Contacts of the helix formed by residues 390 - 411 (chain A) in PDB entry 3U0Z
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 390 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391A SER* 1.3 62.1 + - - +
392A SER* 3.0 16.8 + - - +
393A ARG* 3.0 48.6 + - - +
394A ARG* 3.4 10.0 + - - +
431A LYS* 6.3 2.2 - - - +
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Residues in contact with SER 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ASP* 1.3 76.4 - - - +
392A SER* 1.3 56.0 + - - +
394A ARG* 3.1 24.3 - - - +
395A GLN* 3.2 16.2 + - - +
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Residues in contact with SER 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ASP* 4.2 9.7 + - - -
391A SER* 1.3 77.7 - - - +
393A ARG* 1.3 62.4 + - - +
394A ARG 3.0 5.5 + - - -
395A GLN* 3.7 4.0 + - - +
396A TYR* 3.1 19.8 + - - +
431A LYS* 4.4 12.4 - - - +
432A ILE 2.9 42.9 + - - -
433A PHE* 4.2 16.9 - - - +
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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
----------------------------------------------------------
390A ASP* 3.0 40.4 + - - +
392A SER* 1.3 79.2 + - - +
394A ARG* 1.3 57.7 + - - +
396A TYR* 4.1 6.0 - - - +
397A GLN* 4.1 28.8 - - - +
430A GLY* 3.4 22.8 + - - +
431A LYS* 3.3 37.1 - - + +
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Residues in contact with ARG 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A ASP 3.4 7.0 + - - +
391A SER* 3.1 16.5 + - - +
392A SER 3.0 1.4 - - - -
393A ARG* 1.3 76.4 - - - +
395A GLN* 1.3 67.9 + - + +
396A TYR 3.2 1.1 - - - -
397A GLN* 3.2 19.8 + - - +
398A GLU* 3.2 35.9 + - + +
401A LYS* 5.3 7.7 - - - +
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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
----------------------------------------------------------
391A SER* 3.2 13.9 + - - +
392A SER* 3.7 10.1 - - - +
394A ARG* 1.3 77.4 - - + +
396A TYR* 1.3 55.8 + - - +
398A GLU* 3.3 6.2 + - - +
399A LYS* 2.8 68.6 + - - +
432A ILE* 4.2 20.3 + - + +
433A PHE* 5.9 1.2 - - - +
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Residues in contact with TYR 396 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392A SER 3.1 11.9 + - - +
393A ARG 4.1 3.6 - - - +
394A ARG 3.2 0.2 - - - -
395A GLN* 1.3 77.4 - - - +
397A GLN* 1.3 82.7 + - + +
399A LYS* 3.7 1.9 - - - +
400A TYR* 3.0 35.0 + + + +
421A HIS* 5.9 0.7 - - - -
424A TYR* 3.6 31.6 - + - +
425A GLU* 3.7 29.8 - - - +
428A TYR* 3.8 15.7 - - + -
430A GLY* 3.1 57.2 + - - +
431A LYS* 3.3 6.3 - - - +
432A ILE* 4.1 12.3 - - + +
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Residues in contact with GLN 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* 4.1 25.7 + - - +
394A ARG* 3.2 15.1 + - - +
396A TYR* 1.3 96.9 - - + +
398A GLU* 1.3 62.4 + - + +
400A TYR* 4.0 4.2 - - + +
401A LYS* 3.1 34.7 + - - +
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Residues in contact with GLU 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 ARG* 3.2 37.7 + - + +
395A GLN* 3.3 7.8 + - - +
397A GLN* 1.3 77.2 - - - +
399A LYS* 1.3 61.1 + - + +
401A LYS* 3.1 20.4 + - + +
402A GLN* 2.9 29.4 + - - +
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Residues in contact with LYS 399 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395A GLN* 2.8 46.9 + - - +
396A TYR 3.7 2.5 - - - +
398A GLU* 1.3 78.0 - - + +
400A TYR* 1.3 57.6 + - - +
402A GLN* 2.8 35.5 + - + +
403A VAL* 2.9 14.4 + - - +
424A TYR* 3.6 18.8 - - - +
432A ILE* 4.0 25.8 - - + +
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Residues in contact with TYR 400 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
396A TYR* 3.0 25.2 + + + +
397A GLN* 4.6 4.5 - - + +
399A LYS* 1.3 77.2 - - - +
401A LYS* 1.3 59.7 + - - +
403A VAL* 3.7 28.7 - - + -
404A GLU* 3.1 50.2 + - + +
407A MET* 4.3 11.2 - - + +
417A ARG 4.6 0.2 + - - -
420A ILE* 4.9 0.7 - - + -
421A HIS* 2.9 59.9 + + - +
424A TYR* 3.9 32.4 + + + -
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Residues in contact with LYS 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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394A ARG* 5.3 7.9 - - - +
397A GLN* 3.1 24.1 + - - +
398A GLU* 3.3 23.3 + - + +
399A LYS 3.1 0.4 - - - -
400A TYR* 1.3 75.4 - - - +
402A GLN* 1.3 64.1 + - - +
404A GLU* 3.6 16.6 + - - +
405A GLN* 3.2 30.6 + - - +
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Residues in contact with GLN 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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398A GLU 2.9 13.1 + - - +
399A LYS* 2.8 27.8 + - + +
401A LYS* 1.3 71.9 - - - +
403A VAL* 1.3 64.5 + - + +
405A GLN* 3.0 26.2 + - - +
406A TYR* 3.1 12.9 + - - +
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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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399A LYS 2.9 14.1 + - - +
400A TYR* 3.7 32.1 - - + +
402A GLN* 1.3 74.5 - - + +
404A GLU* 1.3 66.0 + - - +
406A TYR* 3.0 20.7 + - - +
407A MET* 3.0 22.9 + - + +
420A ILE* 4.1 20.0 - - + -
424A TYR* 4.1 25.1 - - + +
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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 TYR* 3.1 50.3 + - + +
401A LYS* 3.7 17.2 - - - +
403A VAL* 1.3 76.7 - - - +
405A GLN* 1.3 63.3 + - + +
407A MET* 3.5 18.4 + - + +
408A SER* 3.1 26.1 + - - +
417A ARG* 4.8 0.9 + - - -
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Residues in contact with GLN 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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401A LYS* 3.2 19.2 + - - +
402A GLN* 3.0 19.7 + - - +
404A GLU* 1.3 79.5 - - + +
406A TYR* 1.3 54.3 + - - +
408A SER* 3.1 9.8 + - - -
409A PHE* 2.8 34.6 + - - +
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Residues in contact with TYR 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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402A GLN 3.1 7.1 + - - +
403A VAL* 3.0 12.9 + - + +
405A GLN* 1.3 78.1 - - - +
407A MET* 1.3 71.8 + - + +
409A PHE* 3.2 6.8 + + - +
410A HIS* 2.9 68.1 + + + +
412A LEU* 4.8 10.5 - - + -
420A ILE* 6.5 0.4 - - + -
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Residues in contact with MET 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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400A TYR* 4.3 12.8 - - - +
403A VAL* 3.0 15.1 + - + +
404A GLU* 3.5 33.7 - - + +
405A GLN 3.2 0.2 - - - -
406A TYR* 1.3 77.9 - - + +
408A SER* 1.3 51.6 + - - +
410A HIS* 3.0 4.7 + - - +
411A LYS 2.7 31.9 + - - -
412A LEU* 3.5 27.1 + - + -
417A ARG* 3.4 56.8 + - + +
420A ILE* 4.1 26.5 - - + -
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Residues in contact with SER 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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404A GLU* 3.1 15.6 + - - +
405A GLN* 3.3 9.9 - - - -
407A MET* 1.3 73.3 - - - +
409A PHE* 1.3 64.9 + - - +
411A LYS* 2.9 20.8 + - - +
417A ARG* 3.7 21.9 + - - +
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Residues in contact with PHE 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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405A GLN 2.8 16.2 + - - +
406A TYR* 3.2 8.7 + + + +
408A SER* 1.3 74.7 - - - +
410A HIS* 1.3 85.3 + + + +
411A LYS* 3.7 17.4 + - - -
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Residues in contact with HIS 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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406A TYR* 2.9 68.7 + + + +
409A PHE* 1.3 101.6 + + - +
411A LYS* 1.3 73.4 + - - +
412A LEU* 3.3 25.7 + - + +
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Residues in contact with LYS 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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407A MET 2.7 7.1 + - - -
408A SER 2.9 12.8 + - - +
409A PHE* 3.8 17.0 - - - -
410A HIS* 1.3 79.5 - - - +
412A LEU* 1.3 65.0 + - - +
413A PRO* 3.6 4.2 - - - +
417A ARG* 3.5 12.8 - - - +
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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