Contacts of the helix formed by residues 443 - 451 (chain A) in PDB entry 3QFS
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 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246A ARG* 4.9 2.7 - - - +
395A TYR* 3.4 33.2 - - + +
441A ARG 3.8 1.5 - - - +
442A PRO* 1.3 84.9 - - + +
444A ILE* 1.3 65.3 + - - +
445A ASP* 3.5 15.7 - - - +
446A HIS* 3.1 25.0 + - + -
447A LEU* 3.2 10.4 + - - +
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Residues in contact with ILE 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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341A LEU* 4.4 18.6 - - + +
343A ALA* 3.9 25.5 - - + +
345A LEU* 3.6 22.7 - - + -
370A TYR* 3.5 58.1 - - + +
374A LEU* 4.1 9.6 - - + -
442A PRO 3.4 4.5 + - - -
443A PRO* 1.3 71.0 - - - +
445A ASP* 1.3 61.9 + - - +
447A LEU* 3.2 9.9 + - + +
448A CYS* 2.9 31.7 + - - -
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Residues in contact with ASP 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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246A ARG* 2.9 36.6 + - - +
250A LEU* 3.7 37.5 - - + +
351A LEU* 3.7 9.7 - - + +
370A TYR* 3.5 28.3 - - + +
443A PRO* 3.5 18.2 - - - +
444A ILE* 1.3 81.7 + - - +
446A HIS* 1.3 65.2 + - - +
448A CYS* 3.3 5.8 + - - +
449A GLU 3.3 15.4 + - - -
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Residues in contact with HIS 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A ARG* 3.5 48.0 + - + +
391A GLU* 4.0 15.2 + - + -
392A LEU* 6.4 0.2 - - + -
394A GLN* 3.8 15.9 - - - -
395A TYR* 2.6 32.6 + + + -
442A PRO* 5.7 0.7 - - + -
443A PRO* 3.1 19.8 + - + +
445A ASP* 1.3 79.1 - - - +
447A LEU* 1.3 67.3 + - - +
449A GLU* 3.0 18.5 + - - +
450A LEU* 3.1 38.5 + - + +
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Residues in contact with LEU 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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337A LEU* 5.3 4.5 - - + -
341A LEU* 3.9 30.3 - - + -
374A LEU* 5.3 8.5 - - + -
388A VAL* 5.3 0.4 - - + -
392A LEU* 4.1 20.6 - - + -
430A ILE* 4.1 33.7 - - + -
434A LEU* 5.1 2.0 - - + -
442A PRO* 4.9 9.5 - - + +
443A PRO 3.2 12.9 + - - +
444A ILE* 3.2 12.1 + - + +
446A HIS* 1.3 77.8 - - - +
448A CYS* 1.3 62.7 + - - +
450A LEU* 3.1 19.6 + - + +
451A LEU* 3.1 38.4 + - + +
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Residues in contact with CYS 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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351A LEU* 4.1 5.6 - - + -
363A PRO* 4.6 2.1 - - - +
364A PHE* 3.5 30.7 - - + -
370A TYR* 3.9 22.7 - - + -
373A ALA* 4.6 9.6 - - - -
374A LEU* 4.6 11.9 - - - -
378A LEU* 3.8 37.1 - - + +
444A ILE* 2.9 26.5 + - - +
445A ASP* 3.6 7.4 - - - +
446A HIS 3.2 0.4 - - - -
447A LEU* 1.3 77.1 - - - +
449A GLU* 1.3 60.4 + - - +
450A LEU 3.4 0.2 - - - -
451A LEU 4.3 2.5 + - - +
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Residues in contact with GLU 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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246A ARG* 3.0 37.1 + - - +
247A GLN* 2.9 27.3 + - + +
248A TYR* 3.3 43.8 + - + +
351A LEU* 4.8 5.8 - - + -
363A PRO* 4.9 5.8 - - - +
445A ASP 3.3 10.2 + - - +
446A HIS* 3.0 17.7 + - + +
448A CYS* 1.3 76.9 - - - +
450A LEU* 1.3 67.4 + - + +
451A LEU 4.3 3.4 - - - +
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Residues in contact with LEU 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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387A ASN* 4.9 4.8 - - - +
388A VAL* 3.6 34.8 - - + +
391A GLU* 3.8 40.6 - - + -
392A LEU* 3.9 28.7 - - + -
446A HIS* 3.4 38.1 - - + +
447A LEU* 3.1 9.2 + - + +
449A GLU* 1.3 84.7 - - + +
451A LEU* 1.3 62.7 + - - +
452A PRO* 3.8 1.7 - - - +
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Residues in contact with LEU 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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374A LEU* 4.5 9.6 - - + -
378A LEU* 3.8 22.2 - - + +
379A ASP 3.9 12.3 - - - +
380A ILE* 4.0 27.1 - - + -
384A PRO* 5.3 7.2 - - + -
388A VAL* 4.7 14.8 - - + -
430A ILE* 4.7 17.7 - - + -
447A LEU* 3.1 45.4 + - + +
448A CYS 4.3 3.2 + - - +
449A GLU 3.6 3.5 - - - +
450A LEU* 1.3 80.3 - - - +
452A PRO* 1.3 76.8 - - + +
453A ARG* 5.7 0.5 - - - +
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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