Contacts of the helix formed by residues 55 - 65 (chain E) in PDB entry 5DPW
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 THR 55 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E GLU 4.3 6.5 - - - +
54E LEU* 1.3 77.9 - - - +
56E MET* 1.3 64.1 + - - +
57E THR* 3.5 7.6 + - - -
58E GLN* 2.9 37.9 + - - +
59E PHE* 3.0 23.5 + - - +
87E MET 3.7 11.0 - - - -
88E SER* 3.8 17.5 - - - +
89E ALA 3.5 7.2 - - - -
90E THR* 4.8 4.7 - - + -
91E MET* 4.8 2.2 - - - -
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Residues in contact with MET 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E THR* 1.3 73.0 - - - +
57E THR* 1.3 52.9 + - - +
59E PHE* 3.4 5.8 + - - +
60E LEU* 2.8 36.0 + - - +
77E LEU* 4.0 33.6 - - + +
79E VAL* 4.4 4.7 - - + -
85E VAL* 3.7 23.6 - - + -
86E SER 3.8 16.2 - - - +
87E MET* 3.4 27.4 + - + +
89E ALA 3.2 11.6 + - - +
91E MET* 4.2 7.6 - - - +
94E ILE* 3.8 18.4 - - + -
107E MET* 3.5 35.4 - - + -
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Residues in contact with THR 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72A THR* 5.1 16.2 + - + +
74A ALA* 6.1 0.3 - - - +
55E THR* 3.7 8.5 - - - +
56E MET* 1.3 78.6 - - - +
58E GLN* 1.3 63.9 + - + +
60E LEU* 3.1 8.1 + - - +
61E SER* 2.8 29.3 + - - -
87E MET* 3.3 29.8 + - - +
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Residues in contact with GLN 58 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53E GLU 4.5 0.9 - - - +
54E LEU* 3.5 30.6 - - + +
55E THR* 2.9 40.9 + - - +
57E THR* 1.3 79.9 - - + +
59E PHE* 1.3 58.4 + - - +
61E SER* 3.3 10.2 + - - -
62E ILE* 2.8 31.6 + - + +
11F TYR* 4.0 21.8 + - - +
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Residues in contact with PHE 59 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29E VAL* 4.0 7.0 - - + -
31E VAL* 4.0 17.7 - - + -
48E PHE* 4.0 23.3 - + + -
50E VAL* 3.4 37.9 - - + -
54E LEU* 3.9 8.5 - - + +
55E THR 3.0 16.8 + - - +
56E MET* 3.6 5.6 - - - +
58E GLN* 1.3 75.5 - - - +
60E LEU* 1.3 59.5 + - - +
62E ILE* 3.1 13.7 + - + +
63E ILE* 2.8 57.2 + - + +
77E LEU* 4.7 2.7 - - + -
91E MET* 4.1 15.9 - - + -
107E MET* 3.7 35.7 - - + -
9F VAL* 4.8 3.6 - - + -
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Residues in contact with LEU 60 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56E MET 2.8 20.1 + - - +
57E THR* 3.1 6.5 + - - +
59E PHE* 1.3 71.1 - - - +
61E SER* 1.3 59.2 + - - +
63E ILE* 3.1 5.3 + - - +
64E ARG* 2.8 34.0 + - + +
74E ALA* 6.4 1.1 - - + -
75E PHE* 4.2 40.2 - - + +
76E TYR* 4.9 0.4 - - - -
77E LEU* 3.3 43.7 - - + +
87E MET* 4.2 16.8 - - + -
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Residues in contact with SER 61 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57E THR* 2.8 13.7 + - - -
58E GLN* 3.3 13.5 - - - -
60E LEU* 1.3 77.8 - - - +
62E ILE* 1.3 53.2 + - - +
64E ARG* 3.1 9.6 + - - +
65E SER* 2.8 43.5 + - - -
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Residues in contact with ILE 62 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E PHE* 4.9 8.5 - - + -
54E LEU* 3.7 22.9 - - + -
58E GLN* 2.8 11.8 + - + +
59E PHE* 3.3 17.7 - - + +
61E SER* 1.3 76.7 - - - +
63E ILE* 1.3 64.2 + - - +
65E SER* 3.4 15.9 + - - -
66E ARG* 3.5 16.7 + - + +
7F VAL* 5.9 1.6 - - + -
9F VAL* 3.3 46.7 - - + -
11F TYR* 5.1 12.3 - - + +
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Residues in contact with ILE 63 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E VAL* 4.4 16.4 - - + -
43E LEU* 4.4 18.9 - - + +
48E PHE* 5.0 8.1 - - + -
59E PHE* 2.8 59.4 + - + +
60E LEU* 3.1 6.0 + - - +
62E ILE* 1.3 74.8 - - - +
64E ARG* 1.3 62.7 + - - +
66E ARG* 3.0 24.4 + - - +
67E MET* 3.8 13.3 + - + +
75E PHE* 4.0 20.6 - - + -
77E LEU* 3.8 29.4 - - + -
109E TYR* 5.1 1.3 - - + -
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Residues in contact with ARG 64 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60E LEU* 2.8 24.9 + - + +
61E SER* 3.6 8.3 - - - +
63E ILE* 1.3 74.6 - - - +
65E SER* 1.3 57.5 + - - +
66E ARG 3.1 0.2 - - - -
67E MET* 2.9 29.7 + - - +
69E LEU* 3.2 32.3 - - + +
71E ALA* 2.8 50.9 + - - +
73E GLU 2.9 25.9 + - - +
74E ALA* 3.2 17.9 - - - +
75E PHE* 4.2 18.7 - - + -
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Residues in contact with SER 65 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61E SER* 2.8 26.7 + - - -
62E ILE* 3.6 10.7 - - - -
63E ILE 3.2 0.2 - - - -
64E ARG* 1.3 76.4 - - - +
66E ARG* 1.3 58.6 + - - +
67E MET 3.2 4.6 + - - +
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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