Contacts of the helix formed by residues 55 - 65 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G GLU 4.3 6.7 - - - +
54G LEU* 1.3 77.3 - - - +
56G MET* 1.3 58.9 + - - +
57G THR* 3.6 7.0 + - - -
58G GLN* 2.7 44.3 + - - +
59G PHE* 2.9 29.3 + - - +
87G MET 3.9 10.1 - - - +
88G SER* 4.1 16.4 - - - +
89G ALA 3.4 8.7 - - - +
90G THR* 4.8 4.5 - - + -
91G MET* 4.9 1.3 - - - -
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Residues in contact with MET 56 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55G THR* 1.3 72.8 - - - +
57G THR* 1.3 57.6 + - - +
59G PHE* 3.7 4.6 - - - +
60G LEU* 2.8 31.5 + - - +
77G LEU* 3.7 37.7 - - + +
79G VAL* 4.3 7.0 - - + -
85G VAL* 3.6 31.0 - - + -
86G SER 4.3 2.0 - - - +
87G MET* 3.5 28.2 + - + +
89G ALA 3.3 13.5 + - - +
91G MET* 4.2 7.6 - - - +
94G ILE* 4.0 20.4 - - + -
107G MET* 3.6 32.3 - - + +
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Residues in contact with THR 57 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55G THR* 3.1 8.2 + - - +
56G MET* 1.3 74.7 - - - +
58G GLN* 1.3 71.1 + - + +
60G LEU* 3.0 6.4 + - - +
61G SER* 2.9 24.2 + - - -
87G MET* 3.6 34.1 + - - +
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Residues in contact with GLN 58 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53G GLU 4.6 0.3 - - - +
54G LEU* 3.5 28.3 - - + +
55G THR* 2.7 47.3 + - - +
57G THR* 1.3 82.8 - - + +
59G PHE* 1.3 58.2 + - - +
61G SER* 3.2 8.6 + - - -
62G ILE* 2.8 38.1 + - + +
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Residues in contact with PHE 59 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29G VAL* 3.9 7.4 - - + -
31G VAL* 3.7 20.9 - - + -
48G PHE* 4.0 20.4 - + + -
50G VAL* 3.5 33.9 - - + -
54G LEU* 3.8 10.0 - - + +
55G THR 2.9 16.6 + - - +
56G MET* 3.7 4.5 - - - +
58G GLN* 1.3 72.3 - - - +
60G LEU* 1.3 62.1 + - - +
62G ILE* 3.0 18.7 + - + +
63G ILE* 2.8 45.8 + - + +
77G LEU* 4.3 4.5 - - + -
91G MET* 4.0 14.1 - - + -
107G MET* 3.4 41.5 - - + -
9H VAL* 4.7 1.6 - - + -
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Residues in contact with LEU 60 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56G MET 2.8 20.3 + - - +
57G THR* 3.0 6.3 + - - +
59G PHE* 1.3 71.7 - - - +
61G SER* 1.3 58.4 + - - +
63G ILE* 3.1 5.5 + - - +
64G ARG* 2.8 31.5 + - + +
75G PHE* 3.8 48.7 - - + +
76G TYR* 5.0 0.7 - - - -
77G LEU* 3.7 34.3 - - + +
87G MET* 4.0 19.7 - - + -
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Residues in contact with SER 61 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57G THR* 2.9 13.4 + - - -
58G GLN* 3.3 13.0 + - - -
60G LEU* 1.3 76.3 - - - +
62G ILE* 1.3 60.0 + - - +
64G ARG* 3.2 7.4 + - - +
65G SER* 2.8 37.8 + - - -
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Residues in contact with ILE 62 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48G PHE* 4.7 9.0 - - + -
54G LEU* 4.8 7.2 - - + -
58G GLN* 2.8 30.9 + - + +
59G PHE* 3.0 29.4 + - + +
61G SER* 1.3 79.8 + - - +
63G ILE* 1.3 65.6 + - + +
65G SER* 2.8 23.2 + - - +
66G ARG* 3.5 10.8 - - - +
7H VAL* 6.0 1.1 - - + -
9H VAL* 4.2 33.4 - - + -
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Residues in contact with ILE 63 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31G VAL* 3.8 22.0 - - + -
43G LEU* 4.2 24.9 - - + -
48G PHE* 4.8 5.6 - - + -
59G PHE* 2.8 52.5 + - + +
60G LEU* 3.4 5.4 - - - +
62G ILE* 1.3 75.5 - - + +
64G ARG* 1.3 58.7 + - - +
66G ARG* 2.9 31.4 + - - +
67G MET* 3.4 8.5 - - - +
75G PHE* 4.2 18.2 - - + -
77G LEU* 3.7 29.6 - - + -
107G MET* 5.2 0.2 - - - -
109G TYR* 4.9 3.6 - - + -
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Residues in contact with ARG 64 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60G LEU* 2.8 24.0 + - + +
61G SER* 3.8 7.6 - - - +
63G ILE* 1.3 73.0 - - - +
65G SER* 1.3 57.3 + - - +
66G ARG 3.0 0.4 - - - -
67G MET* 3.0 31.1 + - - +
69G LEU* 3.6 27.1 + - + +
70G ARG 2.9 23.8 + - - -
71G ALA* 3.5 16.6 + - - +
73G GLU 2.5 29.4 + - - -
74G ALA* 4.5 5.9 - - - +
75G PHE* 3.6 28.0 - - + -
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Residues in contact with SER 65 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61G SER* 2.8 18.4 + - - -
62G ILE* 2.8 18.9 + - - +
63G ILE 3.1 0.4 - - - -
64G ARG* 1.3 76.4 - - - +
66G ARG* 1.3 60.5 + - - +
67G MET 3.3 5.7 + - - +
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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