Contacts of the helix formed by residues 441 - 449 (chain A) in PDB entry 2GQ3
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 441 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A TYR 3.0 24.2 + - - -
91A LEU* 3.9 0.9 - - - -
92A LEU* 2.9 40.7 + - - +
93A PRO 5.3 0.3 - - - +
403A PRO* 3.9 21.5 - - + +
437A ARG* 2.8 28.9 + - - +
438A THR 3.2 3.7 + - - -
439A THR 3.0 0.6 - - - -
440A VAL* 1.3 88.6 - - - +
442A LEU* 1.3 63.5 + - - +
443A LYS 3.3 2.9 + - - -
444A ALA* 3.3 9.0 + - + +
445A CYS* 3.1 19.5 + - - -
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Residues in contact with LEU 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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431A ILE* 5.4 3.8 - - + -
433A ASP* 3.4 31.6 - - + +
438A THR* 3.1 26.2 - - + +
439A THR* 3.3 16.5 + - - +
440A VAL 3.6 0.6 - - - -
441A ASN* 1.3 78.2 - - - +
443A LYS* 1.3 57.2 + - - +
445A CYS* 3.1 6.8 + - + +
446A ILE* 3.0 43.4 + - + +
456A ILE* 4.6 7.4 - - + -
495A HIS* 3.7 14.6 + - + +
496A ASN* 3.5 33.2 - - - +
499A ALA* 3.8 13.5 - - + -
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Residues in contact with LYS 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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94A GLU* 3.6 34.7 + - + +
95A PRO* 2.6 40.9 + - + +
96A ASP* 4.1 3.1 - - - +
97A ASP* 2.9 43.5 + - - +
98A PHE* 3.6 19.6 - - + +
441A ASN 3.3 0.2 - - - -
442A LEU* 1.3 77.3 - - - +
444A ALA* 1.3 57.7 + - - +
446A ILE* 3.5 9.9 + - + -
447A LYS* 2.9 28.1 + - - +
495A HIS* 5.3 3.0 + - + -
499A ALA* 4.8 10.9 - - + +
502A ALA* 5.9 5.8 - - - -
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Residues in contact with ALA 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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92A LEU* 6.0 2.7 - - + -
93A PRO 4.8 6.3 - - - +
95A PRO* 3.8 25.0 - - + +
403A PRO* 3.8 23.5 - - + +
441A ASN* 3.3 13.7 + - + +
442A LEU 3.3 0.2 - - - -
443A LYS* 1.3 77.5 - - - +
445A CYS* 1.3 58.4 + - - +
447A LYS* 3.5 4.2 - - - +
448A ALA* 3.0 28.8 + - - +
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Residues in contact with CYS 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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402A GLY* 3.5 36.1 - - - -
403A PRO* 3.5 7.0 - - - -
406A VAL* 3.3 36.9 - - + +
431A ILE* 3.9 8.1 - - + +
438A THR* 4.0 26.9 - - + -
441A ASN 3.1 18.6 + - - -
442A LEU* 3.1 13.9 + - + +
444A ALA* 1.3 73.1 - - - +
446A ILE* 1.3 66.2 + - - +
448A ALA 3.3 7.6 + - - -
449A ALA 3.4 0.2 + - - -
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Residues in contact with ILE 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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98A PHE* 3.6 20.6 - - + -
100A ILE* 3.8 17.0 - - + -
431A ILE* 4.4 8.9 - - + +
442A LEU* 3.0 27.8 + - + +
443A LYS* 3.6 8.5 - - - +
445A CYS* 1.3 72.6 - - - +
447A LYS* 1.3 64.7 + - - +
449A ALA* 2.9 15.6 + - - +
450A ALA* 3.1 10.9 + - - -
453A VAL* 4.5 3.3 - - + +
456A ILE* 4.0 30.7 - - + -
499A ALA* 3.8 39.3 - - + +
503A ALA* 3.9 2.7 - - + -
505A PHE* 3.8 14.1 - - + -
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Residues in contact with LYS 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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95A PRO* 3.9 28.2 - - + +
96A ASP* 5.1 6.7 + - - +
98A PHE* 3.3 34.5 - - + -
443A LYS 2.9 18.8 + - - +
444A ALA* 3.5 7.9 - - - +
446A ILE* 1.3 76.5 - - - +
448A ALA* 1.3 56.9 + - - +
450A ALA* 2.9 23.4 + - + +
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Residues in contact with ALA 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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403A PRO* 3.7 26.0 - - + +
406A VAL* 3.9 9.6 - - + -
407A ALA* 4.0 14.8 - - + +
410A CYS* 3.7 14.6 - - - +
444A ALA 3.0 19.6 + - - +
445A CYS 3.3 7.1 + - - +
447A LYS* 1.3 71.6 - - - +
449A ALA* 1.3 57.0 + - - +
450A ALA 3.6 0.6 + - - -
451A ASP* 5.1 2.4 - - - +
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Residues in contact with ALA 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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406A VAL* 3.6 22.2 - - + -
410A CYS* 3.7 16.2 - - - -
429A ILE* 3.8 20.0 - - + -
431A ILE* 3.8 11.9 - - + -
445A CYS 3.4 0.6 + - - -
446A ILE 2.9 7.5 + - - +
448A ALA* 1.3 79.9 - - - +
450A ALA* 1.3 56.1 + - - -
451A ASP* 2.9 14.1 + - - -
452A ARG* 2.9 12.5 + - + +
453A VAL* 3.0 11.2 + - + +
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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