Contacts of the helix formed by residues 64 - 76 (chain F) in PDB entry 2AJQ
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 TYR 64 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F ILE* 4.4 16.6 - - + -
7F ALA* 6.2 0.2 - - - -
8F ALA* 3.5 22.4 + - + +
10F ALA 3.0 19.4 + - - -
11F LEU* 4.0 8.5 - - + -
12F LEU* 3.4 37.9 - - + +
15F VAL* 4.1 4.3 - - - +
60F ASN* 3.2 30.6 + - - +
62F HIS 3.6 0.2 - - - -
63F LYS* 1.3 77.8 - - - +
65F ASP* 1.3 79.1 + - - +
66F VAL 3.4 1.6 - - - -
67F PRO* 3.0 5.0 - - - +
68F ALA* 2.8 51.6 + - + +
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Residues in contact with ASP 65 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ALA* 4.3 1.4 - - - -
6F ILE* 3.4 32.7 + - + +
58F PHE* 3.7 33.4 - - + -
59F HIS 3.7 11.1 - - - +
60F ASN* 3.4 13.7 + - - +
61F GLY* 3.7 12.6 + - - -
64F TYR* 1.3 88.7 - - - +
66F VAL* 1.3 58.4 + - - +
68F ALA* 3.6 2.7 - - - +
69F LEU* 2.8 36.1 + - - +
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Residues in contact with VAL 66 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58F PHE* 4.3 12.6 - - + -
61F GLY 3.0 24.1 + - - +
62F HIS* 4.9 0.7 - - - +
65F ASP* 1.3 71.9 - - - +
67F PRO* 1.3 72.1 - - + +
69F LEU* 3.2 9.3 + - - +
70F THR* 3.2 27.9 + - - +
81F PHE* 5.1 0.9 - - + -
83F LEU* 4.0 35.4 - - + +
88F CYS* 4.1 17.0 - - + -
222F TRP* 3.8 30.3 - - + -
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Residues in contact with PRO 67 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F LEU* 4.1 14.1 - - + +
61F GLY 3.5 1.6 - - - +
62F HIS 3.5 17.3 - - - +
63F LYS 3.4 20.4 - - - +
64F TYR 3.0 20.6 - - - +
66F VAL* 1.3 93.0 - - + +
68F ALA* 1.3 60.5 + - - +
70F THR* 3.2 9.5 + - - +
71F LYS* 3.0 23.4 + - - +
225F ALA* 6.0 0.4 - - + -
229F ARG* 3.8 31.0 - - - +
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Residues in contact with ALA 68 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ILE* 4.6 6.5 - - + -
12F LEU* 3.7 15.7 - - + +
15F VAL* 5.1 5.4 - - + -
64F TYR* 2.8 48.7 + - + +
65F ASP* 3.6 4.7 - - - +
67F PRO* 1.3 78.4 - - - +
69F LEU* 1.3 58.9 + - - +
71F LYS* 3.3 2.6 + - - +
72F LEU* 2.9 39.8 + - + +
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Residues in contact with LEU 69 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ILE* 4.0 20.2 - - + -
18F PHE* 4.7 4.0 - - + -
39F PHE* 3.9 22.0 - - + -
42F TYR* 3.9 20.9 - - + +
43F LEU* 4.3 1.3 - - + -
46F LEU* 3.6 30.1 - - + -
58F PHE* 4.1 17.7 - - + -
65F ASP 2.8 25.9 + - - +
66F VAL* 3.2 3.8 + - - +
68F ALA* 1.3 76.2 - - - +
70F THR* 1.3 57.7 + - - +
72F LEU* 4.6 3.6 - - + +
73F ALA* 3.0 31.1 + - - +
81F PHE* 3.7 23.4 - - + -
83F LEU* 4.6 3.1 - - + -
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Residues in contact with THR 70 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66F VAL* 3.2 16.8 + - - +
67F PRO* 3.5 11.7 - - - +
68F ALA 3.1 0.8 - - - -
69F LEU* 1.3 77.3 - - - +
71F LYS* 1.3 64.7 + - - +
73F ALA* 4.3 1.2 - - - +
74F LYS* 3.5 19.4 + - - +
79F ARG 4.9 1.4 - - - +
80F GLU* 5.7 0.2 - - - +
81F PHE* 2.8 32.0 + - - +
82F HIS* 3.5 28.2 + - + +
83F LEU 5.1 0.2 + - - -
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Residues in contact with LYS 71 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F LEU* 2.9 30.5 + - + +
13F GLU 3.1 17.6 + - - -
14F SER* 3.8 1.6 - - - +
15F VAL* 3.3 39.8 + - + +
67F PRO 3.0 15.4 + - - +
68F ALA* 3.8 5.2 - - - +
70F THR* 1.3 78.8 - - - +
72F LEU* 1.3 63.4 + - - +
74F LYS* 3.2 13.9 + - - +
75F LEU* 3.1 25.1 + - + +
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Residues in contact with LEU 72 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6F ILE* 5.6 3.1 - - + -
8F ALA* 4.2 6.7 - - + -
15F VAL* 3.9 29.8 - - + +
16F THR* 3.3 41.3 - - - +
17F LYS* 4.2 0.9 - - - -
18F PHE* 3.8 33.7 - - + +
39F PHE* 3.9 16.2 - - + -
68F ALA* 2.9 25.3 + - + +
69F LEU* 5.4 1.1 - - + -
71F LYS* 1.3 72.3 - - - +
73F ALA* 1.3 62.1 + - - +
74F LYS 3.0 5.4 - - - -
75F LEU* 3.0 8.7 - - + +
76F GLN* 3.0 30.7 + - - +
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Residues in contact with ALA 73 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39F PHE* 3.7 11.4 - - - -
43F LEU* 3.7 19.3 - - + -
69F LEU 3.0 23.4 + - - +
70F THR 4.3 1.3 - - - +
71F LYS 3.3 0.2 - - - -
72F LEU* 1.3 75.6 - - - +
74F LYS* 1.3 52.4 + - - +
77F LEU* 3.5 4.2 + - - +
78F ASN 3.2 6.4 + - - -
79F ARG* 2.6 40.9 + - + +
81F PHE* 3.7 23.6 - - + -
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Residues in contact with LYS 74 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70F THR 3.5 12.4 + - - +
71F LYS* 3.2 10.5 + - - +
72F LEU 3.0 0.6 - - - -
73F ALA* 1.3 81.6 - - - +
75F LEU* 1.3 60.3 + - + +
76F GLN 3.3 0.2 - - - -
78F ASN* 2.9 46.4 + - - +
79F ARG 3.6 6.1 - - - +
80F GLU* 3.3 27.4 - - - +
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Residues in contact with LEU 75 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F VAL 4.2 6.7 - - - +
16F THR* 4.0 32.1 - - + +
71F LYS* 3.1 24.2 - - + +
72F LEU* 3.0 41.7 - - + +
74F LYS* 1.3 79.6 - - + +
76F GLN* 1.3 63.2 + - + +
78F ASN* 4.6 0.4 - - - -
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Residues in contact with GLN 76 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F THR 3.5 13.3 + - - +
17F LYS* 3.2 33.1 - - - +
18F PHE* 3.3 17.7 + - - +
39F PHE* 3.3 27.0 - - - +
72F LEU* 3.0 15.7 + - - +
75F LEU* 1.3 83.5 - - + +
77F LEU* 1.3 74.5 + - + +
78F ASN* 3.4 1.7 + - - +
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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