Contacts of the helix formed by residues 77 - 90 (chain A) in PDB entry 2QB1
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 SER 77 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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47A LEU* 4.0 20.2 - - - -
48A ARG* 3.8 17.2 + - - +
50A ILE* 3.2 39.2 - - - +
74A SER* 4.1 5.8 + - - -
76A HIS* 1.3 76.2 - - - +
78A GLY* 1.3 67.5 + - - +
79A ASP 3.5 0.4 - - - -
80A VAL* 2.8 25.3 + - - +
81A LEU* 3.2 14.6 + - - -
56B GLU 6.0 0.2 - - - -
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Residues in contact with GLY 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A PHE* 3.5 32.1 - - - +
71A ARG* 4.0 2.2 - - - -
74A SER* 3.0 28.0 + - - -
75A PRO 5.1 1.1 - - - -
76A HIS 3.4 0.8 - - - -
77A SER* 1.3 77.1 - - - +
79A ASP* 1.3 61.5 + - - -
81A LEU* 3.2 7.2 + - - +
82A TYR 3.2 15.4 + - - -
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Residues in contact with ASP 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LYS* 3.7 14.5 - - - +
71A ARG* 3.1 47.9 + - + +
75A PRO 5.8 0.2 + - - -
77A SER 3.1 1.6 + - - -
78A GLY* 1.3 72.0 - - - +
80A VAL* 1.3 80.0 + - - +
82A TYR* 3.4 9.0 - - - +
83A GLU* 3.0 31.7 + - - +
65B LEU* 3.6 9.5 - - - +
69B ASP* 4.2 7.9 - - - +
72B TYR* 5.3 0.2 - - - -
73B ARG* 3.1 39.3 + - - +
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Residues in contact with VAL 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A PHE* 5.1 3.6 - - + -
47A LEU* 3.9 29.8 - - + -
76A HIS 4.7 1.1 - - - +
77A SER 2.8 17.2 + - - +
79A ASP* 1.3 85.4 + - - +
81A LEU* 1.3 61.5 + - - +
83A GLU* 3.9 2.8 - - - +
84A LEU* 2.9 30.4 + - + +
57B MET* 3.5 30.1 - - + -
61B ALA* 4.0 24.0 - - + +
64B LEU* 4.9 7.8 - - + +
65B LEU* 4.1 9.9 - - + -
73B ARG* 3.7 4.9 - - - +
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Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A TRP* 3.3 24.7 - - + -
38A LEU* 3.7 32.1 - - + -
41A ALA* 3.8 21.5 - - + -
47A LEU* 3.8 25.1 - - + -
50A ILE* 4.1 9.0 - - + -
55A PHE* 4.6 14.1 - - + -
70A PHE* 4.0 11.2 - - + -
74A SER* 4.8 5.2 - - - +
77A SER* 3.2 23.6 + - - +
78A GLY* 3.6 9.0 - - - +
80A VAL* 1.3 79.3 - - - +
82A TYR* 1.3 60.6 + - - +
84A LEU* 4.4 4.0 - - + -
85A LEU* 3.1 17.8 + - - +
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Residues in contact with TYR 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A LEU 4.1 9.8 + - - -
66A THR* 3.9 5.2 - - - -
67A LYS* 3.6 55.1 + - + +
70A PHE* 3.4 36.5 - + + -
78A GLY 3.2 12.6 + - - +
79A ASP* 3.4 11.9 - - - +
80A VAL 3.2 0.4 - - - -
81A LEU* 1.3 74.7 - - - +
83A GLU* 1.3 69.5 + - - +
85A LEU* 3.2 5.4 + - - +
86A GLN* 3.0 63.1 + - + +
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Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A LYS* 3.1 21.0 + - - +
79A ASP 3.0 17.3 + - - +
80A VAL* 3.4 5.4 + - - +
82A TYR* 1.3 85.0 - - - +
84A LEU* 1.3 60.7 + - - +
86A GLN* 3.7 12.7 - - - +
87A HIS* 2.8 31.9 + - - +
64B LEU* 3.7 32.5 - - + +
65B LEU* 4.6 1.6 - - + +
66B THR* 4.0 17.7 - - - +
69B ASP* 3.3 22.0 - - - +
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Residues in contact with LEU 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 4.4 10.5 - - + -
37A TRP* 3.5 29.4 - - + +
40A TRP* 3.9 7.9 - - + -
41A ALA* 3.6 18.8 - - + -
45A PHE* 3.5 41.3 - - + -
47A LEU* 6.2 0.2 - - + -
80A VAL* 2.9 19.3 + - + +
81A LEU* 3.7 7.2 - - + +
83A GLU* 1.3 77.2 - - - +
85A LEU* 1.3 57.3 + - - +
87A HIS* 3.3 5.8 + - + +
88A ILE* 2.9 45.9 + - + +
64B LEU* 4.0 17.4 - - + +
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Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A PRO* 3.8 36.1 - - + -
29A TRP* 4.2 11.2 - - + -
37A TRP* 4.1 6.7 - - + -
62A LEU* 4.0 27.4 - - + +
63A LEU* 4.0 22.9 - - + -
70A PHE* 3.9 25.8 - - + -
81A LEU 3.1 12.1 + - - +
82A TYR* 3.2 8.3 + - + +
84A LEU* 1.3 76.5 - - - +
86A GLN* 1.3 76.7 + - - +
88A ILE* 3.1 9.3 + - + +
89A LEU* 2.9 27.5 + - + +
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Residues in contact with GLN 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A LEU* 5.9 0.2 - - - +
82A TYR* 3.0 65.4 + - + +
83A GLU* 3.7 19.1 - - - +
85A LEU* 1.3 83.8 - - - +
87A HIS* 1.3 63.4 + - - +
89A LEU* 3.2 25.4 + - - +
90A ALA* 3.0 23.7 + - - +
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Residues in contact with HIS 87 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A SER* 5.9 0.2 + - - -
16A ILE* 4.1 40.2 + - + +
83A GLU 2.8 18.0 + - - +
84A LEU* 3.4 6.3 - - + +
86A GLN* 1.3 77.0 - - - +
88A ILE* 1.3 67.3 + - + +
90A ALA* 3.5 14.2 + - - +
91A GLN* 3.6 20.8 + - - +
64B LEU* 3.8 26.6 - - + +
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Residues in contact with ILE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A ILE* 5.9 1.6 - - + -
18A LEU* 3.7 40.6 - - + -
24A LEU 5.5 0.7 - - - +
26A PRO* 3.7 27.3 - - + +
29A TRP* 4.2 6.3 - - + -
37A TRP* 3.3 31.6 - - + +
84A LEU* 2.9 34.9 + - + +
85A LEU* 3.1 8.9 + - - +
87A HIS* 1.3 78.8 - - + +
89A LEU* 1.3 64.8 + - - +
91A GLN* 2.9 33.6 + - + +
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Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A GLN* 6.0 0.7 - - + -
26A PRO* 3.6 31.6 - - + -
27A ILE* 5.3 0.9 - - + +
63A LEU* 3.8 32.5 - - + -
85A LEU* 2.9 19.2 + - + +
86A GLN* 3.5 30.1 - - - +
88A ILE* 1.3 77.3 - - - +
90A ALA* 1.3 57.5 + - - +
91A GLN* 3.1 7.5 + - - +
92A ALA* 5.5 2.1 - - - +
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Residues in contact with ALA 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86A GLN 3.0 15.3 + - - +
87A HIS* 3.9 10.3 - - - +
88A ILE 3.2 0.8 - - - -
89A LEU* 1.3 74.3 - - - +
91A GLN* 1.3 65.6 + - - +
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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