Contacts of the helix formed by residues 362 - 376 (chain A) in PDB entry 1ULH
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 362 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87A ARG* 4.5 0.4 - - - -
360A LEU* 3.3 11.9 + - + +
361A GLU* 1.3 77.6 - - - +
363A ASP* 1.3 67.1 + - - +
364A ASP* 3.8 14.0 + - - +
365A LYS* 3.0 38.9 + - + +
366A LEU* 3.2 21.2 + - - +
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Residues in contact with ASP 363 (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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80A ARG* 2.7 33.1 + - - +
86A ARG* 3.1 18.9 + - - +
87A ARG* 2.8 33.4 + - - +
361A GLU 3.8 1.2 + - - -
362A ASP* 1.3 71.0 + - - +
364A ASP* 1.3 68.7 + - - +
366A LEU* 3.0 8.1 + - - +
367A GLU* 2.9 31.5 + - - +
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Residues in contact with ASP 364 (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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362A ASP* 3.4 13.0 + - - +
363A ASP* 1.3 83.7 - - - +
365A LYS* 1.3 58.6 + - - +
367A GLU* 3.4 5.4 + - - +
368A GLN* 3.0 37.0 + - - +
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Residues in contact with LYS 365 (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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360A LEU* 4.4 29.8 - - + -
362A ASP* 3.0 30.5 + - + +
363A ASP 3.4 0.2 - - - -
364A ASP* 1.3 75.7 - - - +
366A LEU* 1.3 59.8 + - - +
368A GLN* 3.6 17.8 - - - +
369A ILE* 3.0 44.3 + - + +
386A ALA* 5.4 10.0 - - - +
389A GLU* 5.6 4.0 + - - -
390A VAL* 6.2 0.2 - - - -
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Residues in contact with LEU 366 (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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87A ARG* 3.4 42.2 - - + +
353A PHE* 3.4 36.1 - - + -
356A LEU* 3.6 31.2 - - + +
357A THR* 4.3 7.4 - - + +
360A LEU* 4.4 9.2 - - + +
362A ASP 3.2 13.4 + - - +
363A ASP* 3.0 11.5 + - - +
365A LYS* 1.3 75.8 - - - +
367A GLU* 1.3 61.2 + - - +
369A ILE* 3.0 9.4 + - + +
370A ARG* 2.9 26.4 + - - +
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Residues in contact with GLU 367 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A ASP 2.9 15.7 + - - +
364A ASP* 3.8 7.0 - - - +
366A LEU* 1.3 77.1 - - - +
368A GLN* 1.3 55.3 + - + +
370A ARG* 3.0 42.8 + - - +
371A LYS* 2.8 51.5 + - + +
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Residues in contact with GLN 368 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364A ASP* 3.0 27.1 + - - +
365A LYS* 3.6 21.5 - - - +
367A GLU* 1.3 77.2 - - + +
369A ILE* 1.3 57.6 + - + +
371A LYS* 4.0 5.8 - - + +
372A ASP* 2.7 43.5 + - - +
378A MET* 5.8 0.4 - - - -
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Residues in contact with ILE 369 (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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353A PHE* 4.2 7.9 - - + -
356A LEU* 4.0 12.1 - - + -
360A LEU* 3.7 28.5 - - + -
365A LYS* 3.0 37.2 + - + +
366A LEU* 3.0 9.3 + - - +
368A GLN* 1.3 77.6 - - + +
370A ARG* 1.3 58.5 + - - +
372A ASP* 4.1 0.2 - - - +
373A TYR* 2.9 33.0 + - + +
378A MET* 3.8 26.5 - - + +
383A LEU* 3.4 31.0 - - + -
386A ALA* 4.7 11.0 - - + -
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Residues in contact with ARG 370 (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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347A CYS* 3.7 25.4 - - + -
353A PHE* 3.6 29.8 - - + -
366A LEU 2.9 8.3 + - - +
367A GLU* 3.0 37.9 + - - +
369A ILE* 1.3 75.4 - - - +
371A LYS* 1.3 90.1 + - - +
374A THR* 2.7 41.9 + - - +
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Residues in contact with LYS 371 (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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367A GLU* 2.8 34.1 + - + +
368A GLN* 4.0 5.4 - - - +
370A ARG* 1.3 95.2 - - - +
372A ASP* 1.3 56.7 + - - +
374A THR* 3.9 1.8 - - - -
375A SER* 2.8 39.6 + - - -
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Residues in contact with ASP 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A GLN* 2.7 35.1 + - - +
369A ILE* 4.1 3.8 - - - +
371A LYS* 1.3 80.0 - - - +
373A TYR* 1.3 60.7 + - - +
375A SER* 3.1 6.0 + - - -
377A ALA* 3.1 29.9 + - + +
378A MET* 2.9 37.8 + - + -
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Residues in contact with TYR 373 (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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331A SER* 3.7 0.2 + - - -
332A GLY 3.7 0.3 + - - -
333A GLY* 3.3 15.7 + - - -
340A HIS* 4.2 7.0 - - - -
345A GLY* 2.9 29.6 + - - -
346A ASN 4.3 4.5 - - - -
347A CYS* 3.5 24.9 - - - -
350A ASP* 2.9 35.4 + - + -
353A PHE* 5.2 1.3 - - + -
369A ILE* 2.9 26.2 + - + +
370A ARG 4.1 1.1 - - - +
372A ASP* 1.3 72.0 - - - +
374A THR* 1.3 63.6 + - - +
376A GLY* 3.5 8.5 + - - -
378A MET* 3.3 30.5 - - + +
379A LEU 4.1 9.6 - - - -
380A THR* 3.2 27.1 + - - +
383A LEU* 3.5 36.7 - - + +
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Residues in contact with THR 374 (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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343A PHE* 3.0 19.1 + - - +
345A GLY* 3.2 22.2 + - - +
347A CYS* 3.4 20.1 - - - +
370A ARG* 2.7 34.7 + - - +
371A LYS* 3.9 1.8 - - - -
373A TYR* 1.3 75.0 - - - +
375A SER* 1.3 65.1 + - - +
376A GLY 3.1 0.2 - - - -
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Residues in contact with SER 375 (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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342A GLN* 3.3 38.9 + - - +
343A PHE 4.0 0.5 + - - -
371A LYS 2.8 22.1 + - - -
372A ASP* 3.1 16.1 + - - -
374A THR* 1.3 73.5 - - - +
376A GLY* 1.3 60.1 + - - +
377A ALA* 3.2 12.5 + - - +
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Residues in contact with GLY 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A HIS* 3.8 22.1 + - - -
341A ARG* 3.6 39.7 + - - -
343A PHE 4.1 2.0 - - - -
372A ASP 3.3 3.4 + - - -
373A TYR 3.5 8.7 + - - -
374A THR 3.1 3.0 - - - -
375A SER* 1.3 80.3 + - - +
377A ALA* 1.3 66.1 + - - +
378A MET 3.4 3.3 + - - +
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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