Contacts of the helix formed by residues 54 - 63 (chain E) in PDB entry 2Q6W
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 GLY 54 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E PHE* 3.3 33.4 + - - -
38E LEU* 4.2 5.1 - - - +
49E ALA* 3.4 7.0 - - - -
51E THR 3.0 6.1 + - - -
53E LEU* 1.3 81.6 - - - +
55E ARG* 1.3 54.6 + - - +
57E VAL* 2.9 7.5 + - - +
58E ALA* 2.8 32.1 + - - +
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Residues in contact with ARG 55 (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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52B GLU* 3.7 40.5 + - + +
55B ARG* 6.0 4.3 - - - +
49E ALA* 3.2 11.7 - - + +
52E GLU* 3.2 12.1 + - - +
54E GLY* 1.3 74.4 - - - +
56E PRO* 1.3 72.9 - - + +
57E VAL 3.2 0.7 + - - -
58E ALA* 3.4 5.0 + - - +
59E GLU* 3.2 20.8 + - - +
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Residues in contact with PRO 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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76D ARG* 4.1 19.7 - - - +
52E GLU 3.6 5.6 - - - +
53E LEU 3.5 16.8 - - - +
55E ARG* 1.3 96.8 - - + +
57E VAL* 1.3 51.5 + - - +
59E GLU* 3.7 6.6 - - + +
60E SER* 2.7 31.1 + - - -
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Residues in contact with VAL 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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73D MET* 5.2 0.4 - - - -
76D ARG* 3.5 27.4 - - - +
37E PHE* 4.9 2.0 - - + -
38E LEU* 3.7 11.2 - - + -
53E LEU 3.7 15.7 - - - +
54E GLY* 2.9 9.1 + - - +
56E PRO* 1.3 74.0 - - - +
58E ALA* 1.3 68.9 + - - +
60E SER* 4.2 2.2 - - - +
61E TRP* 2.8 48.0 + - + +
33F LEU* 3.4 47.1 - - + +
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Residues in contact with ALA 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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38E LEU* 4.0 3.4 - - - +
47E TYR* 3.9 32.5 - - - +
48E ARG* 4.4 1.1 - - - -
49E ALA* 3.9 17.9 - - + +
54E GLY 2.8 14.2 + - - +
55E ARG* 3.4 11.2 - - - +
57E VAL* 1.3 74.1 - - - +
59E GLU* 1.4 54.8 + - - +
62E ASN* 2.5 40.7 + - - +
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Residues in contact with GLU 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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55E ARG 3.2 10.1 + - - +
56E PRO* 3.7 9.0 - - + +
58E ALA* 1.4 76.8 - - - +
60E SER* 1.3 66.3 + - - +
61E TRP 2.8 1.4 + - - -
62E ASN* 3.3 11.4 + - - +
63E SER* 3.4 18.4 + - - -
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Residues in contact with SER 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 PRO 2.7 22.3 + - - -
57E VAL* 3.3 2.9 + - - +
58E ALA 3.2 0.2 + - - -
59E GLU* 1.3 71.9 - - - +
61E TRP* 1.3 65.4 + - - +
63E SER* 3.6 12.5 + - - -
64E GLN* 3.6 15.5 + - - +
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Residues in contact with TRP 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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30E TYR* 3.4 27.6 - + - -
38E LEU* 3.3 23.3 - - + -
47E TYR* 3.4 43.5 - + + -
57E VAL* 2.8 23.7 + - + +
58E ALA 2.7 9.0 + - - +
60E SER* 1.3 75.7 - - - +
62E ASN* 1.3 56.9 + - - +
63E SER 2.9 11.3 + - - -
64E GLN* 3.2 37.6 + - - +
67E LEU* 4.4 5.0 - - + +
68E LEU* 4.1 7.9 - - - +
31F LEU* 3.3 29.2 - - + +
32F PRO 3.1 29.0 + - - -
33F LEU* 3.3 28.1 - - + +
34F GLY 5.4 0.2 + - - -
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Residues in contact with ASN 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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46E GLU* 3.1 29.7 - - - +
47E TYR* 2.6 51.4 - - - +
48E ARG* 5.0 0.2 - - - -
58E ALA* 2.5 26.6 + - - +
59E GLU* 3.3 5.4 + - - +
61E TRP* 1.3 69.1 - - - +
63E SER* 1.3 57.6 + - - +
64E GLN 3.7 0.2 - - - -
65E LYS* 3.0 31.4 - - - +
68E LEU* 3.3 15.3 - - + +
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Residues in contact with SER 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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59E GLU 3.4 11.7 + - - -
60E SER* 3.6 9.5 + - - -
61E TRP 2.9 0.6 - - - -
62E ASN* 1.3 77.0 - - - +
64E GLN* 1.3 60.7 + - - +
65E LYS* 3.1 18.1 + - - +
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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