Contacts of the helix formed by residues 63 - 73 (chain B) in PDB entry 5AIS
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 GLN 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A ALA* 3.4 29.4 - - - +
93A ASP* 3.6 20.5 - - + +
94A THR* 3.2 24.9 + - - +
97A ASP* 3.1 21.6 + - - -
52B PRO 3.9 6.3 + - - -
62B HIS* 1.3 97.6 + - - +
64B SER* 1.3 66.4 + - - +
65B LEU 3.3 1.9 + - - +
66B ALA* 3.2 7.6 + - + +
67B ILE* 3.0 18.8 + - - +
1202B GSH 2.9 36.8 + - - +
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Residues in contact with SER 64 (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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14B ARG* 3.4 30.4 + - - +
17B ILE* 4.5 4.4 - - - +
18B ILE* 4.0 12.1 - - - +
52B PRO* 3.7 20.9 - - - +
63B GLN* 1.3 70.1 - - - +
65B LEU* 1.3 69.7 + - - +
67B ILE* 3.3 3.9 + - - +
68B ALA* 2.8 28.1 + - - +
96B ASP* 5.0 2.3 + - - -
152B TYR* 5.2 1.4 + - - -
1202B GSH 2.8 29.2 + - - -
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Residues in contact with LEU 65 (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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93A ASP* 4.2 15.2 + - - +
17B ILE* 4.7 3.8 - - + -
63B GLN* 3.3 1.0 + - - +
64B SER* 1.3 88.4 + - - +
66B ALA* 1.3 60.7 + - - +
68B ALA* 3.8 3.7 - - - +
69B ARG* 2.9 42.0 + - - +
92B VAL* 3.5 33.4 - - + -
93B ASP* 3.7 16.6 - - - +
96B ASP* 3.6 30.1 - - + +
148B TRP* 4.0 14.6 - - + -
152B TYR* 3.9 24.0 - - + +
1202B GSH 4.8 1.7 + - - +
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Residues in contact with ALA 66 (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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86A CYS* 3.5 14.9 - - - +
89A ASP* 3.7 11.5 - - + +
90A ALA* 3.7 33.2 - - - +
93A ASP* 4.6 2.9 + - - +
62B HIS 3.9 4.0 - - - +
63B GLN* 3.2 13.6 + - + +
65B LEU* 1.3 78.0 - - - +
67B ILE* 1.3 57.6 + - - +
69B ARG* 3.7 13.5 - - - +
70B TYR* 3.0 28.1 + - - +
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Residues in contact with ILE 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86A CYS* 4.3 6.3 - - - -
18B ILE* 3.8 26.7 - - + -
52B PRO 4.2 7.2 - - - +
53B ILE 4.5 0.7 - - - -
54B LEU* 3.5 42.0 - - + +
61B LEU* 3.9 25.8 - - + +
62B HIS* 3.7 26.0 - - - +
63B GLN 3.0 23.9 + - - +
64B SER* 3.5 6.1 - - - +
66B ALA* 1.3 73.9 - - - +
68B ALA* 1.3 65.5 + - - +
70B TYR* 3.2 3.1 + - - +
71B LEU* 3.0 27.7 + - + +
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Residues in contact with ALA 68 (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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17B ILE* 4.2 11.2 - - + -
18B ILE* 4.5 3.3 - - + +
21B ILE* 3.6 22.2 - - + -
64B SER 2.8 20.7 + - - +
65B LEU* 3.8 2.7 - - - +
67B ILE* 1.3 72.8 - - - +
69B ARG* 1.3 60.9 + - - +
71B LEU* 3.4 4.4 + - - +
72B THR* 3.0 32.4 + - - +
148B TRP* 3.5 27.8 - - + -
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Residues in contact with ARG 69 (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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69A ARG* 3.5 39.2 - - - +
89A ASP* 3.0 39.5 + - - +
93A ASP* 5.4 4.0 + - - -
65B LEU* 2.9 37.5 + - - +
66B ALA* 3.7 5.6 - - - +
68B ALA* 1.3 73.1 - - - +
70B TYR* 1.3 66.1 + - - +
72B THR* 3.2 9.5 + - - +
73B LYS* 3.1 37.9 + - + +
89B ASP* 3.1 32.1 + - - +
92B VAL* 5.7 0.6 - - - +
93B ASP* 4.7 10.5 + - - -
148B TRP* 4.2 19.1 - - + +
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Residues in contact with TYR 70 (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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82A GLU* 3.4 43.7 - - + +
83A MET* 3.5 30.8 - - + +
86A CYS* 3.8 18.8 - - + -
4B TYR* 4.8 8.5 + + - -
54B LEU* 5.5 0.4 - - + -
56B VAL* 4.8 11.1 - - + +
61B LEU* 4.1 19.5 - - + -
66B ALA 3.0 18.3 + - - +
67B ILE 3.5 4.3 - - - +
69B ARG* 1.3 78.8 - - - +
71B LEU* 1.3 83.7 + - + +
73B LYS* 3.4 22.8 + - - +
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Residues in contact with LEU 71 (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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4B TYR* 4.1 22.4 - - + +
18B ILE* 4.0 19.1 - - + -
21B ILE* 3.8 22.9 - - + -
22B PHE* 3.7 40.2 - - + -
25B LEU* 3.5 18.8 - - + +
27B ILE* 5.2 6.0 - - + +
54B LEU* 4.2 2.5 - - + -
67B ILE* 3.0 28.0 + - + +
68B ALA* 3.8 3.1 - - - +
69B ARG 3.3 0.2 - - - -
70B TYR* 1.3 92.9 - - + +
72B THR* 1.3 61.0 + - - +
73B LYS 3.6 1.6 + - - +
75B THR* 3.8 6.1 - - - +
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Residues in contact with THR 72 (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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21B ILE* 3.6 33.7 - - + -
25B LEU* 4.9 0.7 - - - -
68B ALA 3.0 18.5 + - - +
69B ARG* 3.2 8.8 + - - +
71B LEU* 1.3 74.7 - - - +
73B LYS* 1.3 63.1 + - - +
74B ASN 3.4 0.3 + - - -
75B THR* 2.6 31.7 + - - -
77B LEU* 3.9 18.8 - - + -
78B ALA* 3.5 13.9 - - - +
148B TRP* 3.6 30.0 + - + -
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Residues in contact with LYS 73 (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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69A ARG* 6.2 0.6 - - - +
73A LYS* 5.0 16.4 - - - +
82A GLU* 3.7 30.1 + - + -
85A GLN* 3.0 37.6 + - - +
86A CYS 5.6 0.2 - - - +
89A ASP* 5.2 2.8 + - - -
69B ARG* 3.1 31.2 + - + +
70B TYR* 3.5 20.5 - - - +
71B LEU 3.3 3.7 - - - +
72B THR* 1.3 76.8 - - - +
74B ASN* 1.3 80.7 + - - +
75B THR* 3.3 6.8 + - - +
78B ALA* 4.9 4.0 - - - -
85B GLN* 6.0 4.0 - - - +
189C ASN* 6.2 1.1 - - - +
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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