Contacts of the helix formed by residues 46 - 56 (chain A) in PDB entry 2P18
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 TYR 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A VAL* 3.4 28.9 - - + -
43A ASN 3.6 12.1 - - - +
44A ALA 3.3 12.5 + - - -
45A ASP* 1.3 73.6 - - - +
47A LYS* 1.3 83.2 + - + +
48A PRO* 3.2 4.5 - - - -
49A ILE* 3.0 29.9 + - + +
50A LEU* 3.7 10.5 + - + +
84A GLY* 4.3 8.1 - - - -
87A LYS* 3.6 42.5 - - + +
88A LEU* 4.0 22.8 - - + +
91A GLU* 2.8 40.2 + - + +
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Residues in contact with LYS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA 6.1 0.4 - - - +
45A ASP* 3.5 1.5 - - - +
46A TYR* 1.3 97.4 - - + +
48A PRO* 1.4 62.1 - - + +
50A LEU* 3.0 15.6 + - + +
51A THR* 2.8 32.4 + - - +
91A GLU* 4.9 11.7 - - - -
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Residues in contact with PRO 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 3.7 21.1 - - + +
19A PRO* 4.3 10.5 - - + +
20A THR* 4.6 0.4 - - + -
45A ASP* 3.4 36.1 - - - +
46A TYR 3.2 4.9 - - - -
47A LYS* 1.4 91.7 - - + +
49A ILE* 1.3 59.6 + - - +
51A THR* 3.8 10.4 - - - +
52A TYR* 3.1 22.9 + - - +
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Residues in contact with ILE 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A VAL* 4.1 23.3 - - + -
20A THR* 5.1 1.6 - - + -
26A SER* 3.9 21.3 - - - +
27A TYR 4.9 2.9 - - - +
28A LEU* 4.0 32.5 - - + -
39A ALA* 4.3 7.6 - - + -
42A VAL* 3.8 34.5 - - + -
46A TYR* 3.0 17.9 + - + +
48A PRO* 1.3 74.3 - - - +
50A LEU* 1.3 65.5 + - + +
52A TYR* 3.2 5.2 + - - +
53A ILE* 3.1 32.1 + - + +
69A PHE* 4.5 11.0 - - + -
88A LEU* 4.8 4.3 - - + -
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Residues in contact with LEU 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A TYR* 3.7 19.5 + - + +
47A LYS* 3.0 15.8 + - + +
49A ILE* 1.3 77.3 - - + +
51A THR* 1.3 64.0 + - - +
53A ILE* 3.2 20.4 + - + +
54A GLU* 3.1 24.7 + - - +
69A PHE* 4.7 2.2 - - + -
88A LEU* 4.1 22.0 - - + -
91A GLU* 3.4 29.6 - - - +
92A LEU* 4.6 11.2 - - + -
95A MET* 4.7 12.8 - - + -
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Residues in contact with THR 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A LYS* 2.8 25.3 + - - +
48A PRO* 3.8 9.7 - - - +
50A LEU* 1.3 72.0 - - - +
52A TYR* 1.3 57.8 + - - +
54A GLU* 3.2 4.1 + - - +
55A GLU* 2.9 34.5 + - + +
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Residues in contact with TYR 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 4.4 20.6 - + + -
6A THR* 3.6 12.6 + - - +
16A THR* 3.3 43.0 + - + -
18A VAL* 5.0 5.4 - - + -
28A LEU* 3.7 23.8 - - + -
48A PRO 3.1 14.2 + - - +
49A ILE* 3.5 9.4 - - - +
50A LEU 3.2 0.2 - - - -
51A THR* 1.3 77.9 - - - +
53A ILE* 1.3 54.1 + - - +
55A GLU* 5.1 0.2 - - - -
56A HIS* 2.6 72.7 + + + +
57A LEU* 3.5 27.5 - - + +
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Residues in contact with ILE 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 3.8 22.9 - - + -
37A LEU* 4.0 16.2 - - + -
49A ILE* 3.1 18.8 + - + +
50A LEU* 3.2 15.2 + - + +
52A TYR* 1.3 77.5 - - - +
54A GLU* 1.3 59.0 + - + +
57A LEU* 3.2 43.3 + - + +
67A TYR* 5.8 2.9 - - + -
69A PHE* 3.6 36.8 - - + -
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Residues in contact with GLU 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A LEU 3.1 15.5 + - - +
51A THR* 4.1 3.6 - - - +
53A ILE* 1.3 78.4 - - + +
55A GLU* 1.5 69.0 - - - +
57A LEU 4.9 3.1 + - - -
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Residues in contact with GLU 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A THR* 2.9 22.6 + - + +
54A GLU* 1.5 74.7 - - - +
56A HIS* 1.4 85.2 + - + +
57A LEU 5.0 0.7 - - - -
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Residues in contact with HIS 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 3.3 39.4 + + - -
52A TYR* 2.6 65.7 + + + +
54A GLU 3.8 0.2 - - - -
55A GLU* 1.4 89.7 - - + +
57A LEU* 1.3 64.9 + - + +
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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