Contacts of the helix formed by residues 71 - 90 (chain B) in PDB entry 3PSR
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 PHE 71 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A ALA* 4.2 5.8 - - + -
83A THR* 4.0 21.8 - - + -
86A HIS* 3.3 41.7 - + + +
12B MET* 5.8 1.6 - - + -
13B ILE* 4.0 29.8 - - + -
16B PHE* 3.5 32.8 - + + -
24B ASP 4.8 1.4 + - - -
70B ASP* 1.3 74.3 - - - +
72B SER* 1.3 59.7 + - - +
74B PHE* 3.2 26.1 - + - +
75B LEU* 3.0 64.9 + - + +
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Residues in contact with SER 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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70B ASP* 3.0 18.3 + - - -
71B PHE* 1.3 78.8 - - - +
73B GLU* 1.3 73.7 + - - +
75B LEU* 3.3 10.8 + - - +
76B SER* 3.1 19.2 + - - -
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Residues in contact with GLU 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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61B LYS* 3.4 28.9 - - - +
62B ASP* 3.2 4.5 - - - +
63B LYS* 3.2 17.4 + - + +
64B ASN* 2.9 15.0 + - - +
68B LYS 2.9 4.7 - - - +
69B ILE* 3.1 11.6 - - + -
70B ASP* 2.8 46.6 + - - +
72B SER* 1.3 84.6 + - - +
74B PHE* 1.3 62.9 + - - +
76B SER* 3.1 10.9 + - - -
77B LEU* 3.1 19.8 + - - +
102B CA 2.5 29.9 - - - -
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Residues in contact with PHE 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B MET* 3.7 15.7 - - + -
15B MET* 3.3 35.4 - - + -
16B PHE* 3.3 45.1 - + + -
26B ILE* 4.8 3.6 - - + -
31B LEU* 5.5 0.9 - - + -
34B MET* 3.9 17.9 - - - -
69B ILE* 3.6 10.4 - - + +
70B ASP 3.0 11.4 + - - +
71B PHE* 3.2 27.8 - + - +
73B GLU* 1.3 74.1 - - - +
75B LEU* 1.3 71.0 + - + +
77B LEU* 2.9 23.8 + - + +
78B LEU* 3.0 38.7 + - + +
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Residues in contact with LEU 75 (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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79A GLY* 3.6 22.2 - - - +
82A ALA* 4.1 10.8 - - + -
83A THR* 3.5 18.8 - - - +
12B MET* 4.7 14.1 - - + -
71B PHE* 3.0 56.8 + - + +
72B SER* 3.3 10.3 + - - +
74B PHE* 1.3 82.5 - - + +
76B SER* 1.3 57.9 + - - +
78B LEU* 3.4 7.9 + - + +
79B GLY* 2.9 24.9 + - - -
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Residues in contact with SER 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B LYS* 3.3 22.2 + - - -
72B SER 3.1 10.5 + - - -
73B GLU* 3.1 12.9 + - - -
74B PHE 3.1 0.6 - - - -
75B LEU* 1.3 77.8 - - - +
77B LEU* 1.3 63.2 + - - +
79B GLY* 2.9 11.9 + - - -
80B ASP* 3.0 16.6 + - - +
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Residues in contact with LEU 77 (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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31B LEU* 3.7 31.0 - - + -
34B MET* 4.5 5.8 - - + -
35B MET* 4.1 18.4 - - - -
53B TYR* 4.2 21.3 - - + +
57B VAL* 4.0 25.6 - - + -
61B LYS* 4.0 15.0 - - + +
69B ILE* 6.0 1.6 - - + -
73B GLU 3.1 10.6 + - - +
74B PHE* 2.9 16.4 + - + +
76B SER* 1.3 75.8 + - - +
78B LEU* 1.3 71.6 + - + +
80B ASP* 2.9 23.3 + - - +
81B ILE* 3.2 15.2 + - + +
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Residues in contact with LEU 78 (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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9A ILE* 4.0 12.3 - - + +
12B MET* 4.5 28.5 - - + -
15B MET* 4.5 5.6 - - + -
34B MET* 5.3 0.7 - - + -
39B PHE* 4.1 30.3 - - + -
74B PHE* 3.0 54.6 + - + +
75B LEU* 3.8 9.4 - - + +
77B LEU* 1.3 85.2 - - + +
79B GLY* 1.3 57.6 + - - +
81B ILE* 3.3 13.9 + - + +
82B ALA* 2.8 32.0 + - - +
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Residues in contact with GLY 79 (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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75A LEU* 4.1 19.5 - - - -
75B LEU 2.9 15.7 + - - -
76B SER* 2.9 6.2 + - - -
78B LEU* 1.3 76.7 - - - +
80B ASP* 1.3 56.8 + - - +
81B ILE 3.1 0.2 + - - -
82B ALA* 3.2 3.0 + - - +
83B THR* 2.7 37.3 + - - -
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Residues in contact with ASP 80 (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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42B PHE* 5.4 0.6 - - - -
53B TYR* 3.6 21.7 + - - +
61B LYS* 2.5 41.9 + - - -
76B SER* 3.0 9.3 + - - +
77B LEU* 2.9 9.5 + - - +
79B GLY* 1.3 75.7 - - - +
81B ILE* 1.3 63.6 + - - +
83B THR* 3.6 8.2 + - - +
84B ASP* 3.0 20.8 + - - +
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Residues in contact with ILE 81 (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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9A ILE* 3.6 16.4 - - + -
35B MET* 4.4 15.7 - - + -
39B PHE* 3.8 44.4 - - + -
42B PHE* 4.5 22.0 - - + -
53B TYR* 4.8 2.0 - - - +
77B LEU* 3.2 16.5 + - + +
78B LEU* 3.6 17.0 - - + +
79B GLY 3.1 0.8 - - - -
80B ASP* 1.3 75.6 - - - +
82B ALA* 1.3 59.5 + - - +
84B ASP* 2.7 27.4 + - - +
85B TYR* 2.9 34.4 + - + -
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Residues in contact with ALA 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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9A ILE* 3.8 25.3 - - + +
12A MET* 6.3 3.1 - - + -
13A ILE* 3.5 9.0 - - + +
71A PHE* 3.8 7.4 - - + -
75A LEU* 3.9 25.1 - - + -
78B LEU 2.8 21.0 + - - +
79B GLY* 3.6 4.0 - - - +
81B ILE* 1.3 72.2 - - - +
83B THR* 1.3 58.2 + - - +
85B TYR 3.2 0.7 + - - -
86B HIS* 2.8 27.4 + - - +
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Residues in contact with THR 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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71A PHE* 3.8 13.2 - - + -
72A SER* 6.0 0.2 - - - -
75A LEU* 3.4 17.3 - - - +
79B GLY 2.7 23.7 + - - -
80B ASP* 3.6 8.1 - - - +
82B ALA* 1.3 74.1 - - - +
84B ASP* 1.3 65.8 + - - +
86B HIS* 3.3 7.2 + - - +
87B LYS* 3.2 35.6 + - + +
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Residues in contact with ASP 84 (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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42B PHE* 4.0 23.1 - - + -
80B ASP 3.0 13.0 + - - +
81B ILE 2.7 15.7 + - - +
83B THR* 1.3 73.0 - - - +
85B TYR* 1.3 62.6 + - + +
87B LYS* 3.2 10.6 + - - +
88B GLN* 2.5 51.0 + - - +
93B ALA 4.9 0.4 - - - +
94B PRO* 3.7 1.1 - - - -
95B CYS* 2.8 32.6 + - - -
96B SER* 3.3 14.2 + - - -
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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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2A ASN* 4.3 8.7 + - - -
6A GLU* 3.7 29.2 + - + +
9A ILE* 4.3 10.1 - - + -
10A ILE* 3.8 33.7 - - + -
13A ILE* 3.3 21.6 - - + +
39B PHE* 5.3 0.4 - + - -
41B ASN* 4.8 1.4 - - - +
42B PHE* 3.7 29.1 + + + +
81B ILE* 2.9 43.5 + - + -
82B ALA 3.7 2.5 - - - +
84B ASP* 1.3 81.7 - - + +
86B HIS* 1.3 64.8 + - - +
88B GLN* 3.2 27.2 + - + +
89B SER* 3.2 17.5 + - - -
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Residues in contact with HIS 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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13A ILE* 3.1 12.0 - - + +
16A PHE* 4.1 4.9 - + - -
17A HIS* 3.9 8.5 - + - -
24A ASP* 2.9 14.5 + - - -
71A PHE* 3.8 47.8 - + + +
103A ZN 2.4 31.0 - - - -
82B ALA 2.8 14.5 + - - +
83B THR* 3.6 8.7 - - + +
84B ASP 3.1 0.2 - - - -
85B TYR* 1.3 77.2 - - - +
87B LYS* 1.3 70.7 + - - +
89B SER* 2.3 31.2 + - - -
90B HIS* 3.3 11.0 + + - -
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Residues in contact with LYS 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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83B THR* 3.2 30.5 - - + +
84B ASP* 3.2 8.5 + - - +
86B HIS* 1.3 84.8 - - - +
88B GLN* 1.3 57.8 + - - +
90B HIS* 2.7 30.7 + - - +
91B GLY 3.4 2.8 + - - -
92B ALA* 3.6 20.8 + - + +
93B ALA 6.0 0.4 - - - +
96B SER* 5.8 9.6 - - - +
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Residues in contact with GLN 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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42B PHE* 5.5 1.0 - - - -
84B ASP* 2.5 38.9 + - - +
85B TYR* 3.5 35.8 - - + +
86B HIS 3.2 0.2 - - - -
87B LYS* 1.3 76.2 - - - +
89B SER* 1.3 54.4 + - - +
90B HIS 3.0 0.2 - - - -
91B GLY* 2.8 26.9 + - - +
92B ALA* 3.3 20.4 - - - +
93B ALA 4.0 2.5 - - - +
94B PRO* 3.2 40.3 - - + +
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Residues in contact with SER 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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13A ILE* 4.3 9.0 - - - -
17A HIS* 3.2 23.0 - - - -
85B TYR 3.2 7.7 + - - -
86B HIS* 2.3 24.2 + - - -
88B GLN* 1.3 78.1 - - - +
90B HIS* 1.3 69.8 + - - +
91B GLY 3.3 1.2 + - - -
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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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17A HIS* 3.4 3.5 + + - -
24A ASP* 3.0 20.7 + - + -
103A ZN 2.2 35.1 - - - -
86B HIS* 3.4 15.0 - + - -
87B LYS* 2.7 15.5 + - - +
89B SER* 1.3 103.5 - - - +
91B GLY* 1.3 56.2 + - - +
92B ALA* 3.6 3.4 + - - +
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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