Contacts of the helix formed by residues 74 - 89 (chain B) in PDB entry 1QQJ
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 GLY 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B MET 3.6 0.6 + - - -
72B GLY 3.3 3.0 - - - -
73B LEU* 1.3 79.9 - - - +
75B GLN* 1.3 64.2 + - - -
76B ALA 3.4 2.7 - - - -
77B ALA 3.2 4.9 + - - -
78B TRP* 3.1 37.2 + - - +
208B PRO* 3.5 24.0 - - - -
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Residues in contact with GLN 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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74B GLY* 1.3 68.5 - - - -
76B ALA* 1.3 61.7 + - - +
78B TRP* 3.6 29.8 - - + +
79B LYS* 2.8 61.0 + - + +
222B HIS* 3.9 25.3 + - - +
223B GLU* 3.5 42.3 + - + +
267B ASP* 5.4 1.2 - - - +
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Residues in contact with ALA 76 (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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54B ALA* 3.9 12.9 - - + +
73B LEU 6.1 0.2 - - - +
74B GLY 3.4 0.4 - - - -
75B GLN* 1.3 77.3 - - - +
77B ALA* 1.3 57.1 + - - +
79B LYS* 3.5 7.6 + - - +
80B GLU* 3.0 29.6 + - - +
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Residues in contact with ALA 77 (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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54B ALA* 3.8 18.7 - - + +
55B LEU* 3.9 20.6 - - + +
70B PHE* 4.5 1.8 - - + -
73B LEU* 3.5 32.2 + - + +
74B GLY 3.2 10.5 + - - +
76B ALA* 1.3 76.7 - - - +
78B TRP* 1.3 63.1 + - + +
80B GLU* 3.3 2.1 + - - +
81B ALA* 2.9 31.2 + - - +
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Residues in contact with TRP 78 (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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19B TYR* 4.4 4.1 + - + +
70B PHE* 3.0 43.6 + + + -
71B MET 3.1 20.1 + - - -
74B GLY* 3.1 17.4 + - - +
75B GLN* 3.2 31.6 + - + +
77B ALA* 1.3 75.7 - - + +
79B LYS* 1.3 63.7 + - + +
81B ALA* 3.3 2.1 + - - +
82B ARG* 3.0 25.9 + - - +
207B GLY* 3.7 11.0 - - - -
208B PRO* 3.7 9.4 - - + -
223B GLU 3.7 18.4 - - - -
225B ILE 3.5 21.3 - - - -
226B PHE* 3.5 46.3 - + + -
265B PRO* 6.4 2.5 - - + -
267B ASP* 5.1 5.8 - - - +
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Residues in contact with LYS 79 (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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75B GLN* 2.8 51.2 + - + +
76B ALA* 3.9 6.5 - - - +
78B TRP* 1.3 73.0 - - + +
80B GLU* 1.3 57.6 + - - +
82B ARG* 3.5 4.2 + - - +
83B ALA* 2.9 30.9 + - - +
267B ASP* 3.2 38.6 + - - +
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Residues in contact with GLU 80 (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 PHE* 5.6 0.2 - - - -
52B GLY* 3.2 25.6 + - - -
53B PRO* 3.2 13.3 - - - +
54B ALA* 2.7 30.3 + - + +
55B LEU* 2.9 33.8 + - + +
76B ALA 3.0 17.7 + - - +
77B ALA 3.7 3.6 - - - +
79B LYS* 1.3 75.4 - - - +
81B ALA* 1.3 59.2 + - - +
83B ALA* 3.3 6.3 + - + +
84B SER* 2.9 39.9 + - - +
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Residues in contact with ALA 81 (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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19B TYR* 4.0 5.8 - - + +
50B PHE* 3.8 12.1 - - + -
55B LEU* 3.6 19.0 - - + +
62B PHE* 4.4 4.0 - - + -
70B PHE* 3.8 23.3 - - + -
77B ALA 2.9 16.7 + - - +
78B TRP 3.7 4.3 - - - +
80B GLU* 1.3 78.8 - - - +
82B ARG* 1.3 57.4 + - - +
84B SER* 3.3 2.4 + - - -
85B LEU* 2.8 37.7 + - + +
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Residues in contact with ARG 82 (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 ILE 4.7 0.6 + - - -
15B GLN* 2.9 31.5 + - - +
16B ASN 2.8 22.4 + - - -
17B LEU* 4.0 13.1 + - + +
19B TYR* 4.0 11.3 + - - +
78B TRP 3.0 16.8 + - - +
79B LYS* 3.7 6.1 - - - +
81B ALA* 1.3 77.6 - - - +
83B ALA* 1.3 56.6 + - - +
85B LEU* 3.3 6.3 + - - +
86B GLN* 2.9 59.9 + - + +
265B PRO* 3.7 17.1 - - - +
267B ASP* 3.7 31.3 + - - +
268B ALA* 3.5 18.2 - - - +
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Residues in contact with ALA 83 (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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79B LYS 2.9 17.6 + - - +
80B GLU* 3.7 7.2 - - + +
82B ARG* 1.3 76.2 - - - +
84B SER* 1.3 63.3 + - - +
86B GLN* 3.4 16.4 + - - +
87B ASN* 3.0 23.7 + - - +
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Residues in contact with SER 84 (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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49B LEU 4.8 5.8 + - - -
50B PHE* 3.7 27.5 - - - -
51B THR 5.4 1.2 + - - -
80B GLU* 2.9 28.0 + - - +
81B ALA 3.6 3.8 - - - -
83B ALA* 1.3 76.4 - - - +
85B LEU* 1.3 56.5 + - - +
87B ASN* 3.3 6.5 + - - +
88B LEU* 2.8 41.2 + - - +
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Residues in contact with LEU 85 (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 LEU* 4.2 15.5 - - + -
19B TYR* 3.9 24.0 - - + +
34B VAL* 3.9 25.4 - - + -
41B LEU* 3.8 30.1 - - + -
43B LEU* 3.8 16.8 - - + -
46B ILE* 4.2 5.2 - - + -
50B PHE* 4.0 16.8 - - + -
81B ALA* 2.8 21.4 + - + +
82B ARG* 3.7 5.2 - - - +
84B SER* 1.3 73.7 - - - +
86B GLN* 1.3 60.2 + - - +
88B LEU* 4.4 3.6 - - + +
89B LEU* 2.9 40.8 + - + +
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Residues in contact with GLN 86 (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 ILE* 3.8 24.3 - - + +
15B GLN* 6.0 0.5 - - - -
17B LEU* 3.9 17.2 - - + +
82B ARG* 2.9 47.7 + - + +
83B ALA* 3.4 18.0 + - - +
85B LEU* 1.3 74.6 - - - +
87B ASN* 1.3 62.3 + - - +
90B SER* 3.2 22.9 + - - -
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Residues in contact with ASN 87 (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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83B ALA 3.0 13.6 + - - +
84B SER* 3.5 10.0 - - - +
86B GLN* 1.3 76.3 - - - +
88B LEU* 1.3 73.1 + - - +
90B SER* 3.1 13.4 + - - -
93B GLN* 3.2 55.3 + - - +
95B ARG* 6.1 0.5 - - - +
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Residues in contact with LEU 88 (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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3B PHE* 3.3 18.2 - - - -
41B LEU* 5.8 0.4 - - + -
46B ILE* 4.2 18.6 - - + -
49B LEU* 4.0 46.9 - - + +
50B PHE* 5.2 2.7 - - + -
84B SER* 2.8 32.3 + - - +
85B LEU* 3.9 7.4 - - + +
87B ASN* 1.3 82.8 - - - +
89B LEU* 1.3 61.2 + - + +
90B SER 3.7 1.2 + - - +
93B GLN* 5.0 5.4 - - - +
95B ARG* 4.1 25.1 - - + -
96B LEU* 3.7 25.6 + - + +
97B ARG 4.7 0.3 + - - -
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Residues in contact with LEU 89 (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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2B SER* 2.7 37.3 + - - +
3B PHE* 3.2 14.3 + - + -
4B ILE* 4.6 0.9 - - + -
14B ILE* 3.9 11.9 - - + -
17B LEU* 3.6 31.6 - - + -
34B VAL* 5.0 2.5 - - + -
36B ILE* 4.3 16.4 - - + -
41B LEU* 4.1 25.8 - - + -
85B LEU* 2.9 24.1 + - + +
88B LEU* 1.3 75.3 - - + +
90B SER* 1.3 66.5 + - - +
96B LEU* 4.5 2.0 - - + -
107B PHE* 3.8 32.5 - - + -
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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