Contacts of the helix formed by residues 91 - 105 (chain B) in PDB entry 1P22
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 ILE 91 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B GLN* 4.1 13.0 - - + +
24B SER* 3.6 34.3 - - - +
52B VAL* 4.8 6.7 - - + -
55B TRP* 3.8 29.6 - - + -
56B CYS* 4.0 21.1 - - - -
86B ALA* 3.0 19.9 + - - +
89B LEU* 3.5 17.9 - - + +
90B ASP* 1.3 72.4 + - - +
92B LYS* 1.3 66.0 + - - +
93B GLY 3.3 1.3 - - - +
94B LEU* 3.0 26.3 + - + +
95B LEU* 3.0 12.9 + - - +
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Residues in contact with LYS 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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23B GLN 5.1 0.8 + - - -
25B VAL* 5.2 8.5 - - + -
90B ASP* 3.2 38.1 + - - +
91B ILE* 1.3 69.7 - - - +
93B GLY* 1.3 66.4 + - - +
95B LEU* 3.3 5.3 + - - +
96B ASP* 3.0 33.3 + - - +
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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
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55B TRP* 4.1 15.0 - - - -
91B ILE* 3.1 3.0 + - - +
92B LYS* 1.3 73.4 - - - +
94B LEU* 1.3 56.1 + - - +
96B ASP* 2.5 32.9 + - - -
97B VAL* 3.0 17.9 + - - -
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Residues in contact with LEU 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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52B VAL* 4.0 33.2 - - + -
55B TRP* 3.5 50.3 - - + +
56B CYS* 5.9 0.2 - - - -
71B PHE* 4.3 10.3 - - + -
72B LEU* 4.8 0.2 - - + -
82B LEU* 5.0 11.0 - - + +
85B ALA* 6.3 0.2 - - + -
86B ALA* 4.0 22.0 - - + +
91B ILE* 3.0 28.1 + - + +
93B GLY* 1.3 70.3 - - - +
95B LEU* 1.3 50.8 + - - +
97B VAL* 4.4 4.0 - - + -
98B THR* 2.6 61.3 + - + +
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Residues in contact with LEU 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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155A HIS* 6.0 1.1 - - + +
156A ILE* 3.8 28.3 - - + -
159A ASN* 5.3 8.3 - - - +
83B ILE* 3.3 32.8 - - + +
86B ALA* 3.7 12.8 - - + +
87B ASN* 4.2 16.8 - - + +
91B ILE 3.0 10.1 + - - +
92B LYS* 3.8 9.0 - - - +
93B GLY 2.8 2.6 + - - -
94B LEU* 1.3 73.4 - - - +
96B ASP* 1.3 68.8 + - - +
98B THR* 3.4 2.1 + - - +
99B CYS* 3.1 48.1 + - - -
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Residues in contact with ASP 96 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A TYR* 3.7 12.8 + - - +
92B LYS* 3.0 26.1 + - - +
93B GLY* 2.5 16.9 + - - +
95B LEU* 1.3 79.1 - - - +
97B VAL* 1.3 53.5 + - + +
99B CYS* 2.9 6.5 + - - +
100B LYS* 2.7 56.5 + - - +
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Residues in contact with VAL 97 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B TRP* 4.3 13.2 - - + +
64B ILE 6.3 0.2 - - - +
65B PRO* 4.8 16.6 - - + +
68B ASP* 3.6 24.5 - - - +
72B LEU* 3.7 13.6 - - + +
93B GLY* 3.0 17.9 + - - +
94B LEU* 4.2 7.0 - - + +
96B ASP* 1.3 75.0 - - + +
98B THR* 1.3 61.5 + - - +
100B LYS* 3.7 25.0 - - + +
101B THR* 2.8 27.7 + - - -
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Residues in contact with THR 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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72B LEU* 3.9 24.9 - - + -
79B LEU* 3.9 13.2 - - + +
82B LEU* 4.5 11.2 - - + -
83B ILE* 3.5 25.3 - - - +
86B ALA* 4.6 0.2 - - - +
94B LEU* 2.6 45.0 + - + +
95B LEU* 3.4 9.9 + - - -
97B VAL* 1.3 74.0 - - - +
99B CYS* 1.3 65.3 + - - +
101B THR* 3.7 4.4 + - - -
102B VAL* 3.3 23.0 + - - +
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Residues in contact with CYS 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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156A ILE* 3.9 22.9 - - - -
159A ASN* 5.3 5.2 - - + -
160A ILE* 3.6 33.9 - - + +
163A TYR* 4.2 16.2 - - + +
83B ILE* 4.4 4.5 - - - -
95B LEU* 3.1 32.6 + - - +
96B ASP* 2.9 4.5 + - - +
98B THR* 1.3 76.9 - - - +
100B LYS* 1.3 66.7 + - - +
101B THR 2.9 1.6 - - - -
102B VAL* 2.8 7.8 + - - +
103B ALA* 2.8 20.4 + - - +
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Residues in contact with LYS 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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163A TYR* 3.7 31.7 + - + -
64B ILE 4.5 19.7 - - - +
65B PRO* 5.8 4.0 - - + -
96B ASP* 2.7 34.4 + - - +
97B VAL* 3.7 30.6 - - + +
99B CYS* 1.3 70.5 - - - +
101B THR* 1.3 56.0 + - - +
103B ALA* 3.1 10.2 + - - +
104B ASN* 2.8 43.1 + - - +
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Residues in contact with THR 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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65B PRO* 5.6 4.5 - - - +
72B LEU* 3.5 27.0 - - + +
79B LEU* 4.3 18.4 - - + -
97B VAL 2.8 21.0 + - - -
98B THR* 3.8 8.5 - - - -
99B CYS 2.8 2.4 + - - -
100B LYS* 1.3 74.8 - - - +
102B VAL* 1.3 64.1 + - - -
103B ALA 3.2 0.2 + - - -
104B ASN* 3.3 13.9 + - + +
105B MET* 3.1 33.2 + - + +
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Residues in contact with VAL 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A PHE* 3.5 48.0 - - + -
145A ILE* 5.3 0.9 - - + -
160A ILE* 4.1 19.5 - - + -
79B LEU* 4.1 6.3 - - + -
83B ILE* 3.7 21.5 - - + -
98B THR 3.3 17.3 - - - +
99B CYS 2.8 8.4 + - - +
101B THR* 1.3 72.2 - - - +
103B ALA* 1.3 62.7 + - - +
105B MET* 3.2 14.3 + - - +
106B ILE* 3.1 26.6 + - + +
118B PHE* 4.2 9.9 - - + -
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Residues in contact with ALA 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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160A ILE* 3.8 17.6 - - - +
163A TYR* 3.8 31.6 - - + -
164A LEU* 4.1 10.8 - - + +
99B CYS 2.8 11.1 + - - +
100B LYS* 3.2 10.3 - - - +
102B VAL* 1.3 72.3 - - - +
104B ASN* 1.3 54.9 + - - +
105B MET 2.8 4.6 + - - -
106B ILE* 2.7 28.2 + - - +
107B LYS* 3.0 14.8 + - - +
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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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65B PRO* 5.6 7.1 - - - +
69B GLN* 5.0 12.1 - - - +
100B LYS* 2.8 29.4 + - - +
101B THR* 3.5 14.1 + - + +
103B ALA* 1.3 71.9 - - - +
105B MET* 1.3 59.7 + - + +
106B ILE 3.4 0.6 + - - -
107B LYS* 4.0 21.3 - - - +
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Residues in contact with MET 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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144A PHE* 4.7 0.7 - - + -
76B GLN* 3.2 27.4 - - - +
79B LEU* 4.4 15.7 - - - -
101B THR* 3.1 21.9 + - + +
102B VAL* 3.5 16.2 - - - +
103B ALA 2.8 3.8 + - - -
104B ASN* 1.3 77.2 - - + +
106B ILE* 1.3 59.4 + - - +
107B LYS 4.4 2.1 - - - +
114B ILE* 5.1 2.4 - - - +
117B THR* 4.0 27.6 + - + +
118B PHE* 3.3 32.0 - - + -
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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