Contacts of the helix formed by residues 64 - 74 (chain B) in PDB entry 1QAG
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 ARG 64 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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62B ASP* 3.0 33.7 + - + +
63B GLY* 1.3 73.7 - - - +
65B LYS* 1.3 59.8 + - + +
67B LEU* 2.7 32.5 + - - +
68B ASP* 3.0 11.4 + - - +
80B LYS* 3.9 45.0 - - + +
81B GLU 3.3 22.0 + - - -
82B ARG* 3.7 26.5 + - - +
83B GLY 4.8 3.2 + - - -
84B SER* 6.2 0.2 - - - +
92B ASN* 4.3 5.5 - - - +
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Residues in contact with LYS 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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45B PHE* 3.7 16.7 - - + -
50B LYS* 5.0 2.8 - - - +
51B PRO* 3.3 41.2 + - - +
52B PRO 4.6 3.6 - - - -
53B ILE* 3.7 26.7 - - + -
59B ASP* 3.7 18.2 - - + +
60B LEU* 3.7 21.1 + - + -
62B ASP* 4.3 2.0 + - - +
64B ARG* 1.3 80.6 - - + +
66B LEU* 1.3 63.7 + - - +
68B ASP* 2.9 24.7 + - - +
69B LEU* 2.9 22.0 + - - +
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Residues in contact with LEU 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B ILE* 5.2 1.3 - - + -
60B LEU* 3.5 49.3 + - + +
63B GLY* 3.4 7.9 + - - +
64B ARG 3.3 1.0 - - - -
65B LYS* 1.3 78.2 - - - +
67B LEU* 1.3 62.3 + - - +
69B LEU* 3.6 13.3 - - + +
70B LEU* 3.1 33.2 + - - +
93B VAL* 5.5 1.3 - - + -
96B VAL* 3.8 23.1 - - + -
115B ILE* 4.3 9.9 - - + -
126B LEU* 3.8 28.3 - - + -
127B LEU* 5.3 2.2 - - + -
130B ILE* 3.7 30.1 - - + -
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Residues in contact with LEU 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B GLY 3.0 12.5 + - - +
64B ARG 2.7 12.7 + - - +
66B LEU* 1.3 75.4 - - - +
68B ASP* 1.3 62.9 + - - +
70B LEU* 3.5 4.1 + - + +
71B GLU* 3.0 27.8 + - - +
78B LEU* 4.0 28.9 - - + +
79B PRO 3.5 21.3 - - - +
80B LYS* 4.0 19.3 - - + -
92B ASN* 3.6 30.7 - - + +
95B ARG* 4.0 22.7 - - + +
96B VAL* 3.9 20.6 - - + +
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Residues in contact with ASP 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B PHE* 4.1 10.5 - - + -
50B LYS* 3.4 22.8 + - + +
64B ARG* 3.0 11.6 + - - +
65B LYS* 2.9 31.3 + - - +
67B LEU* 1.3 72.7 - - - +
69B LEU* 1.3 69.2 + - - +
71B GLU* 2.6 32.4 + - - +
72B GLY 2.9 11.4 + - - -
80B LYS* 3.2 26.8 + - - -
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Residues in contact with LEU 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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40B TRP* 4.0 11.7 - - + -
41B ILE* 3.4 39.3 - - + -
44B ARG* 4.1 16.2 - - + -
45B PHE* 3.7 16.0 - - + -
50B LYS* 5.1 1.1 - - - +
65B LYS 2.9 11.7 + - - +
66B LEU* 3.6 15.5 - - + +
68B ASP* 1.3 76.0 - - - +
70B LEU* 1.3 56.7 - - + +
72B GLY* 3.7 1.0 + - - -
73B LEU* 2.9 51.8 + - + +
127B LEU* 4.4 5.4 - - + -
130B ILE* 3.6 34.5 - - + -
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Residues in contact with LEU 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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66B LEU* 3.1 22.0 + - + +
67B LEU* 3.8 6.5 - - + +
68B ASP 2.8 1.6 + - - -
69B LEU* 1.3 75.2 - - + +
71B GLU* 1.3 55.9 + - - +
73B LEU* 3.7 5.3 - - + +
74B THR* 2.4 42.6 + - + +
78B LEU* 4.2 10.3 - - + -
96B VAL* 3.5 42.0 - - + +
99B VAL* 4.5 14.4 - - + -
100B LEU* 3.5 26.9 - - + -
130B ILE* 4.9 14.6 - - + -
134B TRP* 4.0 21.1 - - + -
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Residues in contact with GLU 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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50B LYS* 4.6 4.9 + - - +
67B LEU* 3.0 9.9 + - - +
68B ASP* 2.6 32.6 + - - +
70B LEU* 1.3 69.7 - - - +
72B GLY* 1.3 56.1 + - - +
74B THR* 2.9 5.1 + - - -
75B GLY* 2.5 37.0 + - - -
76B THR 2.7 23.4 + - - +
77B SER* 3.4 12.1 + - - -
78B LEU* 2.9 45.4 + - + +
80B LYS* 5.6 2.8 - - - -
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Residues in contact with GLY 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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48B SER* 5.9 3.8 - - - -
50B LYS* 3.5 18.0 - - - +
68B ASP 2.9 7.2 + - - -
69B LEU 4.1 0.9 - - - -
71B GLU* 1.3 80.5 - - - +
73B LEU* 1.3 61.9 + - - +
74B THR 3.2 0.7 + - - -
75B GLY* 3.5 8.8 + - - -
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Residues in contact with LEU 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40B TRP* 4.6 14.8 - - + -
44B ARG* 5.1 10.8 - - + +
69B LEU* 2.9 50.9 + - + +
70B LEU* 3.7 9.0 - - + +
71B GLU 3.2 0.2 - - - -
72B GLY* 1.3 76.2 - - - +
74B THR* 1.3 59.0 + - - +
130B ILE* 3.6 21.8 - - + -
134B TRP* 3.3 58.1 + - + +
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Residues in contact with THR 74 (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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70B LEU* 2.4 31.0 + - + +
71B GLU* 3.2 4.7 + - - -
73B LEU* 1.3 76.7 - - - +
75B GLY* 1.3 64.6 + - - +
76B THR* 3.2 25.1 + - - -
78B LEU* 5.1 2.9 - - - +
99B VAL* 5.3 6.9 - - + +
103B ASN* 4.6 8.7 - - - +
134B TRP* 3.6 35.0 - - + +
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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