Contacts of the helix formed by residues 96 - 102 (chain A) in PDB entry 1QGI
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 ALA 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79A PRO* 3.7 20.4 - - + +
82A PHE* 4.0 7.7 - - + +
83A LYS* 3.9 16.1 - - + +
95A SER* 1.3 73.2 - - - +
97A ASP* 1.3 63.3 + - - +
99A ALA* 3.1 4.5 + - - +
100A LEU* 3.0 27.3 + - - +
109A MET* 3.7 29.1 - - + +
114A LEU* 4.1 11.9 - - + -
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Residues in contact with ASP 97 (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 SER* 3.2 9.3 + - - +
96A ALA* 1.3 78.2 - - - +
98A GLY* 1.3 61.7 + - - +
100A LEU* 3.3 8.1 + - - +
101A LYS* 3.0 48.7 + - - +
107A GLY 5.4 1.3 - - - -
108A LYS* 3.5 13.9 - - - +
109A MET* 2.8 43.6 + - - +
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Residues in contact with GLY 98 (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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86A ASP* 3.6 21.1 - - - -
95A SER* 3.0 15.0 + - - -
97A ASP* 1.3 76.0 - - - +
99A ALA* 1.3 61.7 + - - +
101A LYS* 3.4 12.8 + - - +
102A ARG* 3.0 26.2 + - - +
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Residues in contact with ALA 99 (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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82A PHE* 3.1 45.1 - - + +
85A TYR* 4.2 11.9 - - + -
86A ASP* 3.7 9.9 - - + -
95A SER 3.1 6.5 + - - +
96A ALA 3.1 9.2 + - - +
98A GLY* 1.3 74.3 - - - +
100A LEU* 1.3 65.2 + - - +
102A ARG* 3.2 7.1 + - - +
103A LEU* 3.1 29.2 + - - +
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Residues in contact with LEU 100 (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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82A PHE* 4.0 25.1 - - + -
96A ALA 3.0 17.9 + - - +
97A ASP* 3.3 6.3 + - - +
99A ALA* 1.3 75.8 - - - +
101A LYS* 1.3 57.5 + - + +
103A LEU* 3.2 3.5 + - - +
104A GLY 2.9 8.5 + - - -
105A ILE* 2.9 68.1 + - + +
107A GLY* 3.5 35.4 - - - +
108A LYS* 3.9 2.9 - - - +
114A LEU* 3.8 30.7 - - + -
116A ILE* 4.6 4.3 - - + -
123A PHE* 4.8 2.7 - - + -
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Residues in contact with LYS 101 (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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97A ASP* 3.0 40.0 + - - +
98A GLY* 3.5 11.0 - - - +
100A LEU* 1.3 76.8 - - + +
102A ARG* 1.3 63.0 + - - +
104A GLY* 2.9 15.1 + - - -
105A ILE 5.0 2.2 - - - +
108A LYS* 5.4 12.1 - - - +
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Residues in contact with ARG 102 (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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85A TYR* 4.5 8.7 - - + +
86A ASP* 2.7 27.5 + - - +
89A LYS* 3.4 49.1 + - - +
90A GLY 4.3 0.8 - - - -
91A ALA* 3.6 28.7 - - - +
98A GLY 3.0 16.6 + - - +
99A ALA* 3.2 8.7 + - - +
101A LYS* 1.3 76.7 - - - +
103A LEU* 1.3 63.4 + - + +
104A GLY 3.5 0.3 + - - -
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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