Contacts of the helix formed by residues 46 - 55 (chain E) in PDB entry 2Q9Q
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 LEU 46 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E ALA 4.2 5.6 - - - +
11E GLU* 3.2 13.1 + - + +
13E GLU 2.8 19.9 + - - +
15E VAL* 3.6 29.8 - - + -
44E VAL 3.6 0.6 + - - -
45E PRO* 1.3 70.3 - - - +
47E TRP* 1.3 61.0 + - - +
49E ALA* 3.3 2.2 + - + -
50E ILE* 3.0 39.3 + - + +
95E LEU* 3.4 34.5 - - + -
98E LEU* 3.4 34.3 - - + -
99E LEU* 3.7 24.2 - - + -
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Residues in contact with TRP 47 (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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11E GLU* 3.1 51.8 + - + +
12E LYS* 4.5 3.2 - - - +
28E LEU* 4.3 14.1 - - + -
45E PRO* 3.3 24.3 - - + +
46E LEU* 1.3 76.9 - - - +
48E LEU* 1.3 81.4 + - + +
50E ILE* 4.2 5.8 - - - +
51E ASN* 3.5 18.4 + - - +
77F ILE* 4.1 14.4 - - + -
80F MET* 3.5 43.6 - - + +
81F GLU* 4.1 28.9 - - + -
84F ARG* 3.5 43.8 - - - +
145G SER 5.3 1.4 - - - +
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Residues in contact with LEU 48 (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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26E ILE* 5.9 1.1 - - + -
33E LEU* 3.9 20.9 - - + -
36E PHE* 4.5 9.4 - - + -
44E VAL* 3.8 26.0 - - + -
45E PRO* 2.9 14.5 + - + +
47E TRP* 1.3 87.8 - - + +
49E ALA* 1.3 56.0 + - - +
51E ASN* 3.0 5.6 + - - +
52E LEU* 2.8 54.8 + - + +
77F ILE* 3.7 34.1 - - + -
80F MET* 3.6 25.6 - - + -
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Residues in contact with ALA 49 (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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15E VAL* 3.4 33.0 - - + -
17E ILE* 3.7 19.3 - - + -
44E VAL* 3.8 8.4 - - + +
45E PRO 3.2 2.2 + - - +
46E LEU* 3.6 7.4 - - + +
48E LEU* 1.3 79.8 - - - +
50E ILE* 1.3 56.9 + - - +
52E LEU* 3.4 7.0 + - - +
53E LYS* 2.8 31.4 + - - +
60E LEU* 3.8 14.1 - - + +
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Residues in contact with ILE 50 (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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11E GLU* 5.9 1.6 - - - +
46E LEU* 3.0 39.8 + - + +
47E TRP* 4.2 5.8 - - - +
49E ALA* 1.3 74.8 - - - +
51E ASN* 1.3 57.9 + - - +
53E LYS* 3.4 5.0 + - - +
54E GLN* 2.9 50.7 + - - +
60E LEU* 4.2 6.7 - - + -
98E LEU* 4.1 20.0 - - + +
99E LEU* 4.2 9.6 - - + -
102E HIS* 3.5 44.6 - - + +
145G SER 5.3 6.3 - - - +
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Residues in contact with ASN 51 (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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47E TRP 3.5 12.1 + - - +
48E LEU 3.0 8.6 + - - +
50E ILE* 1.3 76.9 - - - +
52E LEU* 1.3 65.4 + - - +
54E GLN* 3.2 15.4 + - - +
55E ARG* 2.8 67.9 + - - +
73F LEU* 5.3 0.7 - - - +
77F ILE* 5.9 0.3 - - - +
80F MET* 3.7 33.9 - - + +
145G SER* 3.6 22.9 + - - +
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Residues in contact with LEU 52 (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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17E ILE* 3.6 26.9 - - + -
21E PHE* 4.3 27.8 - - + -
36E PHE* 4.6 4.3 - - + -
44E VAL* 5.1 0.2 - - + -
48E LEU* 2.8 55.4 + - + +
49E ALA* 3.7 1.3 - - - +
51E ASN* 1.3 80.1 - - - +
53E LYS* 1.3 64.9 + - - +
55E ARG* 2.9 9.5 + - - +
56E GLN 2.9 4.0 + - - -
57E LYS* 2.8 26.7 + - + -
58E CYS* 3.6 14.6 - - + -
73F LEU* 4.7 17.7 - - + -
77F ILE* 4.9 5.8 - - + -
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Residues in contact with LYS 53 (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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49E ALA 2.8 19.2 + - - +
50E ILE* 3.5 8.5 - - - +
52E LEU* 1.3 76.4 - - - +
54E GLN* 1.3 55.7 + - + +
56E GLN* 2.7 28.8 + - - +
58E CYS* 3.8 21.2 - - - +
59E ARG* 4.9 0.7 - - - +
60E LEU* 3.3 24.7 - - + -
102E HIS* 3.7 19.5 + - + +
103E ALA* 3.5 7.3 - - - +
105E ASP* 3.2 19.3 + - - -
106E ASN* 2.5 38.6 + - - +
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Residues in contact with GLN 54 (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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50E ILE* 2.9 43.3 + - + +
51E ASN* 3.2 12.5 + - - +
53E LYS* 1.3 77.7 - - + +
55E ARG* 1.3 59.6 + - + +
56E GLN* 3.1 13.3 + - - +
102E HIS* 3.8 22.2 - - + +
145G SER 3.4 28.9 + - - -
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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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51E ASN* 2.8 44.1 + - - +
52E LEU* 2.9 12.5 + - - +
54E GLN* 1.3 75.0 - - + +
56E GLN* 1.3 70.6 + - - +
57E LYS* 3.0 21.9 + - + +
73F LEU* 4.2 26.8 - - - +
76F SER* 4.3 20.8 + - - -
80F MET* 6.1 1.0 - - - -
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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