Contacts of the helix formed by residues 442 - 454 (chain A) in PDB entry 5CHG
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 442 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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440A HIS 3.6 0.6 + - - -
441A ARG* 1.3 72.2 - - - +
443A ILE* 1.3 62.0 + - - +
444A PHE* 3.5 3.3 - - - +
445A SER* 4.3 4.4 + - - -
446A ARG* 3.1 33.3 + - - +
471A GLN* 5.7 3.8 + - - +
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Residues in contact with ILE 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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403A ALA* 5.3 4.5 - - + +
406A PHE* 4.0 15.3 - - + -
407A ASN* 4.9 4.3 - - + -
410A LEU* 3.9 32.8 - - + -
432A ILE* 5.2 8.5 - - + -
439A SER 3.3 26.2 - - - +
440A HIS* 3.4 14.8 + - - +
441A ARG 3.1 1.1 - - - +
442A GLY* 1.3 78.8 - - - +
444A PHE* 1.3 58.7 + - - +
446A ARG* 3.1 27.7 + - - +
447A LEU* 2.7 53.8 + - + +
493A VAL* 5.3 5.2 - - + -
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Residues in contact with PHE 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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440A HIS 4.7 1.4 + - - -
442A GLY 3.5 2.1 - - - +
443A ILE* 1.3 82.3 - - - +
445A SER* 1.3 67.7 + - - +
447A LEU* 3.8 5.2 - - + +
448A LEU* 3.2 45.4 + - + +
463A SER 4.5 9.4 - - - -
466A GLU* 4.8 13.7 - - - -
471A GLN* 3.7 54.5 - - + +
472A LYS 3.6 28.7 - - - -
473A TYR* 3.6 25.8 - - + -
491A ILE* 4.2 9.0 - - + -
493A VAL* 3.8 21.9 - - + +
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Residues in contact with SER 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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442A GLY 4.3 5.2 + - - -
443A ILE 3.4 0.6 - - - -
444A PHE* 1.3 86.4 - - - +
446A ARG* 1.3 59.9 + - - +
448A LEU* 3.6 6.8 + - - +
449A ASP* 3.1 26.9 + - - +
452A ARG* 5.2 1.0 + - - -
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Residues in contact with ARG 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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406A PHE* 3.7 44.9 + - + +
441A ARG 4.8 2.6 + - - -
442A GLY* 3.1 20.5 + - - +
443A ILE* 3.1 33.9 + - - +
445A SER* 1.3 77.6 - - - +
447A LEU* 1.3 60.2 + - - +
449A ASP* 3.4 7.3 + - - +
450A SER* 2.8 29.6 + - - -
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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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399A VAL* 4.1 12.6 - - + +
402A ALA* 3.9 15.0 - - + +
403A ALA* 3.8 33.0 - - + +
406A PHE* 4.4 4.2 - - + -
432A ILE* 3.5 31.6 - - + -
443A ILE* 2.7 33.8 + - + +
444A PHE* 3.8 6.7 - - + +
446A ARG* 1.3 70.9 - - - +
448A LEU* 1.3 61.0 + - + +
450A SER* 3.2 3.7 + - - -
451A LEU* 3.0 40.1 + - + +
491A ILE* 4.5 13.0 - - + -
493A VAL* 5.7 1.8 - - + -
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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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444A PHE* 3.2 44.0 + - + +
445A SER* 3.9 5.8 - - - +
447A LEU* 1.3 75.5 - - + +
449A ASP* 1.3 66.8 + - - +
451A LEU* 3.3 1.5 + - + -
452A ARG* 3.0 50.8 + - - +
457A LEU* 3.7 12.7 - - + +
463A SER 4.9 3.1 - - - +
473A TYR* 3.6 51.8 - - + -
491A ILE* 4.3 15.5 - - + -
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Residues in contact with ASP 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 SER 3.1 18.8 + - - +
446A ARG* 3.5 8.5 - - - +
448A LEU* 1.3 76.7 - - - +
450A SER* 1.3 61.4 + - - +
452A ARG* 3.3 18.2 + - - +
453A GLN* 2.5 59.2 + - - +
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Residues in contact with SER 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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402A ALA* 4.1 17.9 + - - +
405A ALA* 6.0 0.7 - - - +
406A PHE* 4.0 20.9 - - - -
446A ARG 2.8 17.4 + - - -
447A LEU* 3.4 7.4 - - - -
449A ASP* 1.3 79.2 - - - +
451A LEU* 1.3 63.1 + - - +
453A GLN* 3.4 12.2 + - - +
454A GLU* 3.4 23.1 + - - +
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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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398A THR 3.9 9.4 - - - +
399A VAL* 4.3 9.2 - - + -
402A ALA* 3.8 22.9 - - + -
447A LEU* 3.0 30.6 + - + +
448A LEU* 3.3 0.9 + - - -
450A SER* 1.3 73.8 - - - +
452A ARG* 1.3 64.9 + - - +
454A GLU* 3.4 13.3 - - - +
455A GLY 3.3 2.6 + - - -
456A PHE* 3.0 52.7 + - + +
457A LEU* 3.6 26.9 - - + -
491A ILE* 4.3 22.9 - - + -
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Residues in contact with ARG 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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445A SER 5.2 0.6 + - - -
448A LEU* 3.0 52.9 + - - +
449A ASP* 3.7 17.7 + - - +
450A SER 3.3 0.2 - - - -
451A LEU* 1.3 78.1 - - - +
453A GLN* 1.3 59.3 + - + +
455A GLY* 3.0 18.4 + - - -
457A LEU* 3.9 26.4 - - + +
460A ASP* 3.3 36.2 + - - -
463A SER* 5.8 2.4 + - - -
473A TYR* 4.6 2.2 - - - -
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Residues in contact with GLN 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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449A ASP* 2.5 45.1 + - - +
450A SER* 3.6 9.9 - - - +
452A ARG* 1.3 73.1 - - + +
454A GLU* 1.3 62.1 + - - +
455A GLY* 3.0 6.2 + - - -
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Residues in contact with GLU 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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398A THR* 3.8 21.8 - - - +
402A ALA* 4.0 12.6 - - - +
450A SER* 3.4 9.3 + - - +
451A LEU* 3.4 32.2 - - - +
453A GLN* 1.3 77.9 - - - +
455A GLY* 1.3 59.4 + - - +
456A PHE* 3.5 7.8 + - - +
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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