + - + +
396A ARG* 4.4 0.5 + - - -
637A ASP* 3.3 42.0 - - + -
661A ILE* 3.3 44.4 + - + -
662A LYS* 3.6 31.0 - - + -
663A GLN* 3.2 36.7 + - - +
697A LEU* 4.5 0.9 - - - +
1202A SO4 3.0 20.2 + - - +
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Residues in contact with THR 389 (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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387A GLU* 3.4 23.7 + - - +
388A TYR* 1.3 81.6 - - + +
390A GLU* 1.3 64.7 + - - +
392A ASP* 3.7 5.0 - - - +
393A ARG* 3.4 19.4 + - - +
661A ILE* 4.0 23.3 - - + -
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Residues in contact with GLU 390 (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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386A LYS* 3.9 39.7 + - + +
387A GLU* 3.1 17.2 + - + +
388A TYR 3.1 0.8 - - - -
389A THR* 1.3 80.4 + - - +
391A ARG* 1.3 64.1 + - - +
393A ARG* 3.5 10.4 + - - +
394A ILE* 3.3 33.1 + - - +
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Residues in contact with ARG 391 (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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384A ARG* 3.1 47.0 - - - +
386A LYS* 2.6 41.9 + - + +
387A GLU 3.0 12.7 + - - +
388A TYR* 2.9 22.8 + - - +
390A GLU* 1.3 73.9 - - - +
392A ASP* 1.3 62.2 + - - +
394A ILE* 3.2 6.3 + - - +
395A GLN* 2.8 41.3 + - - +
611A PRO* 3.8 25.8 - - + +
635A GLU 3.8 3.2 + - - -
636A PHE 3.5 11.1 + - - -
637A ASP* 2.7 30.9 + - - +
1202A SO4 2.7 36.5 + - - -
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Residues in contact with ASP 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A TYR* 2.6 52.4 + - + +
389A THR* 3.7 6.7 - - - +
391A ARG* 1.3 73.2 - - - +
393A ARG* 1.3 57.6 + - - +
395A GLN* 3.7 8.3 - - - +
396A ARG* 2.5 70.3 + - - +
663A GLN* 3.5 10.2 + - - -
697A LEU* 5.8 1.0 - - - +
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Residues in contact with ARG 393 (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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389A THR 3.4 8.8 + - - +
390A GLU* 3.8 15.7 - - - +
391A ARG 3.3 0.4 - - - -
392A ASP* 1.3 80.5 - - - +
394A ILE* 1.3 63.7 - - + +
396A ARG* 3.9 5.5 - - - +
397A GLU* 3.0 25.9 + - - +
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Residues in contact with ILE 394 (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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386A LYS* 5.5 4.0 - - + -
390A GLU* 3.4 28.5 - - - +
391A ARG* 3.2 8.9 + - - +
393A ARG* 1.3 78.3 - - + +
395A GLN* 1.3 62.6 + - - +
397A GLU* 3.2 5.7 + - - +
398A ARG* 3.0 24.4 + - + +
611A PRO* 4.7 8.1 - - + +
612A GLU* 3.7 34.3 - - + +
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Residues in contact with GLN 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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384A ARG* 3.9 1.2 - - - +
391A ARG* 2.8 27.5 + - - +
392A ASP* 3.8 6.5 - - - +
394A ILE* 1.3 74.2 - - - +
396A ARG* 1.3 57.1 + - + +
398A ARG* 3.2 6.2 + - - +
399A LEU* 2.9 39.6 + - + +
611A PRO 3.0 24.6 + - - +
612A GLU 3.7 15.5 - - - +
613A THR 3.1 8.5 + - - -
614A GLN* 3.0 42.0 + - + +
637A ASP* 2.9 36.1 + - - +
663A GLN* 5.1 1.7 + - - -
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Residues in contact with ARG 396 (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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388A TYR* 4.4 0.8 + - - -
392A ASP* 2.5 52.2 + - - +
393A ARG* 3.9 4.3 - - - +
395A GLN* 1.3 74.3 - - + +
397A GLU* 1.3 58.0 + - - +
399A LEU* 4.5 3.6 - - - +
400A ASN* 2.9 30.1 + - - +
401A LEU 4.5 1.8 + - - +
614A GLN* 5.6 3.8 - - - +
663A GLN* 3.3 32.5 + - - +
696A GLU* 3.0 42.0 + - - +
697A LEU* 4.6 4.2 - - - +
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Residues in contact with GLU 397 (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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393A ARG 3.0 17.5 + - - +
394A ILE* 3.7 6.1 - - - +
396A ARG* 1.3 77.4 - - - +
398A ARG* 1.3 58.8 + - - +
400A ASN* 3.2 22.2 + - - +
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Residues in contact with ARG 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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394A ILE* 3.0 19.9 + - + +
395A GLN* 3.2 6.5 + - - +
397A GLU* 1.3 79.6 - - - +
399A LEU* 1.3 62.7 + - + +
400A ASN* 5.2 0.8 - - - +
570A GLY* 5.4 3.0 + - - -
571A ILE 4.8 2.4 + - - -
572A LYS* 3.7 57.4 + - - +
612A GLU* 3.1 51.7 + - + +
613A THR* 4.3 4.6 + - - +
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Residues in contact with LEU 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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395A GLN* 2.9 22.5 + - + +
396A ARG* 4.5 2.7 - - - +
398A ARG* 1.3 91.6 - - - +
400A ASN* 1.3 73.6 + - - +
401A LEU* 3.9 26.9 - - + +
525A PRO* 5.0 9.1 - - + +
572A LYS* 3.8 36.6 - - + +
573A ILE* 4.2 17.7 - - + -
612A GLU 5.6 0.9 - - - +
614A GLN* 3.9 38.1 - - + +
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Residues in contact with ASN 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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396A ARG 2.9 17.1 + - - -
397A GLU* 3.2 26.9 + - - +
398A ARG 5.2 0.9 - - - +
399A LEU* 1.3 81.2 - - - +
401A LEU* 1.3 62.0 + - - +
402A PRO* 4.2 2.6 - - - +
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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