Contacts of the helix formed by residues 81 - 97 (chain B) in PDB entry 2AFW
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 SER 81 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B GLU* 4.8 3.4 - - - -
77B ARG* 3.5 2.3 - - - -
78B TYR* 2.7 60.0 + - - -
79B PRO 3.2 1.4 + - - -
80B GLY* 1.3 82.2 - - - +
82B PRO* 1.4 76.7 - - - +
83B GLY* 3.4 4.0 + - - -
84B SER* 3.0 27.4 + - - -
85B TYR* 3.5 5.5 + - - +
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Residues in contact with PRO 82 (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 TYR* 5.7 0.9 - - - +
80B GLY 4.6 0.9 - - - +
81B SER* 1.4 87.8 - - - +
83B GLY* 1.3 55.6 + - - +
85B TYR* 3.2 10.1 + - + +
86B ALA* 2.9 28.0 + - - +
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Residues in contact with GLY 83 (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 ILE* 3.7 14.8 - - - +
76B GLU 3.2 21.0 + - - -
77B ARG* 3.6 8.0 - - - +
81B SER* 3.1 3.4 + - - -
82B PRO* 1.3 75.3 - - - +
84B SER* 1.3 61.9 + - - +
86B ALA* 3.7 3.2 - - - +
87B ALA* 2.9 31.4 + - - +
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Residues in contact with SER 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77B ARG* 3.7 13.8 - - - +
78B TYR 3.4 20.4 - - - -
80B GLY* 4.1 7.7 + - - -
81B SER* 3.0 18.6 + - - -
83B GLY* 1.3 77.9 - - - +
85B TYR* 1.3 63.1 + - - +
87B ALA* 3.7 3.6 - - - +
88B ARG* 3.0 40.5 + - - +
141B TYR* 3.7 12.6 + - - -
199B ASP* 4.1 11.4 + - - -
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Residues in contact with TYR 85 (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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81B SER 3.5 4.9 + - - +
82B PRO* 3.2 10.8 + - + +
84B SER* 1.3 78.4 + - - +
86B ALA* 1.3 59.3 + - - +
88B ARG* 3.3 34.1 + - + +
89B GLN* 2.9 74.3 + - + +
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Residues in contact with ALA 86 (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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72B PRO 6.0 0.4 - - - -
75B ILE* 4.1 15.3 - - + -
82B PRO 2.9 16.7 + - - +
83B GLY* 3.7 5.8 - - - +
85B TYR* 1.3 79.5 - - - +
87B ALA* 1.3 57.3 + - - +
89B GLN* 3.3 14.0 + - - +
90B HIS* 2.9 29.3 + - - +
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Residues in contact with ALA 87 (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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72B PRO 5.6 0.7 - - - -
73B LEU* 3.5 26.7 - - + -
75B ILE* 4.6 4.9 - - + +
77B ARG* 4.1 13.5 - - - -
83B GLY 2.9 17.0 + - - +
84B SER* 3.7 4.7 - - - +
86B ALA* 1.3 76.5 - - - +
88B ARG* 1.3 59.0 + - - +
90B HIS* 3.2 3.1 + - - +
91B ILE* 2.9 35.4 + - - +
141B TYR* 4.0 17.0 - - + -
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Residues in contact with ARG 88 (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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84B SER* 3.0 40.2 + - - +
85B TYR* 3.4 39.0 - - + +
87B ALA* 1.3 76.1 - - - +
89B GLN* 1.3 58.2 + - + +
91B ILE* 3.3 1.7 + - - +
92B MET* 2.9 47.7 + - - +
106B ILE* 4.2 12.9 - - - +
121B SER* 3.8 29.9 + - - -
123B ILE* 3.7 30.2 - - + +
141B TYR* 2.9 36.2 + - - +
199B ASP* 4.6 1.4 + - - -
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Residues in contact with GLN 89 (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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85B TYR* 2.9 66.6 + - + +
86B ALA* 3.6 10.7 - - - +
88B ARG* 1.3 77.0 - - + +
90B HIS* 1.3 57.0 + - - +
92B MET* 3.4 9.0 + - - +
93B GLN* 2.8 56.6 + - - +
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Residues in contact with HIS 90 (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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68B ASN 3.1 21.7 + - - -
69B ASP* 2.8 32.8 - - - -
72B PRO* 3.6 27.6 - - + +
73B LEU* 3.6 22.1 - - + +
86B ALA 2.9 17.0 + - - +
87B ALA* 3.2 6.9 + - - +
89B GLN* 1.3 73.6 - - - +
91B ILE* 1.3 69.9 + - - +
93B GLN* 3.3 10.4 + - + +
94B ARG* 2.9 40.5 + - + +
168B LEU* 4.0 11.7 - - + -
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Residues in contact with ILE 91 (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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73B LEU* 4.5 8.3 - - + -
87B ALA 2.9 21.6 + - - +
88B ARG 3.8 3.4 - - - +
90B HIS* 1.3 82.6 - - - +
92B MET* 1.3 64.0 + - - +
94B ARG* 3.4 1.7 + - - +
95B ILE* 3.1 31.6 + - + +
123B ILE* 3.9 21.5 - - + -
141B TYR* 3.9 23.8 - - + -
164B CYS* 4.4 5.8 - - - -
168B LEU* 4.0 20.6 - - + +
197B PHE* 3.6 53.4 - - + -
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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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88B ARG* 2.9 30.0 + - + +
89B GLN* 3.7 7.9 - - - +
91B ILE* 1.3 77.0 - - - +
93B GLN* 1.3 58.7 + - + +
95B ILE 3.3 0.9 + - - -
96B GLN* 2.9 47.6 + - - +
104B LEU* 3.8 31.8 - - + +
106B ILE* 3.5 41.3 - - + -
123B ILE* 4.5 10.3 - - + -
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Residues in contact with GLN 93 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89B GLN* 2.8 47.7 + - - +
90B HIS* 3.8 8.0 - - + +
92B MET* 1.3 75.6 - - + +
94B ARG* 1.3 62.4 + - + +
96B GLN* 3.4 13.4 + - - +
97B ARG* 3.3 25.7 + - - +
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Residues in contact with ARG 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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64B GLU 5.1 0.8 + - - -
68B ASN* 3.5 40.0 + - - +
69B ASP* 2.6 40.2 + - - +
90B HIS* 2.9 40.0 + - + +
91B ILE 4.0 3.1 - - - +
93B GLN* 1.3 77.5 - - + +
95B ILE* 1.3 59.8 + - - +
97B ARG* 3.1 59.9 + - - +
98B LEU* 3.5 12.4 - - - +
168B LEU* 4.1 12.1 - - + -
172B ARG* 4.3 16.2 - - - +
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Residues in contact with ILE 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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91B ILE* 3.1 35.1 + - + +
92B MET 3.8 2.9 - - - +
94B ARG* 1.3 76.9 - - - +
96B GLN* 1.3 65.5 + - - +
98B LEU* 3.1 26.0 + - + +
100B ALA 5.4 0.2 - - - +
102B TRP* 3.6 28.8 - - + +
104B LEU* 4.1 17.7 - - + -
125B SER* 3.4 36.1 - - - +
168B LEU* 3.8 14.4 - - + -
171B ALA* 5.2 7.0 - - + -
195B LEU* 4.5 8.7 - - + -
197B PHE* 4.0 11.2 - - + -
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Residues in contact with GLN 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* 2.9 38.7 + - - +
93B GLN* 3.4 14.7 + - - +
95B ILE* 1.3 76.0 - - - +
97B ARG* 1.3 59.5 + - - +
98B LEU 3.2 6.8 + - - +
102B TRP* 6.2 0.2 - - - -
104B LEU* 3.4 24.6 - - + +
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Residues in contact with ARG 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 GLN 3.3 14.0 + - - +
94B ARG* 3.1 60.6 + - - +
96B GLN* 1.3 76.9 - - - +
98B LEU* 1.3 79.8 + - + +
99B GLN* 5.4 1.9 - - - +
172B ARG* 4.4 10.7 - - - +
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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