Contacts of the helix formed by residues 393 - 405 (chain A) in PDB entry 5H65
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 HIS 393 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A PHE* 5.5 1.9 - + - -
390A GLU* 5.7 4.8 + - + +
391A VAL 3.5 5.7 + - - -
392A PRO* 1.3 76.2 - - + +
394A GLU* 1.3 65.0 + - - +
395A GLY* 3.3 5.2 - - - +
396A ASP* 2.8 24.0 + - - +
397A LEU* 3.0 22.6 + - - +
297B ARG* 3.0 62.2 + - + +
301B THR* 5.2 15.5 + - + +
305B VAL* 6.1 4.7 - - + -
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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
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393A HIS* 1.3 72.7 - - - +
395A GLY* 1.3 53.3 + - - +
397A LEU* 3.1 9.2 + - - +
398A ASP* 2.7 56.6 + - - +
460A LEU* 4.1 17.1 - - + +
288B PRO* 4.0 24.4 - - - +
290B VAL* 4.1 22.5 - - - +
294B ALA* 6.2 3.8 - - + -
297B ARG* 5.9 0.8 - - - +
298B CYS* 5.6 5.5 - - - -
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Residues in contact with GLY 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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393A HIS* 3.3 3.9 - - - +
394A GLU* 1.3 79.8 + - - +
396A ASP* 1.3 60.9 + - - +
398A ASP* 3.4 10.6 + - - +
399A ILE* 3.1 29.6 + - - +
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Residues in contact with ASP 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 PRO* 3.8 13.5 - - + +
393A HIS* 2.8 41.0 + - - +
395A GLY* 1.3 75.9 - - - +
397A LEU* 1.3 62.2 - - - +
399A ILE* 3.4 7.7 + - - +
400A ILE* 3.3 29.9 + - + +
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Residues in contact with LEU 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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392A PRO* 3.8 17.7 - - + +
393A HIS 3.0 18.3 + - - +
394A GLU* 3.6 6.1 - - - +
396A ASP* 1.3 72.6 - - - +
398A ASP* 1.3 66.4 + - - +
400A ILE* 3.1 8.4 + - + +
401A PHE* 2.9 39.8 + - + -
460A LEU* 4.1 30.1 - - + -
489A SER 4.1 1.3 - - - +
490A ALA* 3.9 15.9 - - + -
491A PRO* 3.8 20.6 - - + -
499A HIS* 4.6 8.5 - - + -
501A TYR* 3.6 27.1 - - - +
575A MET* 5.7 3.1 - - + -
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Residues in contact with ASP 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* 2.7 48.4 + - - +
395A GLY* 3.6 10.5 - - - +
397A LEU* 1.3 72.2 - - - +
399A ILE* 1.3 56.2 + - + +
401A PHE* 3.9 4.8 - - - +
402A GLN* 2.9 34.3 + - - +
460A LEU* 4.0 20.6 + - - +
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Residues in contact with ILE 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 GLY 3.1 18.1 + - - +
396A ASP* 3.6 11.2 - - - +
397A LEU 3.3 0.2 - - - -
398A ASP* 1.3 76.6 - - + +
400A ILE* 1.3 62.5 + - + +
402A GLN* 3.9 8.1 - - - +
403A ASP* 2.9 32.7 + - + +
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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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392A PRO* 6.1 0.4 - - + -
396A ASP* 3.3 20.8 + - + +
397A LEU* 3.1 11.2 + - + +
399A ILE* 1.3 81.3 - - + +
401A PHE* 1.3 58.7 + - + +
403A ASP* 3.3 7.1 + - - +
404A GLY* 2.9 25.3 + - - -
486A LEU* 3.8 28.6 - - + +
487A ASP* 4.0 20.2 - - + +
489A SER* 3.6 32.8 - - - +
490A ALA* 4.0 21.1 - - + +
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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 LEU* 2.9 45.5 + - + +
398A ASP* 4.1 4.0 - - - +
400A ILE* 1.3 72.4 - - - +
402A GLN* 1.3 66.3 + - - +
404A GLY* 3.2 2.5 + - - +
405A ALA* 3.0 21.7 + - - +
457A GLY 4.9 1.4 - - - -
458A GLY 3.5 28.1 - - - +
459A THR* 4.3 8.1 - - + -
460A LEU* 3.9 35.7 - - + +
463A ILE* 3.5 23.3 - - + -
475A PRO* 3.8 18.8 - - + -
486A LEU* 3.6 27.8 - - + -
490A ALA* 4.2 15.0 - - + -
491A PRO* 4.7 6.5 - - + -
494A ILE* 5.4 1.8 - - + -
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Residues in contact with GLN 402 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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398A ASP 2.9 19.8 + - - +
399A ILE* 4.0 7.5 - - - +
401A PHE* 1.3 76.0 - - - +
403A ASP* 1.3 63.0 + - - +
405A ALA* 3.1 22.1 + - + +
406A THR* 3.5 12.2 + - + +
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Residues in contact with ASP 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 ILE* 2.9 23.5 + - + +
400A ILE* 3.5 7.0 - - - +
402A GLN* 1.3 76.7 - - - +
404A GLY* 1.3 58.8 + - - +
406A THR* 2.7 36.7 + - - +
407A LYS* 3.9 8.0 - - - +
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Residues in contact with GLY 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 ILE 2.9 15.5 + - - -
401A PHE* 3.2 5.6 + - - -
403A ASP* 1.3 75.4 + - - +
405A ALA* 1.3 59.9 + - - +
407A LYS* 3.2 28.4 + - - +
457A GLY* 4.4 12.5 + - - -
477A ARG* 6.4 0.2 - - - -
486A LEU* 4.2 21.3 - - - -
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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 PHE 3.0 11.9 + - - +
402A GLN* 3.1 17.0 + - + +
404A GLY* 1.3 74.7 - - - +
406A THR* 1.3 61.5 + - - +
407A LYS 3.3 4.9 + - - +
432A ARG* 3.7 46.3 - - + +
433A LYS 4.8 2.8 + - - +
457A GLY* 3.9 15.4 - - - +
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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