Contacts of the helix formed by residues 75 - 81 (chain A) in PDB entry 1QGH
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 LEU 75 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A THR* 1.3 72.1 - - - +
76A LYS* 1.3 54.5 + - - +
78A PHE* 3.1 10.2 + - + +
79A LEU* 2.6 38.5 + - - +
21C ASN* 4.7 2.5 - - + +
22C VAL* 4.0 24.0 - - + -
25C VAL* 3.7 31.4 - - + -
75C LEU* 4.0 24.0 - - + +
78C PHE* 3.6 39.7 - - + -
79C LEU* 3.7 20.6 - - + -
86C GLU* 2.9 16.3 + - - +
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Residues in contact with LYS 76 (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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74A THR* 3.1 4.0 - - - +
75A LEU* 1.3 81.7 - - - +
77A GLU* 1.3 61.1 + - + +
79A LEU* 3.1 2.8 + - - +
80A GLU* 2.8 65.4 + - + +
79C LEU* 3.6 16.3 - - + +
86C GLU* 3.2 15.2 + - - +
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A PHE* 3.7 34.3 - - + -
73A SER* 2.9 25.8 + - - -
74A THR* 2.8 34.9 + - - +
76A LYS* 1.3 79.2 - - + +
78A PHE* 1.3 64.7 + - - +
80A GLU* 3.2 11.7 + - - +
81A ASN* 2.8 32.1 + - - +
88C PRO* 3.9 23.5 - - + +
89C TYR 5.0 1.0 + - - -
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Residues in contact with PHE 78 (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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17A VAL* 3.7 11.7 - - + -
18A ALA* 3.8 28.7 - - - +
21A ASN* 3.3 39.0 - - + -
22A VAL* 4.8 0.7 - - + -
72A PHE* 3.3 40.2 - - + -
73A SER* 3.8 3.8 - - - -
74A THR 2.9 24.2 + - - -
75A LEU* 3.6 12.3 - - + +
77A GLU* 1.3 75.1 - - - +
79A LEU* 1.3 64.5 + - - +
81A ASN 3.0 1.2 + - - -
82A ALA* 2.9 29.6 + - - +
25C VAL* 3.6 28.5 - - + -
32C TRP* 4.9 5.6 - + - -
75C LEU* 3.7 15.7 - - + -
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A VAL* 5.0 5.6 - - + -
75A LEU 2.6 19.8 + - - +
76A LYS* 3.5 5.6 - - - +
78A PHE* 1.3 76.1 - - - +
80A GLU* 1.3 62.6 + - + +
81A ASN 3.4 0.2 + - - -
82A ALA* 4.0 9.5 + - + +
86A GLU* 3.7 24.0 - - + +
75C LEU* 3.7 19.1 - - + -
76C LYS* 3.6 35.0 - - + +
79C LEU* 4.0 16.4 - - + -
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Residues in contact with GLU 80 (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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76A LYS* 2.8 58.6 + - + +
77A GLU* 3.7 14.7 - - - +
79A LEU* 1.3 79.9 - - + +
81A ASN* 1.3 67.2 + - - +
82A ALA 5.3 0.2 - - - -
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Residues in contact with ASN 81 (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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15A HIS* 2.8 32.2 + - + -
18A ALA* 3.9 5.8 - - + -
72A PHE* 3.3 46.5 - - + -
77A GLU* 2.8 27.6 + - - +
80A GLU* 1.3 90.8 + - - +
82A ALA* 1.3 65.7 + - - +
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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