Contacts of the helix formed by residues 426 - 432 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264B GLU* 3.3 18.2 - - - -
398B GLY 3.1 13.2 - - - -
425B ALA* 1.3 74.5 - - - +
427B CYS* 1.3 62.8 + - - -
428B ALA 3.1 2.1 + - - -
429B LYS* 3.1 22.6 + - - -
450B GLY 3.0 12.5 + - - -
451B GLN 3.3 2.6 - - - -
452B CYS* 3.3 16.8 - - - -
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Residues in contact with CYS 427 (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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263B SER* 3.9 17.3 - - - +
264B GLU* 3.6 6.8 + - + -
287B ALA* 4.1 2.7 - - + -
288B TRP* 3.6 14.4 - - - -
398B GLY 3.0 3.6 + - - -
400B ASP* 3.3 29.2 - - - +
426B GLY* 1.3 68.9 - - - -
428B ALA* 1.3 64.8 + - - +
429B LYS* 2.9 4.0 + - - -
430B TYR* 3.1 33.1 + - + -
1545B SF3 2.4 10.3 - - - -
1546B FSO 2.2 36.5 + - - +
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Residues in contact with ALA 428 (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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396B MET 3.6 13.5 - - - +
397B ALA* 4.0 0.7 - - - -
398B GLY* 2.9 37.6 + - - +
399B CYS 3.6 8.1 - - - +
400B ASP* 3.3 14.4 - - - +
409B TYR* 5.7 0.8 - - + +
427B CYS* 1.3 76.5 - - - +
429B LYS* 1.3 61.7 + - - +
430B TYR 3.0 1.6 + - - -
431B ARG* 3.2 16.6 + - - +
432B TYR* 3.5 13.8 - - + -
484B ALA* 4.2 9.6 - - + -
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Residues in contact with LYS 429 (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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263B SER 5.5 0.4 + - - -
264B GLU* 4.5 3.1 + - - -
266B LEU* 3.8 13.0 - - + +
267B PRO* 3.7 14.5 - - - +
424B THR* 3.6 26.4 + - + +
425B ALA* 4.4 1.3 - - - +
426B GLY 3.1 26.6 + - - +
427B CYS 2.9 0.6 - - - -
428B ALA* 1.3 76.9 - - - +
430B TYR* 1.3 75.2 + - + +
431B ARG 3.1 0.7 - - - -
432B TYR* 3.0 14.1 + - + -
433B ASN* 2.9 47.3 + - + +
448B ASP* 2.8 35.8 + - - +
450B GLY 2.8 27.1 + - - -
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Residues in contact with TYR 430 (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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263B SER* 2.8 38.9 + - - -
266B LEU* 3.4 15.0 - - + +
283B ASN* 3.2 23.0 + - - -
285B GLY 4.0 6.7 - - - -
286B ASN* 3.6 40.9 - - + +
287B ALA* 3.6 26.0 - - + +
365B ILE* 4.6 1.6 - - + -
400B ASP* 4.2 5.4 - - - +
427B CYS* 3.1 29.0 + - + +
428B ALA 3.0 2.4 + - - -
429B LYS* 1.3 89.3 - - + +
431B ARG* 1.3 60.3 + - - +
432B TYR 3.2 0.9 + - - -
433B ASN* 3.4 27.6 + - - +
434B LYS* 4.5 7.3 + - - +
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Residues in contact with ARG 431 (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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289B TRP* 3.4 24.2 - - - -
400B ASP* 2.7 26.1 + - - +
401B GLY 2.9 27.3 + - - -
402B ARG 4.5 1.4 + - - -
403B ALA 3.8 7.5 + - - -
404B LYS* 5.1 2.4 + - - +
406B ARG* 3.5 30.6 - - + +
407B SER* 3.7 21.2 - - - +
409B TYR* 4.0 13.9 - - + -
410B THR* 2.6 40.7 + - - +
428B ALA* 3.2 11.4 + - - +
429B LYS 3.1 1.4 - - - -
430B TYR* 1.3 79.3 - - - +
432B TYR* 1.3 68.3 + - + +
435B LEU* 4.2 2.2 - - - +
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Residues in contact with TYR 432 (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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396B MET* 2.6 52.3 + - + +
409B TYR* 4.1 17.3 - + + -
413B ALA* 3.6 24.5 - - + -
422B ILE* 3.8 23.3 - - + -
424B THR* 2.7 25.1 + - + -
428B ALA* 3.5 12.3 - - + -
429B LYS* 3.0 20.8 + - - -
430B TYR 3.2 0.2 - - - -
431B ARG* 1.3 89.7 - - + +
433B ASN* 1.3 59.4 + - - +
434B LYS 3.3 5.9 + - - +
435B LEU* 3.6 25.6 + - + +
437B LEU* 4.4 1.1 - - + +
446B VAL* 3.9 23.4 - - + +
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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