Contacts of the helix formed by residues 384 - 395 (chain A) in PDB entry 3HOU
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 ASN 384 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378A GLU* 3.9 14.6 + - - +
379A VAL 3.1 18.2 + - - -
380A VAL* 3.6 0.2 - - - -
381A THR* 2.6 40.6 + - - -
383A TYR* 1.3 75.5 - - + +
385A ILE* 1.3 66.2 + - - -
386A ASP* 3.0 3.5 + - - -
387A ARG* 3.2 34.1 + - - +
388A LEU* 2.9 40.8 + - + +
115F THR 5.7 2.4 + - - +
117F PRO* 6.0 3.8 - - - +
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Residues in contact with ILE 385 (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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380A VAL* 3.3 32.3 - - + -
381A THR 2.8 12.4 + - - +
382A PRO* 4.0 6.1 + - + +
383A TYR 3.8 1.0 - - - -
384A ASN* 1.3 73.1 - - - +
386A ASP* 1.3 71.0 + - - +
388A LEU* 3.9 2.4 - - - +
389A THR* 2.3 42.8 + - - +
426A LEU* 3.3 31.1 - - + +
427A GLN* 4.4 0.4 - - - +
428A TYR* 3.8 27.8 - - + +
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Residues in contact with ASP 386 (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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382A PRO 4.9 7.1 - - - +
383A TYR 5.6 1.7 - - - +
384A ASN 3.1 1.2 - - - -
385A ILE* 1.3 86.9 - - - +
387A ARG* 1.3 68.5 + - - +
389A THR* 3.1 5.8 + - - -
390A GLN* 3.0 23.1 + - - +
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Residues in contact with ARG 387 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 3.0 40.3 + - - -
384A ASN* 3.2 33.6 + - - +
386A ASP* 1.3 80.3 - - - +
388A LEU* 1.3 65.7 + - - +
390A GLN* 3.1 8.9 + - - +
391A LEU* 3.1 30.2 + - + +
434A ARG* 4.1 4.6 - - - +
437A MET* 3.8 29.8 - - - +
115F THR 5.9 1.4 + - - -
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Residues in contact with LEU 388 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378A GLU* 3.1 36.3 - - + +
379A VAL 4.0 3.8 - - - +
380A VAL* 3.8 21.8 - - + +
384A ASN* 2.9 47.1 + - + +
385A ILE 3.9 0.2 - - - +
387A ARG* 1.3 78.8 - - - +
389A THR* 1.3 59.6 + - - +
391A LEU* 3.1 18.3 + - + +
392A VAL* 2.9 33.9 + - - +
426A LEU* 3.7 12.1 - - + -
432A VAL* 3.9 24.4 - - + +
434A ARG* 4.5 2.0 - - - -
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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
----------------------------------------------------------
385A ILE* 2.3 38.3 + - - +
386A ASP* 3.1 5.8 + - - -
388A LEU* 1.3 74.6 - - - +
390A GLN* 1.3 57.8 + - - +
392A VAL* 3.3 4.9 + - + +
393A ARG* 2.8 52.5 + - + +
424A ILE 4.5 16.4 - - - +
425A GLN* 5.1 2.0 - - - -
426A LEU* 3.8 25.2 + - + +
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Residues in contact with GLN 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 ASP 3.0 11.3 + - - +
387A ARG* 3.2 14.1 - - - +
389A THR* 1.3 79.0 - - - +
391A LEU* 1.3 53.8 + - + +
393A ARG* 3.6 28.1 + - - +
394A ASN* 2.6 55.6 + - - +
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Residues in contact with LEU 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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387A ARG* 3.1 29.1 + - + +
388A LEU* 3.1 19.5 + - + +
390A GLN* 1.3 75.9 - - + +
392A VAL* 1.3 65.9 + - - +
394A ASN* 2.9 15.1 + - + +
395A GLY 2.9 12.6 + - - -
400A PRO* 3.4 38.4 - - + +
401A GLY* 3.6 20.1 - - - +
402A ALA* 3.7 4.8 + - + -
432A VAL* 5.4 0.4 - - + -
434A ARG* 4.1 31.4 - - + -
437A MET* 4.5 11.7 - - - -
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Residues in contact with VAL 392 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388A LEU 2.9 20.5 + - - +
389A THR* 3.7 9.0 - - + +
391A LEU* 1.3 75.6 - - - +
393A ARG* 1.3 65.0 + - - +
395A GLY* 3.2 11.1 + - - -
402A ALA* 4.4 2.0 - - - -
405A VAL* 3.5 17.5 - - + -
415A LEU* 3.2 41.7 - - + +
421A ALA* 4.6 7.2 - - - +
424A ILE* 4.2 17.0 - - + -
426A LEU* 4.2 5.8 - - + -
432A VAL* 3.5 28.5 - - + -
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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* 2.8 40.0 + - + +
390A GLN* 3.7 28.1 + - - +
392A VAL* 1.3 77.1 - - - +
394A ASN* 1.3 64.1 + - - +
395A GLY* 3.4 1.0 + - - -
421A ALA 4.9 8.3 - - - -
422A GLY* 4.3 22.8 + - - +
423A ASP 5.6 2.1 + - - +
424A ILE 5.9 0.2 + - - -
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Residues in contact with ASN 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 GLN* 2.6 50.0 + - - +
391A LEU* 3.0 11.8 - - - +
393A ARG* 1.3 75.2 - - - +
395A GLY* 1.3 56.3 + - - +
398A GLU* 3.3 57.4 + - - +
400A PRO* 3.1 28.2 + - - +
401A GLY* 4.2 0.7 - - - -
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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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391A LEU 2.9 8.5 + - - -
392A VAL 3.2 10.0 + - - -
393A ARG 4.2 0.7 - - - -
394A ASN* 1.3 80.5 - - - +
396A PRO* 1.3 69.5 - - - +
397A ASN* 3.1 9.2 + - - -
398A GLU 3.8 4.3 - - - +
401A GLY* 3.3 9.2 - - - -
402A ALA 3.2 18.6 + - - -
435A HIS* 3.7 0.9 + - - -
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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