Contacts of the helix formed by residues 91 - 106 (chain B) in PDB entry 6ACQ
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 ARG 91 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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89B VAL* 3.3 27.8 + - + +
90B GLU* 1.3 80.0 - - - +
92B MET* 1.3 68.0 + - - +
93B ASP* 3.0 15.1 + - - +
94B ILE* 3.3 32.0 - - + +
95B LYS* 2.9 23.2 + - - +
119B LEU* 3.9 4.1 - - - +
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Residues in contact with MET 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ARG* 1.3 70.3 - - - +
93B ASP* 1.3 57.0 + - - +
95B LYS* 3.5 1.0 + - - +
96B LYS* 2.8 52.1 + - + +
119B LEU* 3.9 28.6 - - + +
120B SER* 3.6 36.8 - - - +
123B GLU* 3.5 39.7 - - + +
124B VAL* 3.4 22.9 - - + -
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Residues in contact with ASP 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ARG* 3.0 16.7 + - - +
92B MET* 1.3 77.5 - - - +
94B ILE* 1.3 86.8 + - - +
96B LYS* 3.5 10.2 + - - +
97B GLN* 3.4 20.1 + - - +
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Residues in contact with ILE 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B ALA* 5.2 3.8 - - + -
89B VAL* 4.5 19.5 - - + +
91B ARG* 3.1 51.0 + - + +
93B ASP* 1.3 86.6 + - - +
95B LYS* 1.3 64.8 + - + +
97B GLN* 2.9 24.0 + - - +
98B ILE* 3.0 28.1 + - + +
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Residues in contact with LYS 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLU* 2.7 44.4 + - - +
88B ALA* 4.2 2.2 + - - +
89B VAL 2.7 29.9 + - - -
90B GLU* 3.7 11.1 + - - -
91B ARG 2.9 16.3 + - - +
92B MET* 3.6 5.4 - - - +
94B ILE* 1.3 81.5 - - - +
96B LYS* 1.3 62.2 + - - +
98B ILE* 3.6 5.9 + - - +
99B PHE* 3.1 38.0 + - + -
114B SER* 3.8 12.3 - - - +
116B THR* 4.1 5.4 - - + +
119B LEU* 3.5 29.6 - - + -
124B VAL* 4.2 19.1 - - + -
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Residues in contact with LYS 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B MET* 2.8 41.0 + - + +
93B ASP* 3.8 9.4 - - - +
94B ILE 3.1 0.4 - - - -
95B LYS* 1.3 77.2 - - - +
97B GLN* 1.3 57.4 + - - +
99B PHE* 3.4 2.9 + - - +
100B ALA* 2.9 28.9 + - - +
123B GLU* 2.9 44.1 + - - +
124B VAL* 4.4 8.5 - - - -
126B SER* 5.8 0.7 - - - -
127B ALA* 3.7 28.9 - - + +
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Residues in contact with GLN 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B ASP 3.4 10.5 + - - +
94B ILE* 2.9 12.9 + - - +
96B LYS* 1.3 77.2 - - - +
98B ILE* 1.3 54.9 + - - +
100B ALA* 2.9 13.0 + - - +
101B ASP* 2.7 63.0 + - - +
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Residues in contact with ILE 98 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 4.2 26.0 - - + -
30B ARG* 5.4 9.0 - - - +
75B LEU* 5.4 9.2 - - + -
86B GLU* 4.3 10.3 - - + -
88B ALA* 4.3 17.5 - - + -
94B ILE* 3.0 22.9 + - + +
95B LYS* 3.7 7.4 - - - +
97B GLN* 1.3 77.4 - - - +
99B PHE* 1.3 74.8 + - + +
101B ASP* 3.4 9.6 + - - +
102B LEU* 2.8 53.3 + - + +
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Residues in contact with PHE 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B GLU* 3.9 28.5 - - + -
95B LYS* 3.1 30.0 + - + +
96B LYS 3.9 3.8 - - - +
97B GLN 3.2 0.8 - - - -
98B ILE* 1.3 83.6 - - + +
100B ALA* 1.3 61.2 + - - +
102B LEU* 3.9 6.8 - - + +
103B ASP* 2.9 30.5 + - - +
112B LEU* 3.6 44.7 - - + +
113B ALA 3.7 25.4 - - - -
114B SER* 4.0 8.5 - - - -
124B VAL* 3.5 28.5 - - + +
128B THR* 3.5 18.3 - - + +
134B VAL* 4.1 13.0 - - + -
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Residues in contact with ALA 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B LYS 2.9 19.6 + - - +
97B GLN* 3.3 18.6 - - - +
99B PHE* 1.3 74.6 - - - +
101B ASP* 1.3 66.2 + - - +
103B ASP* 3.3 6.0 + - - +
104B ASN* 3.1 29.8 + - - +
127B ALA* 3.7 21.1 + - + +
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Residues in contact with ASP 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU* 3.8 22.6 - - + +
97B GLN* 2.7 46.3 + - - +
98B ILE* 3.5 7.3 - - - +
100B ALA* 1.3 72.9 - - - +
102B LEU* 1.3 56.9 + - - +
104B ASN* 2.9 13.7 + - - +
105B ILE* 2.9 33.9 + - + +
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B ILE* 4.5 4.0 - - + -
75B LEU* 3.6 32.1 - - + +
78B ALA* 4.1 10.1 - - + -
84B VAL* 4.0 23.3 - - + -
86B GLU* 5.6 2.0 - - + -
98B ILE* 2.8 48.6 + - + +
99B PHE* 3.9 11.0 - - + +
101B ASP* 1.3 72.2 - - - +
103B ASP* 1.3 59.6 + - - +
105B ILE* 4.2 4.7 - - + -
106B CYS* 2.8 52.0 + - - +
112B LEU* 3.8 20.6 - - + -
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Residues in contact with ASP 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B PHE 2.9 20.5 + - - +
100B ALA* 3.5 7.0 - - - +
101B ASP 3.2 0.2 - - - -
102B LEU* 1.3 76.4 - - - +
104B ASN* 1.3 66.0 + - - +
106B CYS 3.9 0.7 - - - +
112B LEU* 4.2 2.4 - - + +
127B ALA 5.0 0.3 - - - +
128B THR* 3.6 13.5 - - + -
129B LYS* 2.8 44.4 + - - +
130B ARG* 2.9 52.3 + - - +
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Residues in contact with ASN 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ALA* 3.1 21.2 + - - +
101B ASP* 2.9 8.5 + - - +
103B ASP* 1.3 85.1 + - - +
105B ILE* 1.3 65.1 + - + +
106B CYS 3.6 2.4 + - - +
129B LYS* 6.0 1.2 - - - +
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Residues in contact with ILE 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B LEU* 3.6 51.6 - - + +
76B ASN* 4.1 24.9 - - - +
79B ALA* 3.7 37.6 - - + +
101B ASP* 2.9 22.4 + - + +
102B LEU* 3.8 5.8 - - - +
104B ASN* 1.3 79.0 - - + +
106B CYS* 1.3 66.6 + - - +
107B LYS 3.9 0.2 + - - -
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Residues in contact with CYS 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B ALA* 3.6 24.9 - - - +
79B ALA 3.5 7.0 - - - +
84B VAL* 4.2 11.9 - - - -
102B LEU* 2.8 46.9 + - - +
103B ASP 3.9 2.6 - - - +
104B ASN 3.5 2.5 - - - +
105B ILE* 1.3 78.1 - - - +
107B LYS* 1.3 68.1 + - - +
108B PRO* 4.4 0.7 - - - +
110B THR* 3.5 21.8 - - + +
112B LEU* 4.4 2.0 - - + -
130B ARG* 2.9 16.0 + - - +
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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