Contacts of the helix formed by residues 44 - 54 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11D PHE* 5.2 1.4 - - - -
42D ILE* 3.8 1.0 - - - +
43D HIS* 1.3 82.0 - - - +
45D LEU* 1.3 59.6 + - - +
46D GLU* 3.5 15.6 + - - +
47D GLU* 3.0 23.8 + - - +
48D SER* 2.9 28.4 + - - -
85D TYR* 3.5 17.7 - - - -
9E LYS* 6.2 1.3 - - - -
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Residues in contact with LEU 45 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44D SER* 1.3 73.2 - - - +
46D GLU* 1.3 70.3 + - - +
48D SER* 3.2 4.6 + - - +
49D THR* 2.8 45.4 + - - +
85D TYR* 3.5 26.5 - - + +
87D ASP* 6.1 1.6 - - - +
53E GLU* 3.7 15.5 - - + +
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Residues in contact with GLU 46 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 4.2 14.2 - - + -
44D SER* 3.7 11.8 - - - +
45D LEU* 1.3 94.1 + - - +
47D GLU* 1.3 57.0 + - - +
49D THR* 3.4 2.9 + - - -
50D PHE* 3.0 26.7 + - - +
9E LYS* 3.4 35.1 + - - -
10E MET 6.0 0.4 - - - +
11E PHE* 6.0 0.2 - - - -
50E PHE* 3.8 25.2 - - + -
53E GLU* 3.8 31.5 - - - +
54E LEU* 5.6 2.6 - - - +
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Residues in contact with GLU 47 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D PHE* 3.4 32.1 - - + +
12D ASN* 5.3 1.6 - - - +
14D ARG* 2.8 37.6 + - - -
16D PHE* 3.7 15.2 - - + -
41D SER 4.3 1.8 - - - +
42D ILE* 4.3 6.3 - - + -
43D HIS* 2.8 37.2 + - - +
44D SER* 3.0 20.6 + - - +
46D GLU* 1.3 74.0 - - - +
48D SER* 1.3 66.9 + - - +
50D PHE* 3.2 2.0 + - - +
51D VAL* 3.0 31.2 + - + +
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Residues in contact with SER 48 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42D ILE* 3.7 14.9 - - - +
44D SER 2.9 13.8 + - - -
45D LEU* 3.2 11.6 + - - +
47D GLU* 1.3 75.5 - - - +
49D THR* 1.3 60.9 + - - +
51D VAL* 2.8 27.4 - - - +
52D LYS* 3.0 24.8 + - - +
85D TYR* 3.8 18.2 + - - -
87D ASP* 4.2 12.8 + - - +
104D MET* 5.0 2.3 - - - +
112D TRP* 5.0 4.7 + - - -
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Residues in contact with THR 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45D LEU* 2.8 30.4 + - - +
46D GLU 3.7 3.4 - - - -
48D SER* 1.3 77.1 - - - +
50D PHE* 1.3 62.6 + - - +
52D LYS* 3.4 12.4 + - + +
53D GLU* 3.3 24.9 + - + +
49E THR* 3.3 33.9 - - + -
53E GLU* 3.0 21.9 + - + +
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Residues in contact with PHE 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LYS* 4.1 17.3 - - + -
10D MET 3.3 26.0 - - - -
11D PHE* 3.4 40.2 - + + -
16D PHE* 3.9 18.8 - + - -
46D GLU 3.0 14.1 + - - +
47D GLU 3.5 7.6 - - - +
48D SER 3.2 0.2 - - - -
49D THR* 1.3 77.1 - - - +
51D VAL* 1.3 69.4 + - + +
53D GLU* 3.2 26.4 + - - +
54D LEU* 3.6 24.2 + - + +
11E PHE* 4.3 15.3 - + + -
12E ASN* 5.0 0.7 - - - -
46E GLU* 4.1 27.1 - - + -
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Residues in contact with VAL 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16D PHE* 3.9 36.1 - - + -
40D ALA* 5.4 0.4 - - + -
42D ILE* 4.1 17.0 - - + -
47D GLU* 3.0 20.3 + - + +
48D SER* 2.8 32.1 - - - +
50D PHE* 1.3 82.6 - - + +
52D LYS* 1.3 62.9 + - - +
54D LEU* 2.9 24.6 + - + +
55D THR* 3.6 10.1 + - - +
104D MET* 3.9 19.3 - - + -
124D ILE* 4.6 14.2 - - + +
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Residues in contact with LYS 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48D SER* 3.0 32.1 + - - +
49D THR* 3.6 14.1 - - + +
50D PHE 3.2 0.4 - - - -
51D VAL* 1.3 77.5 - - - +
53D GLU* 1.3 58.4 + - + +
55D THR* 2.6 31.9 + - - -
56D SER 4.0 1.9 - - - +
59D LEU* 3.6 22.5 - - + +
87D ASP* 4.3 9.6 + - - -
104D MET* 3.6 12.1 - - + -
105D ASN* 3.4 21.8 - - - +
109D GLY 4.9 2.2 + - - -
110D LYS* 3.2 35.0 + - - +
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Residues in contact with GLU 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49D THR* 3.3 20.0 - - + +
50D PHE* 3.2 19.0 + - - +
52D LYS* 1.3 77.3 - - + +
54D LEU* 1.3 62.8 + - + +
55D THR 3.2 0.2 - - - -
56D SER* 3.8 12.7 + - - +
59D LEU* 5.5 0.7 - - - -
45E LEU* 3.4 12.5 - - + +
46E GLU* 3.3 54.1 + - + +
49E THR* 3.0 32.1 + - + +
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Residues in contact with LEU 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D LYS* 3.6 30.3 - - + -
16D PHE* 3.4 40.4 - - + +
17D LEU* 4.4 6.7 - - - +
18D PHE* 3.3 31.4 - - + +
50D PHE* 3.8 23.6 - - + +
51D VAL* 2.9 18.6 + - - +
53D GLU* 1.3 78.5 - - + +
55D THR* 1.3 58.6 + - + +
56D SER 3.3 5.7 + - - -
124D ILE* 5.0 6.5 - - + -
46E GLU* 6.1 2.9 - - + +
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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