Contacts of the helix formed by residues 443 - 454 (chain A) in PDB entry 1U7V
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 ASN 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271A PRO* 4.1 11.0 - - + -
273A PHE* 2.7 37.3 + - - +
274A TRP 3.2 4.8 + - - +
275A CYS* 3.1 25.6 + - - +
276A SER* 4.0 10.9 + - - +
291A HIS* 5.4 2.6 - - - -
441A HIS* 3.9 6.4 - - - +
442A LEU* 1.3 68.0 - - - +
444A GLY* 1.3 67.3 + - - +
446A LEU* 3.3 5.2 + - - +
447A GLN* 2.9 25.3 + - - +
356B PRO* 3.4 33.2 - - + +
366B GLN* 5.4 0.2 + - - -
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Residues in contact with GLY 444 (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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271A PRO* 4.1 20.4 - - - +
274A TRP* 4.3 6.6 + - - +
340A TYR* 5.6 3.4 - - - -
443A ASN* 1.3 75.0 - - - +
445A PRO* 1.3 71.3 - - - +
447A GLN* 2.8 17.4 + - - +
448A TRP* 3.1 28.5 + - - -
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Residues in contact with PRO 445 (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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274A TRP 5.5 0.4 - - - +
340A TYR* 5.3 3.8 - - - +
385A PHE* 3.5 33.9 - - + -
387A ASN* 3.6 11.9 - - - +
390A PHE* 3.5 21.0 - - + -
412A CYS* 3.5 20.4 - - - -
442A LEU* 3.4 20.0 - - + +
444A GLY* 1.3 88.4 - - - +
446A LEU* 1.3 57.3 + - - +
448A TRP* 3.2 17.9 + - + +
449A LEU* 2.9 25.6 + - - +
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Residues in contact with LEU 446 (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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409A THR* 4.5 16.6 - - + +
412A CYS* 3.4 28.2 - - + -
413A THR* 5.7 1.8 - - + -
441A HIS* 4.2 23.1 - - + +
442A LEU 3.1 19.1 + - - +
443A ASN* 3.6 5.4 - - - +
445A PRO* 1.3 78.3 - - - +
447A GLN* 1.3 57.1 + - - +
449A LEU* 3.2 5.6 + - + +
450A ASP* 2.9 25.8 + - - +
354B VAL* 3.5 26.6 - - + +
356B PRO* 3.6 17.9 - - + -
366B GLN* 3.7 31.2 - - + +
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Residues in contact with GLN 447 (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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270A GLU* 4.4 7.6 + - - -
271A PRO* 3.5 29.2 - - + +
443A ASN 2.9 12.7 + - - +
444A GLY* 2.8 10.1 + - - +
446A LEU* 1.3 74.7 - - - +
448A TRP* 1.3 70.5 + - + +
450A ASP* 3.2 13.0 + - - +
451A LYS* 3.3 34.8 + - - +
355B ASP* 3.3 23.1 + - - +
356B PRO* 4.0 6.2 - - + +
357B SER* 3.2 26.9 + - - -
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Residues in contact with TRP 448 (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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340A TYR* 5.0 2.9 - - - -
387A ASN* 3.6 50.5 - - + -
390A PHE* 4.2 9.9 - + + -
391A ALA* 5.2 9.4 - - + -
394A LEU* 3.7 21.1 - - + +
444A GLY* 3.1 17.2 + - - -
445A PRO* 3.2 27.3 + - + +
447A GLN* 1.3 83.5 + - + +
449A LEU* 1.3 64.1 + - - +
451A LYS* 3.5 33.6 + - + +
452A VAL* 3.6 8.8 + - - +
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Residues in contact with LEU 449 (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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390A PHE* 4.4 4.5 - - + -
394A LEU* 4.1 19.9 - - + +
405A VAL* 3.3 34.5 - - + +
408A LEU* 3.7 27.6 - - + +
409A THR* 3.6 32.8 - - + -
412A CYS* 4.6 5.2 - - - -
445A PRO 2.9 12.3 + - - +
446A LEU* 3.3 10.3 - - + +
448A TRP* 1.3 77.5 - - - +
450A ASP* 1.3 63.8 + - - +
452A VAL* 2.9 13.7 + - - -
453A LEU* 2.9 22.6 + - + -
354B VAL* 4.0 6.5 - - + -
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Residues in contact with ASP 450 (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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446A LEU 2.9 13.0 + - - +
447A GLN 3.3 9.8 - - - +
449A LEU* 1.3 75.0 - - - +
451A LYS* 1.3 68.5 + - - +
453A LEU* 2.9 14.8 + - - +
454A THR* 2.9 17.4 + - - +
353B TYR* 3.4 12.6 - - - +
354B VAL* 3.6 8.7 - - - +
355B ASP* 3.3 31.2 + - + +
361B ARG* 2.6 49.9 + - - -
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Residues in contact with LYS 451 (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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447A GLN* 3.4 34.6 + - + +
448A TRP* 3.7 26.1 - - + +
449A LEU 3.2 0.2 - - - -
450A ASP* 1.3 81.5 - - - +
452A VAL* 1.3 62.3 + - + +
454A THR* 3.1 19.0 + - - -
455A GLN* 3.4 21.1 - - - +
355B ASP* 5.8 0.4 - - - +
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Residues in contact with VAL 452 (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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394A LEU* 4.1 25.1 - - + +
398A VAL* 4.2 24.9 - - + -
405A VAL* 4.4 10.5 - - + -
448A TRP 3.6 11.2 + - - +
449A LEU 2.9 8.1 + - - +
451A LYS* 1.3 78.7 - - + +
453A LEU* 1.3 61.2 + - - +
455A GLN* 3.6 12.3 + - - +
456A MET* 2.9 40.1 + - + +
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Residues in contact with LEU 453 (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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402A PHE* 3.5 36.4 - - + -
405A VAL* 3.6 18.2 - - + -
406A TYR* 3.9 26.0 - - + +
449A LEU* 2.9 21.7 + - + +
450A ASP 2.9 8.8 + - - +
452A VAL* 1.3 72.9 - - - +
454A THR* 1.3 54.3 + - - +
455A GLN 2.6 17.3 + - - -
456A MET* 2.9 15.6 + - + +
457A GLY 4.4 1.2 + - - +
353B TYR* 3.5 24.2 - - + -
354B VAL* 3.7 42.4 - - + +
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Residues in contact with THR 454 (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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450A ASP* 2.9 29.7 + - - +
451A LYS* 3.1 19.6 + - - -
453A LEU* 1.3 72.1 - - - +
455A GLN* 1.3 63.5 + - - +
457A GLY 5.3 0.4 - - - -
353B TYR* 3.3 30.1 - - + -
361B ARG* 3.8 14.4 - - - +
385B LYS* 4.3 16.9 + - - -
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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