Contacts of the helix formed by residues 62 - 72 (chain B) in PDB entry 2Q3G
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 62 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21B GLY* 4.5 0.7 - - - -
22B LYS* 3.8 20.4 - - + +
23B ASP* 3.4 28.0 - - + -
28B LEU* 5.7 0.2 - - - -
61B LEU* 1.3 77.7 - - - +
63B HIS* 1.3 66.7 + - - +
64B ILE* 3.5 6.1 + - - +
65B GLU* 2.9 46.7 + - - +
66B ALA* 2.9 20.1 + - - +
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Residues in contact with HIS 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 3.3 41.3 + - + +
19B GLN* 3.9 5.3 - - - -
20B GLY 2.8 31.9 + - - +
21B GLY* 4.1 1.2 - - - -
23B ASP* 2.9 10.1 + - - +
24B PHE* 3.7 25.0 - + + -
28B LEU* 4.4 3.3 - - - +
62B THR* 1.3 72.5 - - - +
64B ILE* 1.3 64.5 + - + +
66B ALA* 3.2 7.1 + - - +
67B GLN* 3.0 58.6 + - - +
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Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ASP* 5.1 1.9 + - - +
62B THR* 3.3 5.1 + - - +
63B HIS* 1.3 80.1 - - + +
65B GLU* 1.3 62.3 + - + +
67B GLN* 3.1 20.6 + - - +
68B ASN* 2.8 46.2 + - - +
71B ARG* 4.8 4.5 - - - +
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Residues in contact with GLU 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B LYS* 4.1 4.2 + - - -
60B SER 3.7 6.1 - - - +
61B LEU* 3.4 23.8 - - + +
62B THR* 2.9 49.0 + - - +
64B ILE* 1.3 77.3 - - + +
66B ALA* 1.3 57.7 + - - +
68B ASN* 3.4 13.1 + - - +
69B LYS* 3.0 27.7 + - - +
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Residues in contact with ALA 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B LEU* 4.1 6.5 - - + -
28B LEU* 3.6 37.0 - - + -
53B ILE* 3.9 7.9 - - + +
61B LEU* 4.0 16.5 - - + +
62B THR 2.9 12.7 + - - +
63B HIS 3.5 8.1 - - - +
65B GLU* 1.3 74.1 - - - +
67B GLN* 1.3 65.6 + - - +
69B LYS* 3.2 4.6 + - - +
70B ILE* 3.2 25.5 + - - +
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Residues in contact with GLN 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B ARG* 5.7 5.7 - - - +
18B LEU* 4.2 17.4 - - + +
63B HIS* 3.0 47.1 + - - +
64B ILE* 3.5 22.4 - - - +
66B ALA* 1.3 76.2 - - - +
68B ASN* 1.3 56.0 + - - +
70B ILE* 3.2 6.6 + - - +
71B ARG* 2.9 60.6 + - + +
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Residues in contact with ASN 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64B ILE* 2.8 36.4 + - - +
65B GLU* 3.6 11.1 - - - +
67B GLN* 1.3 72.1 - - - +
69B LYS* 1.3 58.2 + - - +
71B ARG* 2.8 30.6 + - - +
72B ALA* 2.8 36.5 + - + +
2960B EDO 5.6 0.2 - - - -
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Residues in contact with LYS 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53B ILE* 3.5 41.3 - - + +
54B ASP* 4.4 11.5 + - + +
56B GLU* 3.2 33.6 + - + +
61B LEU* 4.8 5.6 - - + -
65B GLU 3.0 14.5 + - - +
66B ALA* 3.2 11.9 + - - +
68B ASN* 1.3 76.6 - - - +
70B ILE* 1.3 63.2 + - - +
72B ALA 4.0 1.2 - - - -
73B CYS* 3.5 19.9 + - - +
2960B EDO 3.1 44.5 + - - +
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TRP* 3.7 30.1 + - + +
16B PHE* 3.6 24.7 - - + -
18B LEU* 3.6 26.9 - - + -
50B VAL* 6.3 0.2 - - + -
53B ILE* 3.9 25.8 - - + -
66B ALA 3.2 15.9 + - - +
67B GLN* 3.6 6.5 - - - +
68B ASN 3.2 0.4 - - - -
69B LYS* 1.3 74.4 - - - +
71B ARG* 1.3 69.7 + - + +
73B CYS* 3.0 25.3 + - - -
77B LEU* 4.0 17.0 - - + -
79B LEU* 4.9 2.2 - - + -
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Residues in contact with ARG 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TRP* 5.8 0.4 - - - +
64B ILE* 4.6 6.3 + - - +
67B GLN* 2.9 56.3 + - + +
68B ASN* 2.8 30.1 + - - +
70B ILE* 1.3 77.9 - - + +
72B ALA* 1.3 57.6 + - + +
73B CYS* 3.4 1.8 + - - -
74B GLY 5.0 1.4 + - - -
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B ASN* 2.8 19.1 + - + +
69B LYS 4.0 2.9 - - - -
71B ARG* 1.3 76.6 - - - +
73B CYS* 1.3 59.1 + - - +
74B GLY 3.4 3.8 + - - -
2960B EDO 3.7 29.5 - - - -
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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