Contacts of the helix formed by residues 370 - 379 (chain B) in PDB entry 1UES
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 ARG 370 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A PHE* 3.9 17.0 - - - -
366B THR 3.0 27.1 + - - -
367B TYR* 2.9 41.1 + - + +
368B GLN* 2.8 21.8 + - - -
369B ASN* 1.3 86.9 - - - +
371B ARG* 1.3 62.9 + - - +
372B ALA* 3.3 3.1 - - - -
373B ASP* 3.3 27.8 + - + +
374B HIS 3.1 15.9 + - - -
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Residues in contact with ARG 371 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A TRP* 5.5 3.6 - - - -
315B GLY 3.0 26.1 + - - -
316B THR* 3.9 17.8 + - + +
318B LEU 2.7 26.3 + - - -
320B GLY* 2.9 27.7 + - - +
358B VAL* 3.1 32.8 + - + +
360B GLU* 4.8 5.7 + - - +
363B TYR* 2.9 44.0 + - + +
369B ASN 2.8 12.9 + - - +
370B ARG* 1.3 71.5 - - - +
372B ALA* 1.3 62.8 + - - +
374B HIS* 3.1 6.6 + - - +
375B LEU* 3.0 31.4 + - + +
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Residues in contact with ALA 372 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ASN* 5.6 0.5 - - - +
316B THR* 3.7 31.7 + - + +
370B ARG* 3.3 0.9 - - - -
371B ARG* 1.3 78.5 - - - +
373B ASP* 1.3 66.9 + - - +
375B LEU* 3.4 4.8 + - - +
376B LYS* 3.1 39.2 + - - +
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Residues in contact with ASP 373 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
367B TYR* 3.9 11.9 - - + -
370B ARG* 3.3 36.9 + - + +
371B ARG 3.2 0.6 - - - -
372B ALA* 1.3 76.6 - - - +
374B HIS* 1.3 67.4 + - - +
376B LYS* 3.2 24.0 + - - +
377B ASP* 3.0 29.7 + - - +
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Residues in contact with HIS 374 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B VAL* 3.6 16.6 + - - +
219B ILE* 4.3 4.5 - - + -
277B TYR* 4.3 6.6 + - - -
357B ASP 4.5 6.4 + - - -
362B ALA 4.0 11.9 + - - -
363B TYR* 3.5 36.6 - + + +
367B TYR* 3.3 41.9 - - + -
370B ARG 3.1 7.7 + - - +
371B ARG* 3.1 11.0 + - - +
373B ASP* 1.3 77.8 - - - +
375B LEU* 1.3 77.7 + - + +
377B ASP* 3.2 2.4 + - - +
378B LEU* 3.0 52.4 + - + +
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Residues in contact with LEU 375 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311B PHE 5.0 0.2 - - - +
312B ASN* 3.6 41.5 - - + +
315B GLY* 3.6 13.0 - - - -
316B THR* 3.6 22.0 - - - +
356B PHE* 3.7 34.8 - - + -
357B ASP 5.0 0.4 - - - +
358B VAL* 4.1 13.5 - - + -
371B ARG* 3.0 19.9 + - + +
372B ALA 3.8 6.3 - - - +
374B HIS* 1.3 85.8 - - + +
376B LYS* 1.3 63.6 + - - +
378B LEU* 3.3 22.3 + - + +
379B TRP* 3.3 15.8 + - - -
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Residues in contact with LYS 376 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312B ASN* 4.2 17.9 - - + +
372B ALA* 3.1 25.1 + - - +
373B ASP* 3.2 25.6 + - - +
375B LEU* 1.3 76.3 - - - +
377B ASP* 1.3 64.7 + - - +
379B TRP* 3.2 27.6 + - - +
380B SER 4.9 0.3 + - - -
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Residues in contact with ASP 377 (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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217B PRO* 6.1 0.3 - - - +
218B VAL* 3.6 17.4 - - + +
367B TYR* 2.5 38.9 + - - +
373B ASP* 3.0 17.2 + - - +
374B HIS 3.6 2.9 - - - +
375B LEU 3.2 0.2 - - - -
376B LYS* 1.3 80.0 - - - +
378B LEU* 1.3 57.9 + - - +
379B TRP 3.2 1.7 + - - -
380B SER* 2.8 27.9 + - - -
381B ILE 4.4 0.2 + - - -
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Residues in contact with LEU 378 (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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218B VAL* 3.7 19.5 - - + -
219B ILE* 4.2 5.8 - - + -
277B TYR* 4.7 3.1 - - + +
281B PHE* 3.9 23.1 - - + -
356B PHE* 3.4 51.6 - - + -
357B ASP 5.3 0.7 - - - +
374B HIS* 3.0 41.5 + - + +
375B LEU* 3.3 15.8 + - + +
377B ASP* 1.3 74.0 - - - +
379B TRP* 1.3 65.8 + - - +
381B ILE* 3.1 26.5 + - + +
382B VAL* 3.5 11.2 - - - +
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Residues in contact with TRP 379 (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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286B GLY* 3.4 17.2 - - - -
287B GLY 4.4 2.3 + - - +
304B PHE* 4.6 1.3 - + + -
307B PHE* 3.6 20.4 - + - -
308B LYS* 3.9 41.7 - - + +
311B PHE* 3.5 38.8 - + + -
312B ASN* 2.9 31.8 + - - +
354B LEU* 3.8 13.2 - - + -
356B PHE* 3.6 14.4 - + - -
375B LEU 3.3 8.7 + - - -
376B LYS* 3.2 25.4 - - - +
377B ASP 3.2 0.2 - - - -
378B LEU* 1.3 78.0 - - - +
380B SER* 1.3 61.8 + - - +
381B ILE 3.3 0.5 + - - -
382B VAL* 3.5 13.0 + - + +
384B TRP* 3.8 33.4 + + - -
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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