Contacts of the helix formed by residues 362 - 376 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87B ARG* 3.5 3.3 - - - +
360B LEU* 4.2 8.0 - - + +
361B GLU* 1.3 77.7 - - - +
363B ASP* 1.3 68.8 + - - +
364B ASP* 3.3 10.4 + - - +
365B LYS* 3.4 32.9 + - + +
366B LEU* 3.1 22.7 + - - +
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Residues in contact with ASP 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B ARG* 4.5 11.1 + - - -
83B HIS* 4.9 0.3 - - - +
86B ARG* 2.8 42.7 + - - +
87B ARG* 3.3 25.4 + - - +
361B GLU* 5.2 0.2 - - - -
362B ASP* 1.3 75.6 + - - +
364B ASP* 1.3 62.6 + - - +
366B LEU* 3.7 5.4 + - - +
367B GLU* 3.0 27.7 + - - +
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Residues in contact with ASP 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B ASP* 3.2 9.0 + - - +
363B ASP* 1.3 79.0 - - - +
365B LYS* 1.3 61.6 + - - +
367B GLU* 3.3 9.9 + - - +
368B GLN* 2.8 28.6 + - - +
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Residues in contact with LYS 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B LEU* 4.2 22.3 - - + +
362B ASP* 3.3 28.5 + - + +
364B ASP* 1.3 78.2 - - - +
366B LEU* 1.3 52.7 + - - +
368B GLN* 2.9 19.7 + - - +
369B ILE* 2.7 56.7 + - + +
386B ALA* 6.0 4.4 - - - +
389B GLU* 5.8 1.8 + - - -
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Residues in contact with LEU 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87B ARG* 3.5 41.3 - - + +
353B PHE* 3.7 22.4 - - + -
356B LEU* 3.7 40.8 - - + +
357B THR* 3.9 12.6 - - + +
360B LEU* 3.6 16.0 - - + +
362B ASP 3.1 14.7 + - - +
363B ASP* 3.8 5.4 - - - +
365B LYS* 1.3 79.4 - - - +
367B GLU* 1.3 58.1 + - - +
369B ILE* 3.3 6.6 + - + +
370B ARG* 3.0 26.5 + - - +
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Residues in contact with GLU 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B ASP 3.0 19.2 + - - +
364B ASP* 3.5 11.9 - - - +
365B LYS 3.1 0.2 - - - -
366B LEU* 1.3 76.9 - - - +
368B GLN* 1.3 62.3 + - - +
370B ARG* 2.8 47.4 + - - +
371B LYS* 2.9 42.9 + - - +
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Residues in contact with GLN 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364B ASP 2.8 14.2 + - - +
365B LYS* 2.9 25.0 + - - +
367B GLU* 1.3 75.2 - - - +
369B ILE* 1.3 74.6 + - - +
370B ARG 3.1 0.2 - - - -
371B LYS* 4.7 3.1 - - - +
372B ASP* 2.9 56.9 + - - +
378B MET* 5.0 5.1 - - - +
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Residues in contact with ILE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B CYS* 4.8 0.3 - - - -
353B PHE* 4.4 5.8 - - + -
356B LEU* 4.1 16.8 - - + -
360B LEU* 4.0 22.7 - - + -
365B LYS* 2.7 35.5 + - + +
366B LEU* 3.3 6.9 + - - +
368B GLN* 1.3 91.6 - - - +
370B ARG* 1.3 58.4 + - - +
372B ASP 4.1 0.4 - - - -
373B TYR* 3.1 27.2 + - - +
378B MET* 3.5 19.0 - - + +
383B LEU* 3.3 30.2 - - + +
386B ALA* 4.7 13.9 - - + -
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Residues in contact with ARG 370 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347B CYS* 3.9 26.3 - - + -
353B PHE* 3.8 17.5 - - + -
366B LEU 3.0 12.7 + - - +
367B GLU* 2.8 50.7 + - - +
368B GLN 3.1 0.4 - - - -
369B ILE* 1.3 76.1 - - - +
371B LYS* 1.3 93.3 + - - +
373B TYR 3.4 1.0 + - - -
374B THR* 2.7 37.5 + - - +
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Residues in contact with LYS 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367B GLU* 2.9 40.7 + - - +
368B GLN* 4.3 4.3 - - - +
370B ARG* 1.3 102.3 - - - +
372B ASP* 1.3 63.4 - - - +
374B THR* 3.2 7.8 + - - -
375B SER* 2.8 32.9 + - - -
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Residues in contact with ASP 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368B GLN* 2.9 43.6 + - - +
369B ILE* 4.2 2.0 - - - +
371B LYS* 1.3 84.3 - - - +
373B TYR* 1.3 62.2 + - - +
375B SER* 3.0 19.7 + - - -
377B ALA* 3.1 16.3 + - - +
378B MET* 3.1 32.1 + - + +
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Residues in contact with TYR 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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331B SER* 3.0 21.0 + - - -
333B GLY* 3.4 13.7 - - - -
345B GLY* 3.1 42.0 + - - -
346B ASN 4.1 2.5 - - - -
347B CYS* 4.2 17.7 - - - -
350B ASP* 3.7 15.4 + - + -
353B PHE* 5.5 0.2 - - + -
369B ILE 3.1 21.0 + - - +
370B ARG 4.0 2.2 - - - +
372B ASP* 1.3 76.5 - - - +
374B THR* 1.3 63.0 + - - +
376B GLY* 3.7 5.9 + - - -
378B MET* 3.7 13.8 - - + +
379B LEU 4.3 2.9 + - - +
380B THR* 2.7 52.8 + - - +
383B LEU* 3.6 36.4 - - + +
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Residues in contact with THR 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B GLY 3.1 22.4 + - - +
345B GLY 3.5 14.6 + - - +
347B CYS* 4.1 12.5 + - - +
370B ARG* 2.7 29.1 + - - +
371B LYS* 3.4 7.3 - - - -
373B TYR* 1.3 78.6 - - - +
375B SER* 1.3 63.7 + - - +
376B GLY 3.2 0.9 + - - -
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Residues in contact with SER 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B GLY 4.9 3.1 + - - -
371B LYS 2.8 17.9 + - - -
372B ASP* 3.0 15.8 + - - -
374B THR* 1.3 73.2 - - - +
376B GLY* 1.3 56.4 + - - +
377B ALA* 3.2 17.4 + - - +
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Residues in contact with GLY 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344B GLY* 4.8 11.4 - - - -
372B ASP 3.2 4.0 + - - -
373B TYR 3.7 5.8 + - - -
374B THR 3.2 5.7 - - - -
375B SER* 1.3 78.2 + - - +
377B ALA* 1.3 63.3 + - - +
378B MET 3.4 3.0 + - - -
379B LEU* 3.9 17.1 + - - +
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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