Contacts of the helix formed by residues 45 - 57 (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 ASN 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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135A SER* 3.9 24.9 - - - +
8B SER* 4.0 1.1 - - - -
9B SER* 3.3 17.2 + - - -
10B ASP* 3.3 10.1 - - - +
43B ASN 4.0 2.0 + - - -
44B VAL* 1.3 77.4 - - - +
46B ALA* 1.3 74.8 + - - +
47B ALA* 3.2 9.2 + - - +
48B ILE* 3.6 26.9 - - + +
49B LEU* 2.9 26.9 + - - +
81B GLU* 5.6 7.2 - - - +
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Residues in contact with ALA 46 (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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8B SER* 3.8 22.3 - - - +
10B ASP* 3.1 22.9 + - + +
12B GLU* 3.3 30.5 - - + +
14B PHE* 3.3 13.8 - - + -
45B ASN* 1.3 73.2 + - - +
47B ALA* 1.3 67.5 + - - +
49B LEU 3.1 1.0 + - - -
50B LYS* 3.1 18.0 + - - +
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Residues in contact with ALA 47 (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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135A SER* 2.9 45.4 - - - +
45B ASN* 3.2 7.0 + - - +
46B ALA* 1.3 79.3 - - - +
48B ILE* 1.3 59.8 + - - +
50B LYS* 3.3 22.5 - - - +
51B LYS* 3.5 6.8 + - - +
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Residues in contact with ILE 48 (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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135A SER* 4.0 20.0 - - - +
44B VAL* 4.1 18.4 - - + -
45B ASN* 3.6 22.5 + - + +
46B ALA 3.3 0.4 - - - -
47B ALA* 1.3 74.5 - - - +
49B LEU* 1.3 70.8 + - - +
51B LYS* 3.2 11.3 + - + +
52B VAL* 2.9 28.6 + - + +
78B THR* 4.1 7.2 - - - +
81B GLU* 3.6 46.4 - - + +
82B LEU* 3.9 16.4 - - + +
85B ALA* 4.2 13.2 - - + -
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Residues in contact with LEU 49 (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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6B LEU* 3.2 33.0 - - + +
8B SER* 4.4 10.8 - - - +
14B PHE* 3.3 28.7 - - + -
41B LEU* 3.8 22.4 - - + -
44B VAL* 3.9 18.4 - - + -
45B ASN 2.9 21.1 + - - +
46B ALA* 3.1 6.8 + - - +
48B ILE* 1.3 70.6 - - - +
50B LYS* 1.3 66.9 + - - +
52B VAL* 2.8 28.4 + - + +
53B ILE* 3.0 30.7 + - + +
89B LEU* 4.8 2.2 - - + -
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Residues in contact with LYS 50 (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 PHE* 3.8 24.2 - - + -
46B ALA 3.1 8.9 + - - +
47B ALA* 3.3 15.0 - - - +
49B LEU* 1.3 79.4 - - - +
51B LYS* 1.3 73.2 + - + +
53B ILE* 3.0 5.7 + - - +
54B GLN* 2.8 43.3 + - + +
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Residues in contact with LYS 51 (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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135A SER* 5.8 5.4 - - - -
47B ALA 3.5 7.0 + - - +
48B ILE* 3.2 12.5 + - + +
50B LYS* 1.3 96.4 - - + +
52B VAL* 1.3 59.4 + - - +
54B GLN* 3.2 30.5 - - - +
55B TRP 3.6 4.7 + - - -
71B PHE* 2.7 61.6 - - + +
74B VAL* 5.5 8.1 - - + -
82B LEU* 4.2 17.9 - - + -
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Residues in contact with VAL 52 (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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48B ILE* 2.9 33.2 - - + +
49B LEU* 2.8 18.1 + - + +
51B LYS* 1.3 70.1 - - - +
53B ILE* 1.3 55.8 + - + +
54B GLN 3.2 1.1 - - - -
55B TRP* 3.0 7.8 + - - +
56B CYS* 2.7 47.4 + - - +
82B LEU* 4.8 6.5 - - + -
85B ALA* 5.2 3.8 - - + -
89B LEU* 4.1 27.8 - - + -
91B ILE* 4.8 4.9 - - + -
94B LEU* 4.0 22.9 - - + -
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Residues in contact with ILE 53 (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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6B LEU* 3.7 25.6 - - + -
14B PHE* 4.5 9.4 - - + -
15B GLU 5.6 0.4 - - - +
16B VAL* 3.7 27.1 - - + -
20B ILE* 4.5 7.0 - - + -
49B LEU* 3.0 45.3 + - + +
50B LYS* 3.6 6.1 - - - +
52B VAL* 1.3 71.7 - - + +
54B GLN* 1.3 57.7 + - - +
55B TRP 3.0 4.9 - - - -
56B CYS* 4.3 5.8 - - + +
57B THR* 2.9 47.4 + - + +
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Residues in contact with GLN 54 (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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50B LYS* 2.8 26.0 + - + +
51B LYS* 3.2 38.6 - - - +
52B VAL 3.2 0.2 - - - -
53B ILE* 1.3 75.0 - - - +
55B TRP* 1.3 56.7 + - - +
57B THR* 4.0 13.9 + - - +
58B HIS* 4.6 0.7 - - - +
67B TRP* 3.2 39.3 - - - -
71B PHE* 3.8 12.5 - - - -
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Residues in contact with TRP 55 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23B GLN* 3.8 13.9 - - - -
51B LYS 3.6 11.2 - - - +
52B VAL* 3.2 11.6 - - - +
53B ILE 3.0 0.4 - - - -
54B GLN* 1.3 79.8 - - - +
56B CYS* 1.3 76.2 + - - +
57B THR 3.2 1.8 - - - -
58B HIS* 3.3 7.2 + - - -
59B HIS* 2.9 58.9 + + + -
67B TRP* 4.4 7.9 - + - -
68B ASP* 3.0 23.4 + - - -
71B PHE* 3.4 30.7 - + + -
91B ILE* 3.8 19.1 - - + -
93B GLY* 4.1 10.1 - - - -
94B LEU* 3.5 48.6 - - + +
97B VAL* 4.3 6.9 - - + +
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Residues in contact with CYS 56 (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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20B ILE* 3.5 29.3 - - + +
21B ALA* 5.5 2.2 - - - -
23B GLN* 3.4 39.0 + - - +
52B VAL* 2.7 28.1 + - - +
53B ILE* 4.3 5.4 - - - +
55B TRP* 1.3 85.3 - - - +
57B THR* 1.3 63.7 + - - +
59B HIS 4.0 3.6 + - - +
91B ILE* 4.0 26.7 - - - -
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Residues in contact with THR 57 (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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20B ILE* 4.4 26.9 - - + +
53B ILE* 2.9 35.0 + - + +
54B GLN* 4.0 12.1 + - - +
56B CYS* 1.3 76.0 - - - +
58B HIS* 1.3 60.8 + - - +
59B HIS* 2.6 23.9 + - - +
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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