Contacts of the helix formed by residues 440 - 450 (chain A) in PDB entry 3C5R
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 ASP 440 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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435A ALA* 2.9 17.0 + - + +
438A LYS* 3.3 13.4 - - + +
439A GLY* 1.3 75.3 - - - +
441A ILE* 1.3 56.1 + - - +
442A PRO* 3.2 20.5 - - - +
443A SER* 2.6 32.7 + - - -
444A VAL* 2.9 31.3 + - - +
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Residues in contact with ILE 441 (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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439A GLY 3.1 11.3 + - - +
440A ASP* 1.3 70.5 - - - +
442A PRO* 1.4 68.7 - - + +
444A VAL* 3.1 2.7 + - - +
445A GLU* 2.8 44.5 + - - +
475A LYS* 3.6 38.6 - - + -
476A VAL* 4.0 16.6 - - + -
479A LEU* 4.0 17.3 - - + -
535B ASP* 3.4 32.5 - - + +
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Residues in contact with PRO 442 (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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440A ASP* 3.2 12.8 - - - +
441A ILE* 1.4 94.2 - - + +
443A SER* 1.3 56.3 + - - +
445A GLU* 3.6 11.2 - - + +
446A TYR* 3.0 31.4 + - - +
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Residues in contact with SER 443 (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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431A LEU* 6.4 0.9 - - - -
435A ALA* 3.6 15.5 - - - -
440A ASP* 2.6 33.8 + - - -
441A ILE 3.3 0.4 - - - -
442A PRO* 1.3 74.4 - - - +
444A VAL* 1.3 67.2 + - - +
446A TYR* 3.3 4.1 + - - +
447A LEU* 2.9 36.6 + - - +
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Residues in contact with VAL 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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432A LEU* 4.2 13.5 - - + -
435A ALA* 3.7 30.5 - - + +
436A SER* 4.0 5.6 - - - +
440A ASP 2.9 20.5 + - - +
441A ILE* 3.8 5.8 - - - +
443A SER* 1.3 77.0 - - - +
445A GLU* 1.3 58.6 + - - +
447A LEU* 3.4 1.6 + - - +
448A LEU* 2.9 53.1 + - + +
476A VAL* 3.9 30.1 - - + -
479A LEU* 4.2 13.5 - - + -
480A LEU* 4.6 2.9 - - + -
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Residues in contact with GLU 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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441A ILE* 2.8 27.9 + - - +
442A PRO* 3.6 10.9 - - - +
444A VAL* 1.3 79.1 - - - +
446A TYR* 1.3 57.2 + - - +
448A LEU* 3.8 3.3 - - - +
449A GLN* 2.8 52.5 + - + +
475A LYS* 4.6 10.9 + - - -
479A LEU* 4.0 30.6 - - + +
483A HIS* 5.3 1.0 - - + -
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Residues in contact with TYR 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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442A PRO 3.0 19.0 + - - +
443A SER* 3.9 4.3 - - - +
445A GLU* 1.3 75.0 - - - +
447A LEU* 1.3 69.2 + - + +
449A GLN* 3.3 13.1 + - - +
450A ASN* 2.7 67.1 + - + +
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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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431A LEU* 4.0 35.0 - - + +
432A LEU* 3.8 42.4 - - + +
435A ALA* 4.6 3.8 - - + -
443A SER* 2.9 27.4 + - - +
444A VAL 3.7 2.7 - - - +
446A TYR* 1.3 83.9 - - + +
448A LEU* 1.3 60.2 + - - +
450A ASN* 3.2 4.9 + - - +
451A GLY 3.1 6.6 + - - -
452A SER* 3.0 43.3 + - - +
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Residues in contact with LEU 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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432A LEU* 4.1 10.5 - - + -
444A VAL* 2.9 41.2 + - + +
445A GLU* 4.0 2.0 - - - +
447A LEU* 1.3 74.8 - - - +
449A GLN* 1.3 63.0 + - - +
450A ASN 3.2 0.5 + - - -
451A GLY* 3.3 11.6 + - - -
452A SER 3.6 21.2 + - - +
454A PRO* 3.8 20.0 - - + -
479A LEU* 3.8 27.8 - - + +
480A LEU* 3.8 14.4 - - + -
483A HIS* 3.4 44.6 - - + +
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Residues in contact with GLN 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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445A GLU* 2.8 42.3 + - + +
446A TYR* 3.5 22.9 + - - +
448A LEU* 1.3 75.6 - - - +
450A ASN* 1.3 65.6 + - - +
451A GLY 3.4 0.6 + - - -
483A HIS* 4.0 12.7 + - + +
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Residues in contact with ASN 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 TYR* 2.7 69.9 + - + +
447A LEU* 3.2 5.6 + - - +
448A LEU 3.1 0.4 - - - -
449A GLN* 1.3 85.5 + - - +
451A GLY* 1.3 58.4 + - - +
452A SER* 3.7 0.7 - - - -
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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