Contacts of the helix formed by residues 49 - 61 (chain G) in PDB entry 2H61
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 GLU 49 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33G LYS* 6.4 0.7 - - - -
46G GLU 5.8 0.2 - - - +
47G ILE* 3.7 6.3 - - - +
48G LYS* 1.3 91.5 + - + +
50G GLN* 1.3 65.8 + - - +
51G GLU* 4.2 7.9 - - + +
52G VAL* 2.9 40.0 + - + +
53G VAL* 3.4 8.9 + - - -
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Residues in contact with GLN 50 (chain G).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29G LYS* 4.3 9.3 - - - +
48G LYS 4.4 0.6 + - - -
49G GLU* 1.3 71.2 - - - +
51G GLU* 1.3 65.5 + - - +
53G VAL* 3.4 20.0 + - - +
54G ASP* 2.8 60.1 + - - +
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Residues in contact with GLU 51 (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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49G GLU* 3.1 7.6 + - + +
50G GLN* 1.3 80.2 - - - +
52G VAL* 1.3 59.2 + - + +
54G ASP* 3.3 12.4 + - + +
55G LYS* 3.0 29.3 + - - +
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Residues in contact with VAL 52 (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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47G ILE* 3.8 30.3 - - + -
48G LYS 5.9 0.4 - - - +
49G GLU* 2.9 39.2 + - + +
51G GLU* 1.3 77.4 - - + +
53G VAL* 1.3 64.0 + - - +
55G LYS* 3.4 6.3 + - - +
56G VAL* 3.1 29.3 + - + +
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Residues in contact with VAL 53 (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 LYS* 3.6 42.8 - - + +
32G LEU* 5.0 4.3 - - + +
33G LYS* 3.8 26.2 - - + +
47G ILE* 3.4 31.0 - - + -
49G GLU 3.9 5.2 - - - +
50G GLN* 3.5 22.2 - - - +
52G VAL* 1.3 73.9 - - - +
54G ASP* 1.3 66.7 + - - +
56G VAL* 3.0 6.9 + - - +
57G MET* 3.0 23.0 + - + +
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Residues in contact with ASP 54 (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 LYS* 2.7 37.4 + - - +
50G GLN* 2.8 48.5 + - - +
51G GLU* 3.6 13.3 - - + +
53G VAL* 1.3 77.6 - - - +
55G LYS* 1.3 56.9 + - - +
57G MET* 3.5 2.1 + - - +
58G GLU* 2.9 31.4 + - - +
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Residues in contact with LYS 55 (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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51G GLU 3.0 17.6 + - - +
52G VAL* 3.6 7.6 - - - +
54G ASP* 1.3 74.4 - - - +
56G VAL* 1.3 67.1 + - + +
58G GLU* 3.2 28.5 + - + +
59G THR* 3.0 33.5 + - - +
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Residues in contact with VAL 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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32G LEU* 3.9 19.1 - - + -
36G ILE* 4.2 9.0 - - + -
47G ILE* 4.5 14.8 - - + -
52G VAL* 3.1 24.1 + - + +
53G VAL* 3.0 8.9 + - - +
55G LYS* 1.3 76.3 - - + +
57G MET* 1.3 64.5 + - - +
59G THR* 3.1 11.1 + - - -
60G LEU* 3.0 33.3 + - + +
76G PHE* 4.1 19.5 - - + -
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Residues in contact with MET 57 (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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27G LEU 3.2 26.2 - - - +
28G LYS 3.8 1.6 - - - +
29G LYS* 3.7 42.6 - - + +
32G LEU* 4.1 18.3 - - + +
53G VAL 3.0 15.4 + - - +
54G ASP 3.8 3.6 - - - +
56G VAL* 1.3 73.9 - - - +
58G GLU* 1.3 66.6 + - - +
60G LEU* 3.0 3.5 + - - +
61G ASP* 2.9 33.2 + - + +
66G GLY* 3.6 25.1 - - - +
67G GLU* 3.5 24.2 - - - +
68G CYS* 3.6 10.1 - - + +
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Residues in contact with GLU 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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54G ASP 2.9 16.8 + - - +
55G LYS* 3.2 44.0 + - + +
57G MET* 1.3 77.5 - - - +
59G THR* 1.3 64.2 + - - +
60G LEU 3.4 0.2 + - - -
61G ASP* 3.7 14.9 + - - +
62G ASN* 5.4 0.3 - - - +
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Residues in contact with THR 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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55G LYS* 3.0 20.1 + - - +
56G VAL* 3.1 14.3 + - - +
58G GLU* 1.3 82.9 - - - +
60G LEU* 1.3 70.4 + - + +
62G ASN* 4.1 11.4 + - - +
79G MET* 6.0 6.5 - - + -
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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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32G LEU* 4.3 13.2 - - + -
56G VAL* 3.0 29.6 + - + +
57G MET* 3.0 5.8 + - - +
59G THR* 1.3 87.9 - - + +
61G ASP* 1.3 60.9 + - - +
62G ASN* 3.2 15.9 + - - +
68G CYS* 3.9 28.5 - - + -
72G GLU* 3.5 28.7 - - - +
75G ALA* 4.9 3.8 - - + -
76G PHE* 3.6 51.8 - - + +
79G MET* 6.2 0.9 - - + -
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Residues in contact with ASP 61 (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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57G MET* 2.9 24.9 + - + +
58G GLU* 3.7 11.3 + - - +
59G THR 3.5 1.2 - - - -
60G LEU* 1.3 74.9 - - - +
62G ASN* 1.3 60.9 + - - +
63G ASP* 2.9 8.0 - - - +
64G GLY* 3.3 17.4 + - - -
65G ASP* 3.3 0.5 - - - +
66G GLY* 2.8 29.0 + - - -
67G GLU 3.5 12.1 - - - +
72G GLU* 3.7 4.7 - - - -
814G CA 2.3 29.3 - - - -
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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