Contacts of the helix formed by residues 389 - 401 (chain A) in PDB entry 6XYY
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 PRO 389 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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387A ALA 3.7 7.9 - - - +
388A LEU* 1.3 90.2 - - + +
390A ARG* 1.3 66.6 + - - +
391A ASP* 3.3 15.5 - - - +
392A LYS* 3.1 23.5 + - + -
393A TYR* 2.9 19.8 + - - +
427A ASN* 4.0 1.1 - - - +
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Residues in contact with ARG 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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389A PRO* 1.3 74.0 - - - +
391A ASP* 1.3 64.5 + - - +
393A TYR* 3.0 43.0 + - - +
394A LEU* 3.0 49.0 + - - +
413A ILE* 4.6 4.9 - - - +
417A THR* 3.3 26.8 - - - +
427A ASN* 4.2 12.3 + - - +
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Residues in contact with ASP 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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389A PRO* 3.4 20.9 - - - +
390A ARG* 1.3 75.1 - - - +
392A LYS* 1.3 85.8 + - - +
394A LEU* 3.3 17.2 + - + +
395A GLU* 2.9 26.6 + - - +
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Residues in contact with LYS 392 (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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379A TYR* 4.1 24.7 - - + -
388A LEU* 4.2 11.7 - - + -
389A PRO* 3.1 25.0 + - + +
391A ASP* 1.3 92.9 + - - +
393A TYR* 1.3 61.0 + - - +
395A GLU* 2.9 33.4 + - - +
396A ILE* 3.1 34.1 + - - +
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Residues in contact with TYR 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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388A LEU* 3.8 14.0 - - + +
389A PRO 2.9 12.2 + - - +
390A ARG* 3.2 38.1 - - - +
392A LYS* 1.3 74.5 - - - +
394A LEU* 1.3 62.8 + - + +
396A ILE* 3.2 1.6 + - - +
397A MET* 2.9 54.7 + - + +
413A ILE* 3.1 31.4 + - + -
416A TYR* 2.9 42.8 + - + +
417A THR* 4.3 2.2 - - + -
427A ASN* 3.9 30.5 - - + -
430A GLN* 4.6 3.4 - - + -
431A ILE* 3.5 27.1 - - + -
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Residues in contact with LEU 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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390A ARG* 3.0 57.1 + - - +
391A ASP* 3.5 15.0 - - + +
393A TYR* 1.3 77.3 - - + +
395A GLU* 1.3 56.4 + - - +
397A MET* 4.6 3.1 - - - -
398A ASN* 2.8 51.3 + - - +
413A ILE* 4.3 23.6 - - + -
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Residues in contact with GLU 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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379A TYR* 2.2 36.9 + - - -
391A ASP 2.9 18.1 + - - +
392A LYS* 2.9 34.6 + - - +
394A LEU* 1.3 75.6 - - - +
396A ILE* 1.3 61.0 + - - +
398A ASN* 4.2 5.8 - - - +
399A ASN* 3.3 21.0 + - - +
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Residues in contact with ILE 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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372A LEU* 4.4 4.7 - - + -
376A PHE* 4.0 14.4 - - + -
379A TYR* 3.8 42.8 - - + -
380A PHE* 3.9 12.6 - - + -
388A LEU* 3.8 26.9 - - + -
392A LYS 3.1 19.1 + - - +
393A TYR 3.9 2.0 - - - +
394A LEU 3.2 0.2 - - - -
395A GLU* 1.3 76.0 - - - +
397A MET* 1.3 65.7 + - - +
399A ASN* 3.0 7.8 + - - +
400A ILE* 3.0 30.5 + - + +
431A ILE* 3.7 28.5 - - + -
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Residues in contact with MET 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 TYR* 2.9 54.5 + - + +
394A LEU 4.0 1.3 - - - +
396A ILE* 1.3 77.2 - - - +
398A ASN* 1.3 62.9 + - - +
399A ASN 3.1 0.3 + - - -
400A ILE* 3.2 3.2 + - - +
401A PHE* 3.1 47.9 + - + +
409A ARG* 5.4 0.4 - - - -
412A ILE* 3.6 32.3 - - + +
413A ILE* 4.0 21.8 - - + -
416A TYR* 4.7 2.0 - - + -
431A ILE* 3.8 35.4 - - + -
434A ALA* 4.1 10.1 - - + -
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Residues in contact with ASN 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 LEU* 2.8 39.7 + - - +
395A GLU* 4.2 4.6 - - - +
397A MET* 1.3 73.7 - - - +
399A ASN* 1.3 57.8 + - - +
402A GLY* 3.1 27.0 + - - -
406A GLN* 5.5 1.0 + - - +
409A ARG* 3.2 32.8 + - - +
413A ILE* 3.6 18.4 - - - +
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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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326A GLY* 5.9 2.6 - - - -
327A ILE* 5.7 2.8 + - - +
376A PHE* 3.4 31.2 - - + -
395A GLU 3.3 14.0 + - - +
396A ILE 3.0 10.4 + - - +
398A ASN* 1.3 77.2 - - - +
400A ILE* 1.3 67.1 + - - +
402A GLY* 3.2 11.3 + - - -
403A LYS* 5.5 2.8 - - - -
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Residues in contact with ILE 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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327A ILE* 4.2 26.7 - - + +
372A LEU* 4.2 6.7 - - + -
376A PHE* 3.8 18.4 - - + -
396A ILE* 3.0 24.2 + - + +
397A MET* 3.2 0.9 + - - -
399A ASN* 1.3 78.1 - - - +
401A PHE* 1.3 92.7 + - + +
402A GLY 3.4 1.6 + - - -
403A LYS* 4.8 11.4 + - - -
431A ILE* 3.7 29.4 - - + -
435A VAL* 3.8 17.0 - - + -
439A PHE* 4.3 16.0 - - + -
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Residues in contact with PHE 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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397A MET* 3.1 49.3 + - + +
398A ASN 3.8 2.7 - - - -
400A ILE* 1.3 99.0 - - + +
402A GLY* 1.3 62.5 + - - +
403A LYS 3.1 3.4 - - - -
404A ALA* 3.1 21.6 + - + +
409A ARG* 3.5 24.9 + - + +
412A ILE* 4.0 25.4 - - + -
413A ILE* 6.3 0.7 - - + -
434A ALA* 4.2 19.7 - - + -
435A VAL* 4.9 1.6 - - - -
438A HIS* 3.9 22.9 - + + -
439A PHE* 5.2 0.4 - + - -
563A TRP* 3.5 29.4 - + - -
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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