Contacts of the helix formed by residues 440 - 449 (chain A) in PDB entry 4C02
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 SER 440 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379A LYS* 3.8 6.5 - - - +
438A ASP 3.7 1.8 + - - -
439A PRO* 1.3 75.6 - - - +
441A PHE* 1.3 65.1 + - - +
442A GLU* 3.4 10.4 + - - +
443A ASP* 2.8 41.1 + - - -
444A MET* 3.1 21.8 + - - +
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Residues in contact with PHE 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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375A ARG* 3.2 70.4 - - + +
379A LYS* 3.5 38.0 - - + +
382A MET* 3.8 15.3 - - + -
387A LEU* 4.2 13.4 - - + +
440A SER* 1.3 72.0 - - - +
442A GLU* 1.3 58.8 + - - +
444A MET* 3.2 6.1 + - - +
445A ARG* 2.8 46.2 + - - +
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Residues in contact with GLU 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 SER* 3.2 9.7 + - - +
441A PHE* 1.3 78.5 - - - +
443A ASP* 1.3 67.1 + - - +
445A ARG* 3.8 27.5 + - - +
446A LYS* 3.0 41.0 + - - +
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Residues in contact with ASP 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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435A VAL* 4.0 9.4 - - + +
436A PRO* 3.7 22.3 - - - +
439A PRO* 3.6 16.2 - - + +
440A SER* 2.8 45.8 + - - +
442A GLU* 1.3 81.3 - - - +
444A MET* 1.3 62.3 + - - +
446A LYS* 3.8 4.3 - - - +
447A VAL* 3.2 27.5 + - - +
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Residues in contact with MET 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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379A LYS* 3.5 26.0 - - + +
380A ARG* 3.4 35.9 - - - +
382A MET 5.2 1.6 - - - +
387A LEU* 3.8 21.1 - - + -
431A PHE* 3.8 19.5 - - + -
435A VAL* 3.9 20.4 - - + -
439A PRO* 3.9 16.2 - - + -
440A SER 3.1 12.7 + - - +
441A PHE* 3.7 5.8 - - - +
443A ASP* 1.3 76.9 - - - +
445A ARG* 1.3 57.0 + - - +
447A VAL* 3.2 3.1 + - + +
448A VAL* 2.8 54.6 + - + +
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Residues in contact with ARG 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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375A ARG* 3.4 30.5 - - - +
387A LEU* 3.5 24.7 + - + +
388A ASP* 3.0 28.0 - - - +
441A PHE* 2.8 30.2 + - - +
442A GLU* 3.8 38.2 + - - +
444A MET* 1.3 71.7 - - - +
446A LYS* 1.3 59.3 + - - +
449A CYS* 2.9 36.9 + - + +
450A VAL* 3.1 15.5 + - + -
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Residues in contact with LYS 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 GLU* 3.0 33.6 + - - +
443A ASP* 3.8 4.9 - - - +
445A ARG* 1.3 78.4 - - - +
447A VAL* 1.3 58.3 + - + +
450A VAL* 3.6 16.3 - - + +
451A ASP* 2.9 59.2 + - - +
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Residues in contact with VAL 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 PHE* 3.7 35.2 - - + -
434A VAL* 3.6 25.1 - - + +
435A VAL* 3.6 20.9 - - + -
443A ASP 3.2 13.9 + - - +
444A MET* 3.2 8.3 + - + +
446A LYS* 1.3 79.6 - - + +
448A VAL* 1.3 61.3 + - + +
451A ASP* 4.4 5.4 - - - -
452A GLN 3.3 6.8 + - - -
453A GLN* 2.9 42.5 + - + +
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Residues in contact with VAL 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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382A MET 4.5 2.0 - - - +
384A PRO* 3.6 38.4 - - + +
387A LEU* 3.9 10.1 - - + -
405A TRP* 3.8 15.9 - - + -
431A PHE* 3.8 34.5 - - + -
444A MET* 2.8 34.7 + - + +
447A VAL* 1.3 78.5 - - + +
449A CYS* 1.3 59.7 + - - +
452A GLN* 3.4 10.0 - - - +
453A GLN 4.4 1.1 - - - +
454A ARG* 3.3 21.7 + - - +
480A GLN* 5.1 0.9 - - - +
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Residues in contact with CYS 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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384A PRO* 3.5 40.4 - - - -
387A LEU* 3.9 14.1 - - - -
388A ASP* 3.4 31.9 - - - +
445A ARG* 2.9 19.3 + - + +
448A VAL* 1.3 77.9 - - - +
450A VAL* 1.3 65.2 + - + +
452A GLN* 3.4 18.9 - - - +
480A GLN* 4.3 6.0 - - - +
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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