Contacts of the helix formed by residues 79 - 92 (chain A) in PDB entry 1QM4
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 79 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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77A MET 4.4 0.2 + - - -
78A ILE* 1.3 75.2 - - - +
80A TYR* 1.3 52.1 + - - +
81A GLN* 3.2 14.6 + - - +
82A ARG* 2.8 81.7 + - + +
83A VAL* 2.9 15.2 + - - +
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Residues in contact with TYR 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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42A VAL* 3.6 30.7 - - + -
46A HIS* 3.0 17.1 + - - -
68A LEU* 3.5 21.3 - - + -
72A ILE* 3.1 10.2 - - - +
78A ILE* 3.9 22.4 - - + -
79A ASP* 1.3 68.4 + - - +
81A GLN* 1.3 60.4 + - - +
83A VAL* 3.7 6.3 - - - +
84A VAL* 2.9 36.6 + - - +
109A VAL* 4.0 29.4 - - + -
111A LEU* 3.2 22.4 - - + +
113A GLN* 2.6 34.5 + - + -
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Residues in contact with GLN 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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79A ASP* 3.2 11.1 + - - +
80A TYR* 1.3 78.4 - - - +
82A ARG* 1.3 57.6 + - - +
84A VAL* 4.0 0.7 - - - +
85A ARG* 2.8 80.6 + - - +
107A VAL* 3.0 37.2 + - - +
109A VAL* 4.4 8.4 - - + +
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Residues in contact with ARG 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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77A MET 5.5 4.2 + - - -
79A ASP* 2.8 60.7 + - - +
81A GLN* 1.3 78.2 - - - +
83A VAL* 1.3 58.1 + - + +
85A ARG* 4.9 3.1 - - - +
86A ASP* 3.0 52.1 + - - +
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Residues in contact with VAL 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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38A ILE* 4.9 0.7 - - - +
41A ALA* 4.2 6.7 - - + +
42A VAL* 3.4 44.9 - - + +
45A ALA* 4.0 14.4 - - + -
78A ILE* 3.8 22.9 - - + -
79A ASP 2.9 15.6 + - - +
80A TYR* 3.4 4.7 + - + +
82A ARG* 1.3 79.8 - - + +
84A VAL* 1.3 60.7 + - - +
86A ASP* 4.2 4.6 - - - +
87A THR* 2.7 30.1 + - - -
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Residues in contact with VAL 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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38A ILE* 3.8 26.0 - - + +
42A VAL* 4.9 0.2 - - + -
66A VAL* 3.8 18.8 - - + -
68A LEU* 4.5 20.9 - - + -
80A TYR 2.9 22.8 + - - +
81A GLN 4.0 0.4 - - - +
83A VAL* 1.3 81.5 - - + +
85A ARG* 1.3 64.0 + - - +
87A THR* 3.3 5.9 + - - -
88A ILE* 3.2 28.7 + - + +
107A VAL* 3.6 39.0 - - + -
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Residues in contact with ARG 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 GLN* 2.8 49.1 + - - +
82A ARG* 4.3 2.7 - - - +
84A VAL* 1.3 71.3 - - - +
86A ASP* 1.3 68.9 + - - +
88A ILE* 3.8 4.3 - - + -
89A LYS* 3.0 20.8 + - - +
102A PHE* 2.8 63.1 + - + +
103A LYS* 4.0 11.4 + - - +
104A THR 4.5 0.2 - - - -
105A CYS* 3.1 31.4 + - - +
106A ASN* 4.8 0.4 - - - +
107A VAL* 3.5 22.4 - - + +
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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 ARG* 3.0 39.9 + - - +
83A VAL* 4.4 4.8 - - - +
85A ARG* 1.3 77.8 - - - +
87A THR* 1.3 58.1 + - - +
89A LYS* 3.3 17.8 + - - +
90A HIS* 2.9 29.1 + - - +
102A PHE* 5.6 1.9 - - - -
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Residues in contact with THR 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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37A GLN* 4.1 3.4 - - + -
38A ILE* 4.0 33.8 - - + +
41A ALA* 3.2 17.7 - - - +
83A VAL 2.7 23.6 + - - -
84A VAL 3.3 6.0 + - - -
85A ARG 3.2 0.8 - - - -
86A ASP* 1.3 77.3 - - - +
88A ILE* 1.3 61.2 + - - +
90A HIS* 3.5 6.0 + - - +
91A ILE* 3.1 34.5 + - + +
373A GLN* 3.6 23.1 + - - +
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Residues in contact with ILE 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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34A ILE* 4.9 8.5 - - + -
38A ILE* 4.3 12.3 - - + -
66A VAL* 4.1 12.1 - - + -
84A VAL* 3.2 33.9 + - + +
85A ARG* 3.8 4.3 - - - +
86A ASP 3.3 0.2 - - - -
87A THR* 1.3 75.0 - - - +
89A LYS* 1.3 63.1 + - - +
91A ILE* 3.5 9.7 + - - +
92A GLY 3.2 5.4 + - - -
93A TYR* 3.0 53.9 + - + +
100A PHE* 4.3 13.9 - - + -
102A PHE* 3.8 16.6 - - + +
105A CYS* 3.8 26.0 - - - -
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Residues in contact with LYS 89 (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 ARG 3.0 17.1 + - - +
86A ASP* 3.5 15.4 + - - +
88A ILE* 1.3 75.3 - - - +
90A HIS* 1.3 60.9 + - - +
92A GLY* 2.9 20.8 + - - -
93A TYR 4.0 2.9 + - - -
94A ASP* 5.5 4.3 - - + +
102A PHE* 3.3 47.9 - - + -
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Residues in contact with HIS 90 (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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28A GLU* 4.3 8.4 + - - -
37A GLN* 4.5 6.0 + - - -
86A ASP 2.9 18.3 + - - +
87A THR* 3.7 7.0 - - - +
89A LYS* 1.3 78.1 - - - +
91A ILE* 1.3 64.5 + - + +
92A GLY* 3.2 0.9 + - - -
169A ARG* 4.1 0.3 + - - -
170A ARG* 2.7 52.2 + - - -
373A GLN* 4.0 21.3 + - - +
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Residues in contact with ILE 91 (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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28A GLU* 3.1 42.2 - - + +
29A GLY* 3.8 1.1 - - - -
34A ILE* 4.2 24.9 - - + -
37A GLN* 3.8 24.2 - - - +
87A THR* 3.1 31.1 + - + +
88A ILE* 3.6 10.8 - - + +
90A HIS* 1.3 78.2 - - + +
92A GLY* 1.3 57.0 + - - +
93A TYR* 3.7 23.1 - - + -
169A ARG* 2.7 20.1 + - - -
170A ARG* 3.9 6.0 + - - +
179A PRO* 3.4 8.7 - - + +
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Residues in contact with GLY 92 (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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88A ILE 3.2 0.4 + - - -
89A LYS 2.9 14.1 + - - -
90A HIS 3.1 1.1 - - - -
91A ILE* 1.3 79.9 - - - +
93A TYR* 1.3 64.3 + - - +
94A ASP* 3.5 11.0 + - - +
98A LYS* 3.7 18.7 + - - +
169A ARG* 4.1 7.9 - - - -
179A PRO* 3.7 14.1 - - - +
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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