Contacts of the helix formed by residues 389 - 405 (chain A) in PDB entry 5CHG
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 ARG 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387A MET 3.6 0.6 + - - -
388A PRO* 1.3 70.1 - - - +
390A GLU* 1.3 79.8 + - - +
392A ALA* 3.3 9.5 + - - -
393A THR* 3.0 30.0 + - - -
418A TYR* 3.1 67.1 + - + +
421A GLY* 3.4 15.2 - - - -
422A LYS 2.9 32.6 + - - +
423A ALA* 3.3 18.8 + - - +
425A CYS* 4.5 6.5 - - - -
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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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388A PRO* 3.0 10.0 + - + -
389A ARG* 1.3 101.1 + - + +
391A GLU* 1.3 64.0 + - - +
393A THR* 3.2 13.8 + - - -
394A GLU* 3.2 27.4 + - - +
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Residues in contact with GLU 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A MET* 4.3 7.4 - - - -
388A PRO* 2.9 29.4 + - + +
390A GLU* 1.3 75.3 - - - +
392A ALA* 1.3 65.9 + - - +
394A GLU* 3.2 14.1 + - - +
395A ILE* 3.1 24.2 + - + +
479A LEU* 3.7 21.2 + - + +
484A ARG* 4.2 20.1 + - - +
485A ARG 4.4 8.7 + - - +
487A ARG* 3.0 49.8 + - - +
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Residues in contact with ALA 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
387A MET* 3.9 9.7 - - - -
388A PRO 3.4 2.4 + - - -
389A ARG* 3.3 17.2 + - - +
390A GLU 3.2 0.4 - - - -
391A GLU* 1.3 80.0 - - - +
393A THR* 1.3 60.9 + - - +
395A ILE* 3.1 4.5 + - - +
396A GLU* 3.0 21.5 + - - +
418A TYR* 3.6 21.5 - - + -
425A CYS* 4.1 9.0 - - - -
428A VAL* 3.9 30.5 - - + +
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Residues in contact with THR 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 ARG* 3.0 14.0 + - - -
390A GLU* 3.2 18.7 + - - +
392A ALA* 1.3 75.6 - - - +
394A GLU* 1.3 63.9 + - + +
396A GLU* 3.0 10.6 + - - +
397A GLN* 3.0 46.2 + - + +
418A TYR* 2.5 31.0 + - - +
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Residues in contact with GLU 394 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
390A GLU* 3.2 15.0 + - - +
391A GLU* 3.2 12.4 + - - +
393A THR* 1.3 79.1 - - + +
395A ILE* 1.3 52.9 + - - +
397A GLN* 3.4 8.1 + - - +
398A THR* 2.5 38.1 + - - -
479A LEU* 3.7 13.4 - - + +
484A ARG* 3.1 34.4 + - - -
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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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387A MET* 4.2 4.5 - - - -
391A GLU* 3.1 17.7 + - + +
392A ALA 3.4 6.7 - - - +
393A THR 3.1 0.4 - - - -
394A GLU* 1.3 74.3 - - - +
396A GLU* 1.3 66.2 + - - +
398A THR* 3.3 8.0 + - - -
399A VAL* 3.1 23.9 + - + +
428A VAL* 3.9 36.3 - - + -
456A PHE* 4.1 12.3 - - + -
477A CYS* 3.9 19.7 - - - -
479A LEU* 3.9 20.9 - - + +
487A ARG* 4.0 22.7 - - + -
489A LEU* 4.1 15.7 - - + -
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Residues in contact with GLU 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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392A ALA 3.0 11.6 + - - +
393A THR* 3.0 13.3 + - - +
395A ILE* 1.3 78.2 - - - +
397A GLN* 1.3 60.9 + - - +
399A VAL* 3.4 3.3 + - - +
400A GLN* 2.8 36.4 + - - +
412A CYS* 3.4 18.7 - - - +
413A VAL* 3.5 2.5 - - - +
414A ALA* 2.8 46.0 + - + +
418A TYR* 4.2 16.0 + - - -
428A VAL* 4.9 0.9 - - + +
430A VAL* 4.6 16.4 - - + -
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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 THR* 3.0 38.6 + - + +
394A GLU* 3.8 7.8 - - - +
396A GLU* 1.3 80.5 - - - +
398A THR* 1.3 61.4 + - - +
399A VAL 3.1 0.7 - - - -
400A GLN* 4.1 12.3 - - - +
401A LYS* 2.8 53.6 + - + +
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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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394A GLU 2.5 25.2 + - - -
395A ILE 3.3 6.3 + - - -
397A GLN* 1.3 76.2 - - - +
399A VAL* 1.3 60.1 + - - +
401A LYS* 4.4 6.1 - - - +
402A ALA* 3.6 21.8 + - - +
451A LEU* 3.9 2.6 - - - +
454A GLU* 3.8 23.9 - - - +
456A PHE* 3.8 33.9 - - + -
479A LEU* 3.7 11.3 - - + +
480A PRO* 5.8 3.8 - - + -
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Residues in contact with VAL 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 ILE 3.1 14.8 + - - +
396A GLU* 3.7 8.3 - - - +
398A THR* 1.3 77.2 - - - +
400A GLN* 1.3 60.3 + - - +
402A ALA* 3.3 2.9 + - - +
403A ALA* 2.9 27.7 + - - +
412A CYS* 4.9 0.4 - - - -
430A VAL* 4.2 21.1 - - + -
432A ILE* 4.1 26.0 - - + -
447A LEU* 4.1 7.6 - - + +
451A LEU* 4.3 12.3 - - + -
456A PHE* 4.3 7.9 - - + -
489A LEU* 4.2 24.5 - - + -
491A ILE* 4.4 13.9 - - + -
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Residues in contact with GLN 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 GLU* 2.8 29.1 + - - +
397A GLN* 3.8 12.4 - - + +
399A VAL* 1.3 74.2 - - - +
401A LYS* 1.3 60.2 + - + +
403A ALA* 3.3 0.9 + - - +
404A GLN* 2.9 61.3 + - - +
410A LEU 4.8 1.0 + - - -
411A LEU* 5.0 0.6 - - - +
412A CYS* 3.3 53.8 + - + +
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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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397A GLN* 2.8 39.5 + - + +
398A THR* 4.4 6.5 - - - +
400A GLN* 1.3 74.8 - - + +
402A ALA* 1.3 62.8 + - - +
404A GLN* 3.3 8.6 + - - +
405A ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 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 THR 3.6 16.7 + - - +
399A VAL 3.3 3.6 + - - +
401A LYS* 1.3 79.9 - - - +
403A ALA* 1.3 60.6 + - - +
405A ALA* 3.6 10.7 - - - +
406A PHE* 3.2 25.3 - - - -
447A LEU* 3.9 9.0 - - + -
450A SER* 4.1 13.7 + - - +
451A LEU* 3.8 20.9 - - + -
454A GLU* 4.0 10.1 - - - +
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Residues in contact with ALA 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 VAL 2.9 18.0 + - - +
400A GLN 3.5 4.3 - - - +
402A ALA* 1.3 74.0 - - - +
404A GLN* 1.3 58.3 - - - +
405A ALA 3.0 4.3 - - - -
406A PHE* 2.9 29.9 + - - +
407A ASN 3.4 3.6 + - - -
410A LEU* 3.5 19.1 - - + +
412A CYS* 3.8 21.5 - - - -
432A ILE* 4.7 1.8 - - + -
443A ILE* 5.3 1.8 - - + -
447A LEU* 3.8 21.7 - - + +
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Residues in contact with GLN 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 GLN* 2.9 49.8 + - + +
401A LYS* 4.0 7.6 - - - +
403A ALA* 1.3 72.3 - - + +
405A ALA* 1.3 59.5 + - - +
406A PHE 3.0 6.7 + - - -
407A ASN* 3.3 24.1 + - - +
408A SER* 3.5 30.3 + - - +
410A LEU* 3.6 21.9 + - + +
412A CYS* 5.5 0.2 - - - -
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Residues in contact with ALA 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 3.1 11.6 + - - +
402A ALA* 3.6 16.8 - - - +
403A ALA 3.0 1.0 - - - -
404A GLN* 1.3 76.6 - - - +
406A PHE* 1.3 65.9 + - + +
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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