Contacts of the helix formed by residues 75 - 81 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F THR* 1.3 70.4 - - - +
76F LYS* 1.3 65.7 + - - +
78F PHE* 3.6 9.8 - - + +
79F LEU* 2.8 28.2 + - - +
21H ASN* 4.3 1.6 - - + +
22H VAL* 4.2 24.0 - - + +
25H VAL* 3.8 31.0 - - + -
75H LEU* 3.9 25.1 - - + +
78H PHE* 3.7 38.8 - - + -
79H LEU* 3.6 21.1 - - + -
86H GLU* 2.8 21.2 + - - +
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Residues in contact with LYS 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74F THR* 3.1 4.0 - - - +
75F LEU* 1.3 77.5 - - - +
77F GLU* 1.3 65.0 + - + +
79F LEU* 3.5 3.4 - - - +
80F GLU* 2.8 60.6 + - + +
79H LEU* 3.5 15.0 - - + +
86H GLU* 3.1 17.7 + - - +
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Residues in contact with GLU 77 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72F PHE* 3.5 36.7 - - + -
73F SER* 2.9 24.5 + - - -
74F THR* 2.8 38.9 + - - +
76F LYS* 1.3 78.3 - - + +
78F PHE* 1.3 64.6 + - - +
80F GLU* 3.2 11.2 + - - +
81F ASN* 2.7 33.7 + - - +
88H PRO* 4.0 23.0 - - + +
89H TYR 4.9 0.7 + - - -
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Residues in contact with PHE 78 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F VAL* 3.8 5.6 - - + -
18F ALA* 3.6 26.0 - - - +
21F ASN* 3.3 44.4 - - + -
22F VAL* 4.8 0.2 - - - -
72F PHE* 3.4 35.7 - - + -
73F SER* 3.8 6.3 - - - -
74F THR 3.0 28.7 + - - -
75F LEU* 3.1 13.0 + - + +
77F GLU* 1.3 76.0 - - - +
79F LEU* 1.3 58.1 + - - +
81F ASN 3.2 0.5 + - - -
82F ALA* 2.9 36.9 + - - +
25H VAL* 3.6 25.8 - - + -
32H TRP* 5.0 5.2 - + - -
75H LEU* 3.7 16.6 - - + -
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Residues in contact with LEU 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22F VAL* 5.0 5.4 - - + -
75F LEU 2.8 18.0 + - - +
76F LYS* 3.5 4.5 - - - +
78F PHE* 1.3 74.4 - - - +
80F GLU* 1.3 64.8 + - + +
81F ASN 3.5 0.2 + - - -
82F ALA* 3.9 9.7 + - + +
86F GLU* 3.8 23.6 - - + +
75H LEU* 3.7 18.6 - - + -
76H LYS* 3.7 36.3 - - + +
79H LEU* 3.9 16.8 - - + -
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Residues in contact with GLU 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76F LYS* 2.8 61.3 + - + +
77F GLU* 3.7 9.9 - - - +
79F LEU* 1.3 81.3 - - + +
81F ASN* 1.3 71.8 + - - +
82F ALA 5.3 0.5 - - - +
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Residues in contact with ASN 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F HIS* 2.8 31.6 + - + -
18F ALA* 4.0 6.1 - - + -
72F PHE* 3.2 45.8 - - + -
77F GLU* 2.7 27.1 + - - +
80F GLU* 1.3 90.7 + - - +
82F ALA* 1.3 62.3 + - - +
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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