Contacts of the helix formed by residues 90 - 109 (chain B) in PDB entry 5A6C
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 90 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B LYS* 5.7 5.9 - - - +
55B SER* 5.1 5.7 + - - -
85B ALA* 2.9 17.9 + - - +
86B ARG* 5.0 0.4 - - - +
88B ILE* 3.3 21.9 - - + +
89B GLY* 1.3 73.1 - - - +
91B GLN* 1.3 59.2 + - - +
92B LEU* 3.5 8.3 + - - +
93B GLY* 3.2 26.0 + - - -
94B GLU* 2.9 30.2 + - - +
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Residues in contact with GLN 91 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLY 3.4 9.0 + - - +
90B ASP* 1.3 72.6 + - - +
92B LEU* 1.3 58.3 + - - +
94B GLU* 3.2 29.6 + - - +
95B ALA 2.9 23.6 + - - -
124B ILE* 3.6 26.4 - - + +
127B GLU* 3.7 25.8 - - - +
128B LEU* 4.2 24.5 - - + +
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Residues in contact with LEU 92 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A ARG* 4.8 3.4 - - - +
223A LEU* 4.7 19.1 - - + +
227A GLU* 3.7 33.9 - - + +
90B ASP* 3.3 7.5 + - - +
91B GLN* 1.3 75.2 - - - +
93B GLY* 1.3 67.6 + - - +
95B ALA* 3.1 12.6 + - + +
96B LYS* 2.9 27.8 + - + +
124B ILE* 5.5 0.7 - - + -
125B SER* 5.1 5.6 - - - +
128B LEU* 3.7 26.5 - - + +
130B ASP* 4.4 16.4 - - + +
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Residues in contact with GLY 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B SER* 5.4 0.2 - - - -
85B ALA* 3.7 6.5 - - - -
90B ASP* 3.2 25.2 + - - -
92B LEU* 1.3 77.9 - - - +
94B GLU* 1.3 56.5 + - - +
96B LYS* 3.1 30.6 + - - +
97B ALA* 2.9 27.9 + - - +
384B CYS* 5.8 0.2 - - - -
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Residues in contact with GLU 94 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82B LEU* 3.6 17.0 - - + +
85B ALA* 3.4 15.7 - - + +
86B ARG* 2.8 44.4 + - + +
90B ASP 2.9 14.3 + - - +
91B GLN* 3.4 30.8 + - - +
93B GLY* 1.3 74.6 - - - +
95B ALA* 1.3 58.1 + - - +
98B SER* 2.9 31.2 + - - -
120B ARG* 4.0 9.7 - - - -
124B ILE* 3.7 14.3 - - + +
1388B SO4 4.6 3.1 + - - -
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Residues in contact with ALA 95 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91B GLN 2.9 6.4 + - - +
92B LEU* 3.1 13.0 + - + +
94B GLU* 1.3 76.9 - - - +
96B LYS* 1.3 59.0 + - - +
98B SER* 3.3 3.4 + - - -
99B GLY 2.9 22.9 + - - -
121B HIS* 3.3 32.1 + - + +
124B ILE* 3.4 38.8 - - + -
125B SER* 4.7 4.9 - - - +
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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
----------------------------------------------------------
55B SER* 3.5 10.3 + - - -
59B SER* 3.6 4.3 - - - +
81B ASP* 2.7 43.3 + - - -
92B LEU* 2.9 13.0 + - + +
93B GLY* 3.1 38.1 + - - +
95B ALA* 1.3 74.6 - - - +
97B ALA* 1.3 67.4 + - - +
99B GLY* 3.2 1.7 + - - -
100B ASN* 3.0 31.3 + - - +
121B HIS* 4.6 1.6 - - + -
382B GLU* 3.7 42.7 - - + +
383B ASP 4.7 2.2 - - - +
384B CYS* 3.4 32.5 - - - -
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Residues in contact with ALA 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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78B HIS* 4.1 4.4 - - - +
81B ASP* 3.3 26.7 - - - +
82B LEU* 3.6 32.3 - - + +
93B GLY 2.9 16.8 + - - +
94B GLU 3.9 2.0 - - - +
96B LYS* 1.3 76.8 - - - +
98B SER* 1.3 58.0 + - - +
100B ASN* 3.3 7.7 + - - +
101B LEU* 2.9 32.4 + - - +
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Residues in contact with SER 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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82B LEU* 4.3 7.8 - - - +
94B GLU 2.9 20.1 + - - -
95B ALA* 3.6 5.8 - - - -
97B ALA* 1.3 78.3 - - - +
99B GLY* 1.3 57.1 + - - +
101B LEU* 3.3 7.0 + - - +
102B GLY 2.9 22.3 + - - -
117B CYS* 2.4 41.4 + - - +
120B ARG* 3.2 32.6 + - - +
121B HIS 3.7 0.6 + - - -
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Residues in contact with GLY 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95B ALA 2.9 11.9 + - - -
96B LYS 3.2 3.3 + - - -
98B SER* 1.3 73.2 - - - +
100B ASN* 1.3 64.9 + - - +
102B GLY* 3.3 2.1 + - - -
103B ASN* 3.0 29.8 + - - -
117B CYS 4.7 0.7 - - - -
118B CYS* 4.3 5.9 - - - -
121B HIS* 3.8 30.9 - - - +
140B ASN* 4.5 3.0 + - - -
382B GLU* 5.1 2.9 - - - -
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Residues in contact with ASN 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B SER* 3.7 10.9 + - - -
63B ASN* 3.7 7.7 - - - +
66B PHE* 5.5 0.5 - - - -
78B HIS* 3.3 42.0 + - + +
96B LYS* 3.0 24.6 + - - +
97B ALA* 3.6 4.7 - - - +
99B GLY* 1.3 73.6 - - - +
101B LEU* 1.3 65.9 + - - +
103B ASN* 3.3 7.3 + - - +
104B THR* 2.9 27.4 + - - -
381B GLU* 4.2 4.7 - - - +
382B GLU* 3.1 42.0 + - - +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B LEU* 3.5 47.1 - - + +
78B HIS* 3.6 16.6 - - + +
79B HIS* 3.9 21.1 - - + +
82B LEU* 3.8 30.3 - - + -
97B ALA 2.9 15.8 + - - +
98B SER* 3.5 9.0 - - - +
99B GLY 3.2 0.2 - - - -
100B ASN* 1.3 76.3 - - - +
102B GLY* 1.3 58.1 + - - +
104B THR* 3.2 3.9 + - - -
105B LEU* 2.9 39.0 + - + +
117B CYS* 3.9 16.8 - - - -
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Residues in contact with GLY 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B SER 2.9 11.3 + - - -
99B GLY 3.6 1.1 - - - -
100B ASN 3.3 0.2 - - - -
101B LEU* 1.3 76.2 - - - +
103B ASN* 1.3 56.3 + - - +
106B LYS* 2.9 26.5 + - - +
114B ALA* 3.3 16.3 - - - +
117B CYS* 3.6 14.0 - - - +
118B CYS* 3.5 27.3 - - - -
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Residues in contact with ASN 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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66B PHE* 4.2 10.1 - - + -
99B GLY 3.0 15.7 + - - +
100B ASN* 3.3 9.5 + - - +
102B GLY* 1.3 73.4 - - - +
104B THR* 1.3 66.3 + - - +
106B LYS* 3.3 15.6 + - - +
107B VAL* 3.1 26.2 + - - +
118B CYS* 4.2 1.8 - - - -
140B ASN* 3.6 43.6 + - - +
143B ASN* 5.2 1.9 + - - +
144B VAL* 5.3 1.0 - - - +
379B GLU* 4.2 28.5 - - + +
380B GLU 4.1 11.5 + - - -
381B GLU* 4.8 5.3 - - - +
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Residues in contact with THR 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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66B PHE* 3.7 20.9 - - + -
71B TYR* 3.4 32.3 - - + +
74B ALA* 4.2 4.6 - - + +
75B LEU* 3.6 26.7 - - + +
78B HIS* 3.6 16.5 - - - -
100B ASN 2.9 17.5 + - - -
101B LEU* 3.6 4.9 - - - -
103B ASN* 1.3 76.0 - - - +
105B LEU* 1.3 57.5 + - - +
107B VAL* 3.2 5.9 + - - +
108B LEU* 3.0 29.7 + - + +
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Residues in contact with LEU 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* 3.7 30.5 - - + -
101B LEU* 2.9 30.9 + - + +
104B THR* 1.3 73.7 - - - +
106B LYS* 1.3 59.5 + - - +
108B LEU* 2.9 8.1 + - + +
109B GLY 2.8 25.8 + - - -
110B ASN* 3.1 40.1 + - + +
113B GLU* 3.8 32.1 - - + +
114B ALA* 3.6 15.7 - - + +
117B CYS* 3.9 10.5 - - - -
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Residues in contact with LYS 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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102B GLY 2.9 14.6 + - - +
103B ASN* 3.4 15.6 + - - +
105B LEU* 1.3 74.6 - - - +
107B VAL* 1.3 70.0 + - - +
109B GLY* 3.1 13.5 + - - -
111B PHE* 3.9 16.0 - - + -
114B ALA* 3.7 9.0 - - + +
143B ASN* 4.0 38.2 - - + +
144B VAL* 4.0 13.7 - - + +
147B ALA* 3.8 22.3 - - + +
379B GLU* 3.3 39.1 + - - +
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Residues in contact with VAL 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B PHE* 3.9 22.2 - - + -
71B TYR* 3.6 44.9 - - + +
103B ASN 3.1 13.0 + - - +
104B THR 3.5 7.4 - - - +
106B LYS* 1.3 83.5 - - - +
108B LEU* 1.3 63.0 + - + +
109B GLY* 3.2 1.6 + - - -
379B GLU* 4.2 12.6 - - - +
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Residues in contact with LEU 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B TYR* 3.9 38.8 - - + +
72B ALA* 5.1 3.4 - - - +
75B LEU* 4.0 29.4 - - + -
104B THR* 3.0 18.5 + - + +
105B LEU* 2.9 12.9 + - + +
107B VAL* 1.3 75.2 - - - +
109B GLY* 1.3 59.9 + - - +
110B ASN* 3.3 6.6 + - + +
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Residues in contact with GLY 109 (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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105B LEU 2.8 4.0 + - - -
106B LYS 3.1 12.6 + - - -
107B VAL 3.1 2.3 + - - -
108B LEU* 1.3 78.4 - - - +
110B ASN* 1.3 59.1 + - - +
111B PHE* 3.2 32.1 + - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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