Contacts of the helix formed by residues 78 - 88 (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 GLY 78 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A ILE* 6.2 1.6 - - - -
66A ALA* 4.3 7.0 - - - -
67A THR 2.9 24.7 + - - +
68A THR* 4.6 3.4 - - - -
77A ASP* 1.3 77.2 - - - +
79A PRO* 1.3 66.8 - - - +
81A LEU* 3.0 20.9 + - - +
82A PHE* 3.1 25.5 + - - -
114A LEU* 4.8 1.1 - - - -
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Residues in contact with PRO 79 (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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67A THR 4.1 1.1 - - - +
68A THR 4.5 2.5 - - - +
76A PRO* 3.6 22.7 - - + +
77A ASP 3.5 3.1 - - - -
78A GLY* 1.3 87.6 - - - +
80A ASP* 1.3 60.4 + - - +
82A PHE* 3.3 1.3 + - + -
83A LYS* 2.9 30.4 + - - +
96A ALA* 3.7 13.8 - - + +
109A MET* 3.7 38.1 - - + -
112A SER 3.8 17.0 - - - +
114A LEU* 4.1 15.9 - - + +
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Residues in contact with ASP 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 PRO 5.2 2.7 - - - -
77A ASP* 3.0 24.7 + - + +
79A PRO* 1.3 80.3 - - - +
81A LEU* 1.3 58.2 + - - +
83A LYS* 3.4 11.4 + - - +
84A ALA* 2.9 30.3 + - - +
143A THR* 4.0 13.6 + - + -
147A VAL* 5.6 3.2 - - + +
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Residues in contact with LEU 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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61A ILE* 4.2 16.4 - - + +
64A PHE* 5.0 1.6 - - + -
66A ALA* 4.6 15.5 - - + -
77A ASP 3.1 10.6 + - - +
78A GLY* 3.0 12.7 + - - +
80A ASP* 1.3 76.1 - - - +
82A PHE* 1.3 65.9 + - + +
84A ALA* 3.2 5.2 + - - +
85A TYR* 3.0 19.8 + - - +
136A TRP* 3.8 33.0 - - + -
139A ALA* 3.7 26.0 - - + +
140A MET* 3.7 31.0 - - + +
143A THR* 3.6 16.5 - - + +
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Residues in contact with PHE 82 (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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61A ILE* 3.9 29.8 - - + -
68A THR* 4.4 4.7 - - + -
78A GLY* 3.1 27.5 + - - -
79A PRO 3.8 4.9 - - - +
81A LEU* 1.3 75.6 - - + +
83A LYS* 1.3 67.4 + - - +
85A TYR* 3.1 4.8 + - + +
86A ASP 3.0 18.4 + - - -
96A ALA* 4.0 11.7 - - + +
99A ALA* 3.1 27.9 - - + +
100A LEU* 4.0 19.3 - - + -
103A LEU* 4.1 16.2 - - + -
105A ILE* 4.8 0.7 - - + -
114A LEU* 3.6 26.9 - - + -
123A PHE* 4.1 9.2 - + - -
127A ILE* 4.0 13.7 - - + -
136A TRP* 4.0 25.4 - + - -
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Residues in contact with LYS 83 (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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79A PRO 2.9 16.3 + - - +
80A ASP* 3.7 11.7 - - - +
82A PHE* 1.3 76.2 - - - +
84A ALA* 1.3 58.6 + - - +
86A ASP* 3.1 4.2 + - - +
87A ALA* 2.9 26.8 + - + +
94A PRO* 3.4 39.5 + - + +
95A SER* 3.8 15.3 - - - -
96A ALA* 3.9 7.4 - - + +
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Residues in contact with ALA 84 (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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80A ASP 2.9 17.3 + - - +
81A LEU 3.4 6.1 - - - +
83A LYS* 1.3 77.7 - - - +
85A TYR* 1.3 57.1 + - - +
87A ALA* 3.3 8.4 + - - +
88A ALA* 2.8 29.3 + - - +
139A ALA* 3.7 14.7 - - + +
142A GLU* 4.3 16.3 - - + +
143A THR* 3.7 16.2 - - - +
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Residues in contact with TYR 85 (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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81A LEU 3.0 12.3 + - - +
82A PHE* 3.4 9.2 - + - +
84A ALA* 1.3 75.1 - - - +
86A ASP* 1.3 68.4 + - - +
88A ALA* 3.1 3.1 + - - +
89A LYS* 2.9 63.4 + - + +
99A ALA* 4.2 14.8 - - + -
102A ARG* 4.5 9.5 - - + +
103A LEU* 3.9 39.2 - - + +
130A LEU* 4.0 3.3 - - + +
133A ASP* 3.2 22.1 + - - -
135A ALA* 3.9 2.7 - - + -
136A TRP* 3.7 53.6 - + + -
139A ALA* 3.5 10.1 - - + +
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Residues in contact with ASP 86 (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 3.0 7.6 + - - +
83A LYS 3.4 9.0 - - - +
85A TYR* 1.3 77.4 - - - +
87A ALA* 1.3 62.0 + - - +
89A LYS* 3.3 9.2 + - - +
90A GLY 3.4 0.7 + - - -
91A ALA* 3.1 31.2 + - - +
93A ASN 4.2 2.3 - - - +
94A PRO* 3.3 5.9 - - + +
95A SER* 2.9 40.3 + - - +
98A GLY* 3.6 13.1 - - - -
99A ALA* 3.7 11.4 - - - +
102A ARG* 2.7 40.7 + - - +
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Residues in contact with ALA 87 (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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83A LYS* 2.9 13.4 + - + +
84A ALA* 3.5 11.2 - - - +
85A TYR 3.1 0.2 - - - -
86A ASP* 1.3 73.7 - - - +
88A ALA* 1.3 59.2 + - - +
90A GLY* 2.8 22.0 + - - -
91A ALA 4.0 7.4 + - - +
94A PRO* 3.7 21.9 - - + +
142A GLU* 5.8 2.7 - - - +
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Residues in contact with ALA 88 (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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84A ALA 2.8 20.4 + - - +
85A TYR 3.1 5.4 + - - +
87A ALA* 1.3 72.2 - - - +
89A LYS* 1.3 60.6 + - - +
90A GLY 3.2 1.1 + - - -
135A ALA* 3.6 36.8 - - + +
138A LYS* 4.7 16.8 - - + -
139A ALA* 4.8 1.3 - - + -
142A GLU* 6.1 0.7 - - - +
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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