Contacts of the helix formed by residues 71 - 91 (chain A) in PDB entry 2QE9
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 THR 71 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A THR* 5.9 6.1 - - + -
27A LEU* 6.1 0.2 - - - -
39A LEU* 3.6 6.3 - - - -
69A TYR 3.4 0.6 - - - -
70A GLN* 1.3 86.5 - - + +
72A LEU* 1.3 65.2 + - - +
73A ASN* 3.8 6.6 + - - +
74A LYS* 3.1 35.1 + - + +
75A VAL* 3.1 24.1 + - - +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.8 30.1 - - + +
19A CYS* 3.5 42.0 - - + +
20A HIS* 3.7 44.4 - - + +
27A LEU* 3.9 17.6 - - + +
39A LEU* 3.7 20.5 - - + +
42A LEU* 4.7 0.2 - - + -
71A THR* 1.3 72.6 - - - +
73A ASN* 1.3 59.6 + - - +
75A VAL* 3.3 2.6 + - - -
76A LYS* 2.8 31.5 + - + +
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Residues in contact with ASN 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20A HIS* 4.1 18.7 + - - -
71A THR* 3.3 6.3 + - - +
72A LEU* 1.3 77.3 - - - +
74A LYS* 1.3 59.4 + - + +
76A LYS* 3.4 6.7 + - - +
77A SER* 2.9 35.5 + - - +
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Residues in contact with LYS 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68A ASP* 3.3 28.1 + - - +
69A TYR* 3.6 26.2 - - + -
70A GLN 4.4 4.2 - - - +
71A THR* 3.1 30.5 + - + +
73A ASN* 1.3 73.8 - - + +
75A VAL* 1.3 60.5 + - - +
77A SER* 3.5 6.2 + - - -
78A LEU* 3.0 28.8 + - - +
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Residues in contact with VAL 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16A PHE* 3.7 20.4 - - + -
39A LEU* 3.7 20.4 - - + -
42A LEU* 4.3 2.7 - - + -
43A PHE* 3.9 31.9 - - + +
46A ILE* 3.6 6.8 - - + +
66A PHE* 4.4 5.8 - - + -
69A TYR* 3.3 33.4 - - + +
71A THR 3.1 12.9 + - - +
72A LEU 3.9 3.1 - - - +
74A LYS* 1.3 73.5 - - - +
76A LYS* 1.3 58.5 + - - +
78A LEU* 3.3 6.9 + - - +
79A SER* 2.9 27.5 + - - -
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Residues in contact with LYS 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A ASP* 3.1 40.6 + - - +
16A PHE* 3.6 38.7 - - + +
20A HIS* 6.2 5.2 - - + -
72A LEU* 2.8 18.4 + - + +
73A ASN* 3.7 8.3 - - - +
75A VAL* 1.3 76.8 - - - +
77A SER* 1.3 61.8 + - - +
79A SER* 3.2 4.3 + - - -
80A ASN* 3.1 48.4 + - - +
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Residues in contact with SER 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A ASN* 2.9 20.9 + - - +
74A LYS* 3.8 6.7 - - - -
75A VAL 3.3 0.2 - - - -
76A LYS* 1.3 73.3 - - - +
78A LEU* 1.3 60.7 + - - +
80A ASN* 3.4 8.5 + - - +
81A THR* 2.9 33.5 + - - -
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Residues in contact with LEU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A PHE* 3.6 30.1 - - + -
46A ILE* 3.5 18.2 - - + -
47A ASP 5.9 0.2 - - - +
64A VAL* 4.0 7.0 - - + -
69A TYR* 3.7 32.3 - - + +
74A LYS 3.0 18.4 + - - +
75A VAL* 3.6 4.7 - - - +
77A SER* 1.3 71.9 - - - +
79A SER* 1.3 66.7 + - - +
81A THR* 3.2 9.2 + - + -
82A PHE* 2.9 64.8 + - + -
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Residues in contact with SER 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12A ARG* 3.0 27.2 + - - -
13A ASP* 4.6 1.0 + - - -
16A PHE* 3.6 25.9 - - - -
46A ILE* 3.6 17.0 - - - +
75A VAL 2.9 13.6 + - - -
76A LYS* 3.4 10.1 - - - -
78A LEU* 1.3 76.4 - - - +
80A ASN* 1.3 59.9 + - - +
82A PHE* 3.5 2.9 + - - +
83A ARG* 3.0 36.9 + - - +
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Residues in contact with ASN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76A LYS* 3.1 45.2 + - - +
77A SER* 3.7 9.6 - - - +
79A SER* 1.3 78.2 + - - +
81A THR* 1.3 63.8 + - - +
83A ARG* 3.4 21.1 + - - +
84A THR* 3.2 26.3 + - - -
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Residues in contact with THR 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A SER* 2.9 20.0 + - - -
78A LEU* 3.6 10.3 - - + -
80A ASN* 1.3 76.8 - - - +
82A PHE* 1.3 71.3 + - + +
84A THR* 3.4 16.6 + - - -
85A GLU* 3.7 8.8 + - + +
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Residues in contact with PHE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46A ILE* 3.6 27.8 - - + +
47A ASP* 4.4 8.1 - - + -
49A GLU* 5.8 0.4 - - - +
50A TYR* 3.4 64.1 - + + -
64A VAL* 3.8 24.0 - - + -
78A LEU* 2.9 56.7 + - + +
79A SER* 3.9 3.8 - - - +
81A THR* 1.3 81.4 - - + +
83A ARG* 1.3 58.5 + - - +
85A GLU* 3.2 6.2 + - - +
86A ILE* 2.9 35.3 + - + +
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Residues in contact with ARG 83 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A TRP* 3.4 59.5 + - + +
12A ARG* 3.5 27.1 - - - +
13A ASP* 2.9 39.8 + - - -
79A SER* 3.0 22.3 + - - +
80A ASN* 3.6 19.5 + - - +
81A THR 3.3 0.2 - - - -
82A PHE* 1.3 76.9 - - - +
84A THR* 1.3 63.0 + - - +
86A ILE* 3.2 10.0 + - - +
87A ILE* 2.9 37.5 + - + +
159A TYR* 4.1 23.3 + - - -
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Residues in contact with THR 84 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ASN 3.2 14.5 + - - -
81A THR* 3.6 11.7 - - - -
82A PHE 3.3 0.2 - - - -
83A ARG* 1.3 75.9 - - - +
85A GLU* 1.3 65.1 + - + +
87A ILE* 3.7 9.7 + - - +
88A ASP* 3.5 27.8 + - - +
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Residues in contact with GLU 85 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A TYR* 3.9 25.8 - - + +
53A ILE* 5.4 0.2 - - - -
54A ARG* 3.6 13.0 + - - +
57A GLN* 3.6 25.4 + - - +
59A LYS* 5.4 0.7 + - - -
81A THR* 3.7 6.6 + - + +
82A PHE 3.2 9.0 + - - +
84A THR* 1.3 80.2 - - + +
86A ILE* 1.3 65.8 + - - +
88A ASP* 3.2 20.0 + - - +
89A VAL* 3.1 27.1 + - + +
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Residues in contact with ILE 86 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A PHE* 5.1 0.4 - - + -
9A TRP* 3.6 25.8 - - + -
46A ILE 5.5 0.2 - - - +
49A GLU* 3.4 35.0 - - + +
50A TYR* 4.1 15.0 - - + -
53A ILE* 3.8 36.1 - - + -
82A PHE* 2.9 36.5 + - + +
83A ARG* 3.2 8.9 + - - +
85A GLU* 1.3 75.9 - - - +
87A ILE* 1.3 56.5 + - - +
89A VAL* 3.2 2.9 + - - +
90A LEU* 2.9 40.0 + - + +
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Residues in contact with ILE 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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9A TRP* 3.8 20.4 - - + -
83A ARG* 2.9 33.6 + - + +
84A THR* 3.8 9.6 - - - +
85A GLU 3.3 0.2 - - - -
86A ILE* 1.3 74.6 - - - +
88A ASP* 1.3 63.7 + - - +
90A LEU* 3.4 2.4 + - - +
91A GLN* 2.9 43.6 + - + +
156A ILE* 3.8 28.5 - - + +
159A TYR* 3.3 38.8 - - + +
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Residues in contact with ASP 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57A GLN* 6.4 0.2 - - - +
84A THR* 3.5 18.3 + - - +
85A GLU* 3.2 24.9 + - - +
87A ILE* 1.3 83.0 - - - +
89A VAL* 1.3 59.7 + - + +
91A GLN* 3.4 7.6 + - - +
92A THR* 3.0 31.7 + - + +
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Residues in contact with VAL 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53A ILE* 3.7 36.3 - - + +
56A ILE* 4.4 8.1 - - + -
57A GLN* 3.4 47.3 - - + +
85A GLU* 3.1 14.6 + - + +
86A ILE 3.2 6.9 + - - +
88A ASP* 1.3 76.3 - - + +
90A LEU* 1.3 61.8 + - + +
92A THR* 2.7 26.8 + - - +
114A ARG* 3.7 21.0 + - - +
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Residues in contact with LEU 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2A PHE* 3.2 27.0 - - + -
2A MSE 3.6 39.3 - - + -
5A PHE* 4.2 14.6 - - + -
9A TRP* 4.1 15.7 - - + -
53A ILE* 3.9 21.3 - - + -
56A ILE* 6.0 0.7 - - + -
86A ILE* 2.9 39.0 + - + +
87A ILE* 4.0 4.0 - - - +
89A VAL* 1.3 78.4 - - + +
91A GLN* 1.3 60.2 + - - +
92A THR 3.2 1.4 + - - -
93A HIS* 3.5 8.2 - - - -
114A ARG* 5.0 7.6 - - - +
118A LEU* 4.3 14.6 - - + -
156A ILE* 4.9 4.9 - - + -
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Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
-2A PHE* 4.3 17.2 - - - -
87A ILE* 2.9 36.8 + - + +
88A ASP* 3.8 8.1 - - - +
89A VAL 3.4 0.2 - - - -
90A LEU* 1.3 75.1 - - - +
92A THR* 1.3 56.8 + - - +
93A HIS* 3.7 4.6 + - - +
156A ILE* 4.1 14.0 + - + +
157A HIS* 3.3 39.0 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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