Contacts of the helix formed by residues 46 - 55 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A ALA* 4.1 8.7 - - + +
11A GLU* 3.0 16.1 + - + +
13A GLU 2.8 17.5 + - - +
15A VAL* 4.1 26.7 - - + -
44A VAL 3.6 0.4 + - - -
45A PRO* 1.3 70.9 - - - +
47A TRP* 1.3 57.7 + - - +
49A ALA* 3.2 1.9 + - + -
50A ILE* 2.9 57.8 + - + +
95A LEU* 3.6 32.1 - - + -
98A LEU* 3.6 28.7 - - + -
99A LEU* 4.2 16.2 - - + -
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Residues in contact with TRP 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU* 3.1 50.3 + - + +
12A LYS* 4.6 2.2 - - - +
28A LEU* 3.9 30.3 - - + -
45A PRO* 3.4 24.0 - - + +
46A LEU* 1.3 76.8 - - - +
48A LEU* 1.3 93.4 + - + +
50A ILE* 3.6 6.6 + - - +
51A ASN* 3.2 22.7 + - - +
77B ILE* 4.0 11.7 - - + -
80B MET* 3.8 38.2 - - + +
81B GLU* 4.1 14.8 - - + -
84B ARG* 3.3 47.0 - - - +
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Residues in contact with LEU 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE* 5.3 2.0 - - + -
33A LEU* 3.6 30.1 - - + -
36A PHE* 4.6 10.8 - - + -
44A VAL* 4.0 17.3 - - + -
45A PRO* 2.9 16.6 + - + +
47A TRP* 1.3 100.1 - - + +
49A ALA* 1.3 66.1 + - - +
51A ASN* 3.3 5.4 + - + +
52A LEU* 2.9 45.9 + - + +
77B ILE* 3.7 31.9 - - + -
80B MET* 5.8 0.2 - - - -
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Residues in contact with ALA 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A VAL* 3.5 32.1 - - + -
17A ILE* 3.6 20.9 - - + -
44A VAL* 3.8 8.8 - - + +
45A PRO 3.0 5.4 + - - +
46A LEU* 3.6 6.5 - - + +
48A LEU* 1.3 78.0 - - - +
50A ILE* 1.3 63.2 + - - +
52A LEU* 3.3 5.3 + - - +
53A LYS* 2.9 25.3 + - - +
58A CYS* 4.1 0.3 - - - -
60A LEU* 3.6 13.4 - - + +
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Residues in contact with ILE 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A GLU* 5.9 0.7 - - + -
46A LEU* 2.9 49.9 + - + +
47A TRP* 3.8 7.0 - - - +
49A ALA* 1.3 76.2 - - + +
51A ASN* 1.3 62.6 + - - +
53A LYS* 3.2 6.7 + - - +
54A GLN* 3.0 35.2 + - - +
60A LEU* 5.0 3.4 - - + -
98A LEU* 4.1 37.2 - - + +
99A LEU* 4.6 7.4 - - + -
102A HIS* 3.6 31.9 - - + +
145C SER 5.4 2.9 - - - +
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Residues in contact with ASN 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A TRP 3.2 10.6 + - - +
48A LEU* 3.6 4.9 - - - +
50A ILE* 1.3 80.1 - - - +
52A LEU* 1.3 58.9 + - - +
54A GLN* 3.3 20.7 + - - +
55A ARG* 2.7 65.7 + - - +
77B ILE* 4.6 6.1 - - - +
80B MET* 3.2 42.4 - - + +
145C SER* 4.7 8.5 - - - +
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Residues in contact with LEU 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 4.0 24.7 - - + -
21A PHE* 4.5 8.5 - - + -
36A PHE* 4.3 14.6 - - + -
44A VAL* 5.4 0.2 - - + -
48A LEU* 2.9 44.7 + - + +
49A ALA 3.8 0.7 - - - +
51A ASN* 1.3 75.7 - - - +
53A LYS* 1.3 61.2 + - - +
55A ARG* 3.2 3.7 + - - +
56A GLN 2.9 7.4 + - - -
57A LYS* 2.8 50.9 + - + -
58A CYS* 3.6 16.6 - - + -
73B LEU* 4.6 12.8 - - + -
77B ILE* 4.5 12.8 - - + -
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Residues in contact with LYS 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ALA 2.9 9.5 + - - +
50A ILE* 3.5 7.0 - - - +
52A LEU* 1.3 74.8 - - - +
54A GLN* 1.3 57.6 + - + +
56A GLN* 2.6 31.7 + - - +
58A CYS* 3.6 22.1 - - - +
60A LEU* 3.4 33.2 - - + +
102A HIS* 3.3 23.1 - - + +
103A ALA* 3.9 5.1 - - - +
105A ASP* 2.8 38.4 + - - -
106A ASN* 2.9 22.9 + - - +
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Residues in contact with GLN 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50A ILE* 3.0 24.8 + - + +
51A ASN* 3.4 18.3 + - - +
53A LYS* 1.3 77.6 - - - +
55A ARG* 1.3 59.2 + - - +
56A GLN* 3.1 13.9 + - - +
102A HIS* 3.7 34.0 - - + +
145C SER 3.7 29.8 + - - +
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Residues in contact with ARG 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51A ASN* 2.7 50.7 + - - +
52A LEU* 3.5 8.4 - - - +
54A GLN* 1.3 75.0 - - - +
56A GLN* 1.3 71.0 + - - +
57A LYS* 3.2 25.1 + - + +
73B LEU* 3.2 33.3 - - - +
76B SER* 4.1 19.5 + - - -
77B ILE* 4.6 3.4 - - - +
80B MET* 4.7 1.2 - - - -
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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