Contacts of the helix formed by residues 63 - 75 (chain B) in PDB entry 2QQ6
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 ASP 63 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B ASP* 3.2 18.6 + - - +
62B ARG* 1.3 77.7 - - - +
64B VAL* 1.3 64.1 + - - +
65B GLU 3.5 1.6 - - - -
66B ARG* 3.4 43.8 + - + +
67B LEU* 3.2 26.8 + - - +
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Residues in contact with VAL 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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61B PRO 4.6 4.5 - - - +
62B ARG 3.0 8.5 + - - +
63B ASP* 1.3 71.4 - - - +
65B GLU* 1.3 69.2 + - + +
67B LEU* 2.8 29.0 + - - +
68B TYR* 3.1 10.9 + - - +
93B GLU* 4.1 12.5 - - + +
96B LEU* 3.9 26.1 - - + +
97B TRP* 3.1 73.8 - - + +
100B ALA* 5.6 0.4 - - + -
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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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63B ASP 3.5 0.6 - - - -
64B VAL* 1.3 85.5 - - + +
66B ARG* 1.3 62.6 + - - +
67B LEU 3.3 0.7 + - - -
68B TYR* 3.3 11.0 + - + +
69B GLU* 3.3 30.7 + - + +
93B GLU* 6.1 0.7 - - - -
97B TRP* 5.1 5.8 - - + -
297B ALA* 4.5 24.8 - - + +
301B ARG* 4.5 20.6 + - - +
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Residues in contact with ARG 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TRP* 3.7 40.0 - - + +
59B GLU* 3.2 32.1 + - - -
60B ASP* 4.2 13.1 + - - +
63B ASP* 3.4 44.0 + - + +
64B VAL 3.2 0.8 - - - -
65B GLU* 1.3 79.5 - - - +
67B LEU* 1.3 67.0 + - - +
69B GLU* 3.7 6.1 + - - +
70B LYS* 3.1 28.6 + - - +
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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
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6B ILE* 4.3 10.8 - - + -
55B GLN 5.4 0.9 - - - +
56B LEU* 4.8 6.7 - - + -
59B GLU* 3.7 34.5 - - + +
60B ASP 4.0 14.8 - - - +
61B PRO* 4.0 15.3 - - + -
63B ASP 3.2 18.4 - - - +
64B VAL* 2.8 9.7 + - - +
66B ARG* 1.3 89.0 - - - +
68B TYR* 1.3 64.1 + - - +
70B LYS* 3.3 14.2 + - + +
71B MSE 3.1 32.7 + - + +
96B LEU* 4.2 24.9 - - + -
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Residues in contact with TYR 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 VAL 3.1 10.3 + - - +
65B GLU* 3.7 13.9 - - + +
67B LEU* 1.3 74.8 - - - +
69B GLU* 1.3 69.5 + - + +
71B MSE 3.2 10.4 + - + +
72B ARG* 2.6 65.9 + - + +
86B ILE* 3.8 12.2 - - + +
89B LEU* 3.6 34.3 - - + -
93B GLU* 4.7 22.0 - - + +
270B THR* 4.3 0.9 - - - +
271B ARG* 4.4 1.3 - - - -
293B CYS 4.3 0.9 + - - -
294B GLY* 3.2 40.5 - - - -
297B ALA* 6.1 1.8 - - + -
298B GLU* 3.6 29.6 + - + -
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Residues in contact with GLU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A TRP* 4.2 11.6 - - + -
65B GLU* 3.3 20.1 + - + +
66B ARG* 3.9 6.3 - - - +
68B TYR* 1.3 84.4 - - + +
70B LYS* 1.3 61.1 + - - +
72B ARG* 2.6 39.1 + - - -
73B ARG* 2.9 71.8 + - - +
271B ARG* 2.8 18.4 + - - -
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Residues in contact with LYS 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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181A PHE* 5.7 4.9 - - + -
182A TRP* 4.1 19.9 - - + -
55B GLN* 2.8 54.6 + - + +
59B GLU* 3.4 24.5 + - - +
66B ARG* 3.1 19.5 + - - +
67B LEU* 3.3 19.5 - - + +
68B TYR 3.1 0.4 - - - -
69B GLU* 1.3 77.9 - - - +
71B MSE 1.3 62.5 + - + +
73B ARG* 3.8 1.3 - - - +
74B TRP* 2.8 31.8 + - + +
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Residues in contact with MSE 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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52B MSE 3.7 18.2 - - - +
55B GLN* 4.9 8.7 - - + -
56B LEU* 4.4 15.9 - - + -
67B LEU* 3.1 29.4 + - + +
68B TYR* 3.8 12.8 - - + +
70B LYS* 1.3 82.3 - - + +
72B ARG* 1.3 63.1 + - - +
74B TRP* 2.9 15.7 + - - +
75B ASN* 2.6 26.1 + - - +
89B LEU* 3.3 35.2 - - + +
92B ILE* 4.1 33.4 - - + -
93B GLU* 5.2 3.1 - - + +
96B LEU* 4.3 12.6 - - + -
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Residues in contact with ARG 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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246A GLU* 4.1 18.9 + - - -
68B TYR* 2.6 56.4 + - + +
69B GLU* 2.6 42.4 + - - -
71B MSE 1.3 71.7 - - - +
73B ARG* 1.3 77.1 + - - +
75B ASN* 3.0 19.9 + - - +
76B ILE* 3.7 4.9 + - - +
80B GLY* 4.6 9.2 + - - +
86B ILE* 4.1 17.7 - - + -
89B LEU* 3.8 8.6 - - + +
270B THR* 4.9 9.2 - - - +
271B ARG* 2.6 24.7 - - - +
272B PHE* 3.9 20.5 - - - -
298B GLU* 5.2 0.2 - - - -
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Residues in contact with ARG 73 (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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134A ALA* 4.7 5.7 - - - +
136A HIS* 5.8 0.3 + - - -
181A PHE* 4.3 12.7 + - + -
182A TRP* 2.8 59.0 + - + +
218A ARG* 5.4 2.4 + - - -
69B GLU* 2.9 56.7 + - - +
70B LYS* 4.2 1.8 - - - +
72B ARG* 1.3 87.1 - - - +
74B TRP* 1.3 64.7 + - - +
75B ASN 3.1 1.0 + - - -
76B ILE* 3.1 28.6 + - + +
271B ARG* 5.4 2.0 - - - +
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Residues in contact with TRP 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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132A ASP* 3.3 36.1 - - + -
133A ALA* 3.4 31.9 - - + +
134A ALA* 3.7 32.8 + - + +
136A HIS* 4.7 4.7 - + - -
51B ASN* 5.1 3.2 + - - -
52B MSE 3.5 30.0 - - + +
55B GLN* 3.6 43.2 - - + +
70B LYS* 2.8 24.6 + - + +
71B MSE 2.9 12.7 + - - +
73B ARG* 1.3 77.8 - - - +
75B ASN* 1.3 59.5 + - - +
76B ILE 3.6 0.9 + - - -
77B PHE 5.2 0.3 + - - -
78B THR* 4.3 3.4 + - - +
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Residues in contact with ASN 75 (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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40A ALA* 4.9 5.7 - - - +
48B ILE* 5.9 1.2 - - - +
52B MSE 3.7 31.5 - - - +
71B MSE 2.6 29.1 + - - +
72B ARG* 3.6 10.6 - - - +
73B ARG 3.0 1.2 - - - -
74B TRP* 1.3 81.5 - - - +
76B ILE* 1.3 66.3 + - - +
77B PHE 3.2 2.5 - - - -
78B THR* 2.8 36.8 + - - +
80B GLY* 3.1 26.1 + - - +
85B VAL* 3.8 22.5 - - + +
89B LEU* 4.5 2.8 - - - +
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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