Contacts of the helix formed by residues 357 - 368 (chain B) in PDB entry 1U54
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 PRO 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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226B LEU* 3.9 28.0 - - + -
324B PHE* 5.0 0.4 - - + -
352B ARG* 4.6 2.9 - - - +
355B ASP 3.3 9.8 - - - +
356B CYS* 1.3 107.3 - - + +
358B GLN* 1.3 61.5 + - - +
359B ASP* 3.5 14.1 - - - +
360B ILE* 4.1 21.5 - - + -
361B TYR* 3.2 10.4 + - - +
388B ALA 5.9 0.9 - - - +
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Residues in contact with GLN 358 (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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352B ARG* 2.9 39.9 + - - +
357B PRO* 1.3 74.3 - - - +
359B ASP* 1.3 59.4 + - + +
360B ILE 3.2 2.0 - - - -
361B TYR* 3.2 22.3 + - - +
362B ASN* 2.8 33.8 + - + +
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Residues in contact with ASP 359 (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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357B PRO* 4.2 8.1 - - - +
358B GLN* 1.3 77.4 - - + +
360B ILE* 1.3 65.4 + - - +
362B ASN* 4.1 13.3 + - + +
363B VAL* 3.6 13.9 + - - +
387B GLU 4.5 2.6 - - - +
388B ALA* 3.4 40.8 - - + +
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Residues in contact with ILE 360 (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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226B LEU* 5.5 2.2 - - + +
230B SER* 3.6 24.2 - - - +
320B LEU* 5.5 2.2 - - + -
324B PHE* 3.9 35.0 - - + -
356B CYS* 4.3 8.7 - - - -
357B PRO* 3.8 24.1 + - + +
358B GLN 3.2 0.8 - - - -
359B ASP* 1.3 87.8 + - - +
361B TYR* 1.3 56.5 + - - +
362B ASN 2.9 4.7 - - - -
363B VAL* 2.9 20.2 + - + +
364B MET* 3.4 14.6 + - + +
385B LEU* 4.8 19.5 - - + +
388B ALA* 4.1 22.0 - - + +
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Residues in contact with TYR 361 (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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321B TRP* 5.2 0.2 - + - -
349B ARG* 4.5 8.8 - - - +
350B LEU 2.7 26.4 + - - -
351B PRO* 3.7 3.8 - - - +
352B ARG* 3.3 55.4 + - + -
353B PRO* 4.0 2.7 - - + -
356B CYS* 3.7 7.7 - - - -
357B PRO 3.2 18.8 + - - +
358B GLN* 3.2 22.9 + - - +
360B ILE* 1.3 73.8 - - - +
362B ASN* 1.3 56.8 + - - +
364B MET* 3.7 18.2 - - - +
365B VAL* 3.0 41.0 + - + +
368B TRP* 4.2 11.6 - + - -
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Residues in contact with ASN 362 (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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358B GLN* 2.8 20.8 + - + +
359B ASP* 4.1 13.8 + - - +
360B ILE 2.9 0.4 - - - -
361B TYR* 1.3 78.3 - - - +
363B VAL* 1.3 66.4 + - - +
364B MET 3.2 0.4 - - - -
365B VAL* 3.0 24.9 + - - +
366B GLN* 3.2 31.7 + - - +
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Residues in contact with VAL 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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320B LEU* 4.1 10.8 - - + -
359B ASP 3.6 19.1 - - - +
360B ILE* 2.9 11.7 + - - +
362B ASN* 1.3 74.4 - - + +
364B MET* 1.3 67.4 + - - +
366B GLN* 3.2 10.2 + - - +
367B CYS* 3.2 19.9 + - - -
381B LEU* 3.9 24.9 - - + +
384B PHE* 3.8 35.2 - - + +
385B LEU* 3.9 28.9 - - + +
388B ALA* 5.1 0.7 - - + -
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Residues in contact with MET 364 (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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317B GLY* 4.0 4.0 - - - +
320B LEU* 3.9 25.4 - - + +
321B TRP* 3.8 29.6 - - - +
324B PHE* 4.1 12.6 - - + -
353B PRO* 3.8 25.8 - - + -
356B CYS* 4.1 12.8 - - - -
360B ILE* 3.7 11.7 - - + +
361B TYR* 3.7 18.4 - - - +
362B ASN 3.2 0.2 - - - -
363B VAL* 1.3 79.2 - - - +
365B VAL* 1.3 63.8 + - - +
367B CYS* 3.0 20.0 + - - +
368B TRP* 3.1 48.4 - - + -
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Residues in contact with VAL 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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349B ARG* 5.9 5.6 - - + -
361B TYR* 3.0 48.2 + - + +
362B ASN* 3.0 23.1 + - - +
364B MET* 1.3 75.5 - - - +
366B GLN* 1.3 62.2 + - + +
368B TRP* 3.0 35.7 + - + +
369B ALA* 3.6 1.6 + - - -
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Residues in contact with GLN 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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362B ASN* 3.2 33.9 + - - +
363B VAL* 3.9 6.1 - - - +
364B MET 3.1 0.6 - - - -
365B VAL* 1.3 77.4 - - + +
367B CYS* 1.3 61.4 + - - +
368B TRP 2.9 6.5 + - - -
369B ALA* 3.2 20.0 + - - +
374B ASP 4.9 0.6 - - - +
375B ARG* 4.1 1.2 - - - -
376B PRO* 3.5 25.3 - - + +
381B LEU* 6.1 0.2 - - + -
384B PHE* 3.3 36.8 - - + -
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Residues in contact with CYS 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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313B THR* 3.3 35.7 - - - +
314B TRP* 3.3 13.5 + - - -
316B PHE* 3.9 8.5 - - - -
317B GLY* 3.7 23.3 - - - -
320B LEU* 5.2 0.2 - - - -
363B VAL* 3.2 20.3 + - - -
364B MET* 3.0 10.4 + - - +
366B GLN* 1.3 75.5 - - - +
368B TRP* 1.3 60.3 + - + +
369B ALA 3.5 0.4 - - - -
375B ARG* 2.9 21.3 + - - -
376B PRO* 4.3 1.0 - - - +
381B LEU* 3.6 23.8 - - - -
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Residues in contact with TRP 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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314B TRP* 3.3 51.8 + + + -
317B GLY* 3.3 24.3 - - - -
318B VAL* 3.5 17.5 - - + +
321B TRP* 4.5 2.2 - + + -
349B ARG* 2.6 64.6 + - + +
350B LEU* 4.0 42.0 - - + -
361B TYR* 4.2 9.0 - + - -
364B MET* 3.1 47.8 - - + -
365B VAL* 3.0 16.1 + - + +
366B GLN 2.9 1.2 - - - -
367B CYS* 1.3 82.4 - - - +
369B ALA* 1.3 59.5 + - - +
370B HIS 3.0 0.2 + - - -
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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