Contacts of the helix formed by residues 44 - 55 (chain B) in PDB entry 2PY2
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 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11B PHE* 5.1 1.9 - - - -
42B ILE* 3.7 0.5 - - - +
43B HIS* 1.3 80.0 - - - +
45B LEU* 1.3 59.3 + - - +
46B GLU* 3.5 18.0 + - - +
47B GLU* 3.0 23.7 + - - +
48B SER* 2.9 28.2 + - - -
85B TYR* 3.6 18.8 - - - -
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Residues in contact with LEU 45 (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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44B SER* 1.3 72.8 - - - +
46B GLU* 1.3 70.3 + - - +
48B SER* 3.2 6.7 + - - +
49B THR* 2.9 43.5 + - - +
85B TYR* 3.6 26.0 - - + +
87B ASP* 6.4 0.4 - - - -
53F GLU* 3.8 14.8 - - + +
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Residues in contact with GLU 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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11B PHE* 4.0 12.1 - - + -
12B ASN* 5.8 0.2 - - - +
44B SER* 3.7 17.4 - - - +
45B LEU* 1.3 94.3 + - - +
47B GLU* 1.3 62.1 + - - +
49B THR* 3.4 3.1 + - - -
50B PHE* 3.1 22.3 + - - +
9F LYS* 5.5 15.4 - - + +
10F MET 5.8 0.2 - - - +
50F PHE* 3.5 36.6 - - + -
53F GLU* 3.9 26.9 - - + +
54F LEU* 5.5 4.9 - - + +
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Residues in contact with GLU 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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11B PHE* 3.5 31.3 - - + -
12B ASN* 5.8 0.7 - - - +
14B ARG* 2.5 32.3 + - - -
16B PHE* 3.4 15.9 - - + -
41B SER 4.1 3.8 - - - +
42B ILE* 4.2 6.5 - - + -
43B HIS* 2.7 40.7 + - - +
44B SER* 3.0 21.4 + - - +
46B GLU* 1.3 74.0 - - - +
48B SER* 1.3 65.3 + - - +
50B PHE* 3.2 2.5 + - - +
51B VAL* 2.9 33.0 + - + +
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Residues in contact with SER 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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42B ILE* 3.7 13.8 - - - +
44B SER 2.9 17.5 + - - -
45B LEU* 3.5 10.5 - - - +
47B GLU* 1.3 77.3 - - - +
49B THR* 1.3 56.0 + - - +
51B VAL* 2.8 28.8 - - - +
52B LYS* 3.0 30.5 + - - +
85B TYR* 3.8 16.9 + - - -
87B ASP* 4.2 9.8 + - - +
104B MET* 5.2 1.4 - - - +
112B TRP* 5.1 4.6 + - - -
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Residues in contact with THR 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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45B LEU* 2.9 20.4 + - - +
46B GLU 3.7 3.8 - - - -
48B SER* 1.3 74.1 + - - +
50B PHE* 1.3 65.1 + - - +
52B LYS* 3.4 11.0 + - + +
53B GLU* 3.2 25.7 + - + +
49F THR* 3.5 32.5 - - + -
53F GLU* 2.7 28.7 + - - +
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Residues in contact with PHE 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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9B LYS* 3.9 21.5 - - + -
10B MET 3.3 26.9 - - - -
11B PHE* 3.5 40.8 - + + -
16B PHE* 3.8 22.4 - + - -
46B GLU 3.1 13.4 + - - +
47B GLU 3.2 7.8 + - - +
49B THR* 1.3 76.9 - - - +
51B VAL* 1.3 71.5 + - + +
53B GLU* 3.2 31.0 + - - +
54B LEU* 3.6 18.4 + - + +
11F PHE* 4.6 6.5 - + + -
12F ASN* 5.4 0.2 - - - -
46F GLU* 4.1 26.2 - - + -
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Residues in contact with VAL 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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16B PHE* 4.0 32.1 - - + -
40B ALA* 5.5 0.4 - - + -
42B ILE* 3.9 17.5 - - + -
47B GLU* 2.9 24.1 + - + +
48B SER* 2.8 30.5 - - - +
50B PHE* 1.3 79.9 - - + +
52B LYS* 1.3 61.3 + - - +
54B LEU* 2.8 31.9 + - + +
55B THR* 3.5 9.3 + - - +
104B MET* 3.8 20.6 - - + -
124B ILE* 4.6 15.4 - - + +
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Residues in contact with LYS 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 SER* 3.0 34.5 + - - +
49B THR* 3.7 9.9 - - + +
50B PHE 3.3 0.2 - - - -
51B VAL* 1.3 77.2 - - - +
53B GLU* 1.3 62.5 + - + +
55B THR* 2.7 25.9 + - - -
56B SER 3.7 3.1 - - - +
59B LEU* 3.5 26.4 - - + +
87B ASP* 4.2 9.4 + - - -
104B MET* 3.6 19.5 - - + -
105B ASN* 3.5 17.3 - - - +
109B GLY 4.6 2.2 + - - -
110B LYS* 3.0 35.4 + - - +
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Residues in contact with GLU 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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49B THR* 3.3 19.5 - - + +
50B PHE* 3.2 20.2 + - - +
51B VAL 3.1 0.6 - - - -
52B LYS* 1.3 78.3 - - + +
54B LEU* 1.3 64.1 + - + +
55B THR 3.4 0.3 + - - -
56B SER* 3.5 12.6 + - - -
45F LEU* 3.9 8.1 - - + +
46F GLU* 3.6 44.1 - - + +
49F THR* 3.0 34.3 + - + +
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Residues in contact with LEU 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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9B LYS* 3.6 32.1 - - + -
16B PHE* 3.5 38.8 - - + -
17B LEU* 4.4 8.1 - - - +
18B PHE* 3.4 29.7 - - + +
50B PHE* 3.8 21.5 - - + +
51B VAL* 2.8 19.5 + - - +
53B GLU* 1.3 81.3 - - + +
55B THR* 1.3 56.5 + - + +
56B SER 3.2 4.1 + - - -
124B ILE* 4.8 8.1 - - + -
46F GLU* 6.3 1.8 - - + -
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Residues in contact with THR 55 (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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18B PHE* 3.8 18.8 - - + -
51B VAL 3.7 9.0 - - - +
52B LYS* 2.7 19.8 + - - -
54B LEU* 1.3 77.6 - - - +
56B SER* 1.3 71.3 + - - +
59B LEU* 3.4 6.9 - - - -
60B ILE* 3.3 25.5 + - - +
62B SER* 4.0 5.2 - - - +
104B MET* 4.9 2.7 - - + -
105B ASN* 3.0 27.2 + - - +
124B ILE* 3.6 31.0 - - + -
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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