Contacts of the helix formed by residues 426 - 432 (chain A) in PDB entry 1UPX
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 GLY 426 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A GLU* 3.4 17.9 - - - -
398A GLY 3.1 13.7 - - - -
425A ALA* 1.3 75.3 - - - +
427A CYS* 1.3 59.0 + - - -
428A ALA 3.1 5.5 + - - -
429A LYS* 3.1 20.9 + - - -
450A GLY 3.0 12.7 + - - -
451A GLN 3.3 2.8 - - - -
452A CYS* 3.4 16.6 - - - -
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Residues in contact with CYS 427 (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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263A SER* 3.8 17.7 - - - +
264A GLU* 3.6 7.0 + - + -
287A ALA* 4.0 6.3 - - + -
288A TRP* 3.6 13.7 - - - -
398A GLY 3.1 4.0 + - - -
400A ASP* 3.3 31.8 - - - +
426A GLY* 1.3 67.9 - - - -
428A ALA* 1.3 65.1 + - - +
429A LYS* 2.9 4.0 + - - -
430A TYR* 3.1 28.1 + - + +
1545A SF3 2.3 37.0 - - - -
1546A FSO 2.4 9.3 + - - +
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Residues in contact with ALA 428 (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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396A MET 3.6 20.2 - - - +
397A ALA* 3.9 0.7 - - - -
398A GLY* 2.9 31.1 + - - +
399A CYS 3.6 7.6 - - - +
400A ASP* 3.3 14.2 - - - +
409A TYR* 5.6 0.6 - - + +
426A GLY 3.1 0.6 + - - +
427A CYS* 1.3 76.8 - - - +
429A LYS* 1.3 61.8 + - - +
430A TYR 3.0 1.4 + - - -
431A ARG* 3.2 17.0 + - - +
432A TYR* 3.5 13.4 - - + -
484A ALA* 4.2 9.9 - - + -
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Residues in contact with LYS 429 (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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263A SER 5.5 0.4 + - - -
264A GLU* 4.4 2.8 + - - -
266A LEU* 3.8 13.4 - - + +
267A PRO* 3.7 13.9 - - - +
424A THR* 3.5 18.8 + - + +
425A ALA* 4.4 1.3 - - - +
426A GLY 3.1 23.4 + - - +
427A CYS 2.9 0.2 - - - -
428A ALA* 1.3 78.1 - - - +
430A TYR* 1.3 75.9 + - + +
432A TYR* 3.0 22.0 + - + -
433A ASN* 2.9 47.7 + - + +
448A ASP* 2.8 36.3 + - - +
450A GLY 2.8 28.7 + - - -
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Residues in contact with TYR 430 (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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263A SER* 2.8 39.7 + - - -
264A GLU* 5.9 0.2 - - - -
266A LEU* 3.4 15.3 - - + +
283A ASN* 3.2 22.6 + - - -
285A GLY 3.9 7.2 - - - -
286A ASN* 3.6 39.9 - - + +
287A ALA* 3.6 26.5 - - + +
365A ILE* 5.3 0.4 - - + -
400A ASP* 4.2 5.4 - - - +
427A CYS* 3.1 26.8 + - + +
428A ALA 3.0 1.6 + - - -
429A LYS* 1.3 88.5 - - + +
431A ARG* 1.3 61.5 + - - +
432A TYR 3.2 1.0 + - - -
433A ASN* 3.4 30.2 + - - +
434A LYS* 4.4 10.8 - - - +
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Residues in contact with ARG 431 (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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289A TRP* 3.3 25.1 - - - -
400A ASP* 2.7 27.1 + - - +
401A GLY 2.9 27.9 + - - -
402A ARG 4.5 0.8 + - - -
403A ALA 3.8 7.5 + - - -
404A LYS* 5.0 1.8 + - - +
406A ARG* 3.4 30.1 - - + +
407A SER* 3.6 22.8 - - - +
409A TYR* 4.0 21.1 - - + -
410A THR* 2.7 42.6 + - - +
428A ALA* 3.2 10.7 + - - +
429A LYS 3.1 1.2 - - - -
430A TYR* 1.3 78.2 - - - +
432A TYR* 1.3 59.7 + - + +
435A LEU* 4.2 1.2 - - - +
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Residues in contact with TYR 432 (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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396A MET* 2.6 53.0 + - + +
409A TYR* 4.0 16.6 - + + -
413A ALA* 3.4 25.4 - - + -
422A ILE* 3.8 24.0 - - + -
424A THR* 2.7 25.5 + - + -
428A ALA* 3.5 13.5 - - + -
429A LYS* 3.0 20.2 + - + -
430A TYR 3.2 0.2 - - - -
431A ARG* 1.3 89.9 - - + +
433A ASN* 1.3 59.3 + - - +
434A LYS 3.3 5.6 + - - -
435A LEU* 3.5 26.7 + - + +
437A LEU* 4.3 2.9 - - + +
446A VAL* 4.3 19.0 - - + +
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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