Contacts of the helix formed by residues 57 - 63 (chain G) in PDB entry 1QGN
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 57 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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55G ASN 4.3 0.6 + - - -
56G SER* 1.3 72.7 + - - +
58G GLY* 1.3 56.7 + - - +
60G VAL* 3.6 9.5 - - - +
61G ALA* 2.8 32.8 + - - +
126G LEU* 3.5 11.6 - - + +
242G PRO 4.0 0.5 - - - +
243G LEU* 3.5 34.4 - - + +
246G LYS* 2.8 35.1 + - - -
311G HIS* 6.1 0.2 - - + -
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Residues in contact with GLY 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430F ASP* 4.5 3.4 - - - -
56G SER* 2.9 8.4 + - - -
57G ASP* 1.3 79.3 - - - +
59G SER* 1.3 62.0 + - - +
60G VAL 3.3 0.5 + - - -
61G ALA* 3.5 2.8 + - - +
62G ILE* 3.3 28.2 + - - +
311G HIS* 3.5 42.0 + - - +
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Residues in contact with SER 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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429F GLU* 3.4 17.7 - - - +
430F ASP 2.9 24.3 + - - +
433F ASP* 2.8 31.2 + - - +
54G LEU* 3.5 25.5 - - - +
56G SER* 2.8 5.8 + - - -
58G GLY* 1.3 76.5 - - - +
60G VAL* 1.3 57.3 + - - +
62G ILE* 3.6 0.4 + - - -
63G HIS* 3.1 32.6 + - - +
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Residues in contact with VAL 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49G LYS* 6.1 3.1 - - + -
50G TYR* 5.3 8.3 - - + +
51G ALA 6.0 0.2 - - - +
54G LEU* 4.1 28.5 - - + +
55G ASN 5.4 0.7 - - - -
56G SER 2.9 17.8 + - - +
57G ASP* 3.7 13.0 - - - +
59G SER* 1.3 75.1 - - - +
61G ALA* 1.3 62.0 + - - +
62G ILE 2.9 4.5 - - - -
64G ALA* 2.7 52.9 + - + +
125G ALA* 3.8 16.6 - - + +
126G LEU* 3.7 19.1 - - + +
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Residues in contact with ALA 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57G ASP 2.8 21.2 + - - +
58G GLY* 3.8 6.5 - - - +
60G VAL* 1.3 73.1 - - - +
62G ILE* 1.3 57.9 + - + +
122G LYS* 3.0 30.0 + - - +
126G LEU* 3.9 27.1 - - + +
243G LEU* 5.4 1.6 - - + -
307G MET* 3.5 25.9 - - + +
310G LEU* 4.5 13.5 - - + -
311G HIS* 5.4 2.7 - - - +
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Residues in contact with ILE 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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392F CYS* 3.8 15.5 - - + +
393F GLU* 4.3 9.9 - - + -
428F VAL* 3.6 22.9 - - + -
429F GLU* 4.0 14.4 - - + +
58G GLY 3.3 17.4 + - - +
59G SER 3.7 4.3 - - - +
60G VAL 2.8 1.8 + - - -
61G ALA* 1.3 79.5 - - - +
63G HIS* 1.3 82.7 + - + +
64G ALA 3.6 0.2 - - - -
66G GLU* 3.4 2.3 - - - +
122G LYS* 2.9 20.8 + - - +
307G MET 4.7 0.7 - - - +
308G LYS* 3.3 60.5 + - + +
311G HIS* 4.1 2.5 - - + -
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Residues in contact with HIS 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382F ILE* 3.7 20.1 + - + +
384F TYR* 4.3 8.8 - + - -
393F GLU* 4.2 16.6 - - + +
394F SER 4.7 0.2 + - - -
429F GLU* 2.9 40.3 + - + +
50G TYR* 3.4 6.5 - - - -
54G LEU* 3.8 18.8 - - + +
59G SER 3.1 11.7 + - - -
62G ILE* 1.3 91.1 - - + +
64G ALA* 1.3 66.8 + - - +
65G GLY 3.2 0.5 + - - -
66G GLU* 3.0 16.6 + - + -
67G ARG* 3.1 49.0 + - + +
308G LYS* 6.1 0.4 - - - -
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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