Contacts of the helix formed by residues 84 - 99 (chain A) in PDB entry 1QO0
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 MET 84 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A VAL* 3.8 19.3 - - + -
20A THR* 3.9 30.7 + - + +
58A GLY* 3.7 25.1 - - - +
63A TYR* 5.5 0.9 + - - +
83A TYR* 1.3 80.7 - - + +
85A SER* 1.3 60.0 + - - +
86A HIS* 3.3 33.4 - - + +
87A THR* 2.6 43.1 + - + +
88A ARG 3.3 2.8 + - - -
150A TYR* 3.5 21.8 - - + +
179A LEU* 3.8 24.9 - - + -
206A VAL* 4.4 1.1 - - + -
400A BMD 3.3 7.0 - - - -
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Residues in contact with SER 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A TYR 3.4 0.8 + - - -
84A MET* 1.3 71.3 - - - +
86A HIS* 1.3 57.1 + - - +
88A ARG* 2.9 26.0 + - - +
89A LYS* 2.9 30.5 + - - +
104A TYR* 4.2 0.2 - - - -
109A GLU* 2.5 35.2 + - - -
150A TYR* 4.2 0.6 - - - -
151A ILE* 3.9 16.4 - - - -
152A TYR* 4.7 1.3 - - - -
400A BMD 2.9 24.2 + - - -
88D TYR* 3.9 3.6 - - - -
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Residues in contact with HIS 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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58A GLY 5.0 0.4 - - - -
60A PRO* 3.9 33.8 - - + +
84A MET* 3.3 41.1 - - + +
85A SER* 1.3 71.7 - - - +
87A THR* 1.3 58.5 + - + +
89A LYS* 3.5 3.8 + - - +
90A ALA* 3.1 26.2 + - - +
150A TYR* 3.3 34.0 - + + -
151A ILE* 4.5 2.2 - - + +
179A LEU* 4.5 9.6 - - + -
87D GLU* 6.0 0.9 - - - +
88D TYR* 3.4 19.1 + - - +
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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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58A GLY 4.3 11.7 - - - +
60A PRO* 4.4 12.8 - - + -
63A TYR* 3.5 41.1 - - + +
82A CYS* 3.7 5.4 - - - +
83A TYR 3.3 19.8 + - - -
84A MET* 2.6 35.7 + - + +
86A HIS* 1.3 77.5 - - + +
88A ARG* 1.3 63.5 + - - +
90A ALA* 3.3 5.6 + - - +
91A VAL* 3.2 25.6 + - - +
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Residues in contact with ARG 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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82A CYS* 4.0 9.0 - - - -
84A MET 3.3 0.6 + - - -
85A SER* 2.9 32.5 + - - +
87A THR* 1.3 81.1 + - - +
89A LYS* 1.4 72.8 + - - +
91A VAL* 3.1 3.3 + - - +
92A MET* 3.0 25.3 + - + +
102A LEU* 4.7 5.1 - - + +
104A TYR* 3.1 58.3 + - + +
108A TYR* 3.6 17.5 - - - -
109A GLU* 2.9 22.4 + - - -
112A GLU* 2.7 43.0 + - - +
117A ILE* 4.1 17.9 - - + -
119A TYR* 4.3 2.9 - - - -
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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 SER 2.9 20.3 + - - +
86A HIS 3.5 5.1 + - - +
87A THR 3.4 0.2 - - - -
88A ARG* 1.4 81.2 - - - +
90A ALA* 1.3 57.3 - - - +
92A MET* 3.9 21.5 - - + +
93A PRO* 3.0 26.2 - - - +
111A PHE 5.2 2.0 + - - -
112A GLU* 2.5 39.4 + - - +
87D GLU* 3.3 54.5 + - + +
88D TYR* 3.5 39.9 - - + +
89D GLU* 5.2 6.3 + - - +
113E HIS* 5.2 2.4 + - - -
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Residues in contact with ALA 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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60A PRO* 3.3 32.1 - - + +
61A ASP* 5.4 0.2 - - - -
64A ARG* 3.6 30.2 - - + +
86A HIS 3.1 14.2 + - - +
87A THR 3.5 9.4 - - - +
88A ARG 3.2 0.4 - - - -
89A LYS* 1.3 79.9 - - - +
91A VAL* 1.3 60.4 + - - +
93A PRO* 3.9 8.4 - - - +
94A VAL* 4.3 2.6 - - - +
87D GLU* 5.6 0.4 - - - -
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Residues in contact with VAL 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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13A LEU* 3.7 13.5 - - + -
63A TYR* 3.5 45.1 - - + +
67A ALA* 4.0 11.4 - - + -
79A LEU* 4.6 3.4 - - + -
82A CYS* 3.8 15.7 - - - -
87A THR 3.2 9.1 + - - +
88A ARG 3.1 4.7 + - - +
90A ALA* 1.3 78.6 - - - +
92A MET* 1.3 64.6 + - - +
94A VAL* 2.9 19.2 + - - +
95A VAL* 3.1 30.6 + - + +
102A LEU* 4.3 11.2 - - + -
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Residues in contact with MET 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A ARG* 3.0 16.1 + - - +
89A LYS* 3.9 29.6 - - + +
91A VAL* 1.3 75.6 - - - +
93A PRO* 1.3 70.4 - - + +
95A VAL* 3.2 8.4 + - - +
96A GLU* 2.8 47.6 + - + +
102A LEU* 5.5 0.8 - - - +
112A GLU* 3.5 24.7 - - - +
114A SER* 4.0 3.8 - - - +
117A ILE* 3.6 21.5 - - + -
108D GLN 6.0 2.5 - - - +
113E HIS* 3.4 39.5 - - + +
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Residues in contact with PRO 93 (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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89A LYS 3.0 21.3 - - - +
90A ALA* 3.9 6.7 - - - +
91A VAL 3.5 3.4 - - - -
92A MET* 1.3 98.5 - - + +
94A VAL* 1.3 56.7 + - + +
96A GLU* 4.0 10.4 - - + +
97A ARG* 2.9 59.9 + - + +
87D GLU* 5.8 1.1 - - - +
109D PRO* 4.0 27.6 - - + -
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Residues in contact with VAL 94 (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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64A ARG* 3.9 22.4 - - + +
67A ALA* 4.1 7.4 - - + -
68A GLU* 3.8 47.6 - - + +
71A ILE* 3.7 24.5 - - + -
72A ARG* 5.9 1.1 - - - +
90A ALA 4.3 4.0 - - - +
91A VAL 2.9 11.3 + - - +
93A PRO* 1.3 76.7 - - + +
95A VAL* 1.3 64.1 + - - +
97A ARG* 3.5 18.5 + - - +
98A ALA* 3.3 21.5 + - - +
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Residues in contact with VAL 95 (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 ALA* 5.2 0.2 - - + -
71A ILE* 4.4 7.2 - - + -
79A LEU* 3.8 21.8 - - + -
91A VAL* 3.1 30.2 + - + +
92A MET* 3.5 14.1 - - - +
94A VAL* 1.3 75.7 - - + +
96A GLU* 1.3 65.9 + - + +
98A ALA 3.2 1.2 + - - -
99A ASP 3.1 3.6 + - - -
100A ALA* 3.1 41.5 + - + -
101A LEU 4.8 0.4 - - - +
102A LEU* 4.3 14.4 - - + +
116A ASN* 3.7 30.0 + - + +
117A ILE* 4.8 3.6 - - + -
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Residues in contact with GLU 96 (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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92A MET* 2.8 30.3 + - - +
93A PRO* 4.0 8.7 - - + +
95A VAL* 1.3 70.3 - - - +
97A ARG* 1.3 65.3 + - + +
99A ASP* 3.2 19.4 + - - +
114A SER* 2.6 28.9 + - - +
115A PRO* 4.0 4.6 - - + +
116A ASN* 3.3 26.5 + - + +
97B ARG* 4.8 4.6 - - - -
111E ASP* 5.0 3.8 - - - +
113E HIS* 2.6 37.5 + - - -
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Residues in contact with ARG 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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64A ARG* 6.2 1.0 - - - +
68A GLU* 5.2 3.2 + - - +
72A ARG* 5.7 5.6 - - - +
93A PRO* 2.9 47.5 + - + +
94A VAL* 4.0 20.5 - - - +
95A VAL 3.3 0.2 - - - -
96A GLU* 1.3 77.2 - - + +
98A ALA* 1.3 59.3 + - - +
99A ASP* 3.3 5.0 - - - +
96B GLU 4.7 3.8 - - - -
97B ARG* 3.4 66.5 + - + +
98B ALA* 5.2 0.5 - - - -
99B ASP* 5.1 7.0 - - - -
109D PRO* 4.2 16.2 - - - +
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Residues in contact with ALA 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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71A ILE* 3.7 35.2 - - + -
77A ARG* 3.7 18.4 + - - +
94A VAL 3.3 14.0 + - - +
95A VAL 3.2 4.3 + - - +
96A GLU 3.2 0.6 - - - -
97A ARG* 1.3 78.1 - - - +
99A ASP* 1.3 71.9 + - - +
100A ALA* 3.2 7.1 + - + +
97B ARG 5.4 0.4 - - - -
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Residues in contact with ASP 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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77A ARG* 4.6 2.1 - - - -
95A VAL 3.1 3.4 + - - -
96A GLU 3.2 11.3 + - - +
97A ARG 4.6 4.4 - - - +
98A ALA* 1.3 81.8 - - - +
100A ALA* 1.3 62.2 + - - +
116A ASN* 3.7 13.7 + - - +
308A VAL* 3.7 23.2 - - + +
72B ARG* 3.2 38.0 + - - -
97B ARG* 5.2 7.2 + - - -
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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