Contacts of the helix formed by residues 75 - 97 (chain A) in PDB entry 1QLS
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 PHE 75 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A ILE 5.6 0.2 - - - -
15A LEU* 3.8 12.8 - - + -
16A ILE* 3.8 31.4 - - + -
19A PHE* 3.4 54.3 - + + -
20A GLN* 5.2 1.3 - - - -
30A THR 4.4 1.2 + - - -
74A ASP* 1.3 75.5 - - - +
76A GLN* 1.3 58.2 + - - +
78A PHE* 3.3 10.5 + + - +
79A LEU* 2.9 58.7 + - + +
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Residues in contact with GLN 76 (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 LEU* 5.9 2.0 - - + -
74A ASP* 3.2 11.9 + - - +
75A PHE* 1.3 81.0 - - - +
77A GLU* 1.3 66.1 + - + +
79A LEU* 3.2 21.2 + - - +
80A ASN* 3.2 27.2 + - - +
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Residues in contact with GLU 77 (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* 3.3 32.9 - - - +
66A ASP* 4.2 1.3 - - - -
67A LEU* 3.0 30.9 + - + +
68A ASP* 3.3 12.1 + - - +
73A LEU* 3.2 13.3 - - + -
74A ASP* 2.7 39.7 + - - +
76A GLN* 1.3 74.7 - - + +
78A PHE* 1.3 66.6 + - - +
80A ASN* 3.3 20.9 + - - +
81A LEU* 3.4 8.0 + - - +
102A CA 2.7 29.7 - - - -
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Residues in contact with PHE 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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15A LEU* 4.0 13.5 - - + -
18A ILE* 3.9 23.8 - - + -
19A PHE* 3.7 32.5 - + + -
32A ILE* 3.9 21.5 - - + -
37A PHE* 6.5 0.2 - + - -
40A PHE* 3.6 33.2 - + - -
73A LEU* 4.4 15.6 - - + +
74A ASP 2.9 15.9 + - - +
75A PHE* 3.6 13.5 - + - +
77A GLU* 1.3 78.8 - - - +
79A LEU* 1.3 68.5 + - + +
81A LEU* 3.1 21.5 + - + +
82A ILE* 3.1 34.9 + - + +
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Residues in contact with LEU 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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15A LEU* 3.8 30.3 - - + -
75A PHE* 2.9 59.6 + - + +
76A GLN* 3.2 11.6 + - - +
78A PHE* 1.3 82.9 - - + +
80A ASN* 1.3 56.3 + - - +
82A ILE* 3.2 6.3 + - + +
83A GLY* 2.9 27.5 + - - -
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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
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65A LEU* 4.4 10.9 + - + +
67A LEU* 3.7 28.1 - - - +
76A GLN* 3.2 24.7 + - - +
77A GLU* 3.3 13.3 + - - +
79A LEU* 1.3 74.2 - - - +
81A LEU* 1.3 57.5 + - - +
83A GLY* 4.5 1.3 - - - +
84A GLY* 2.8 28.1 + - - +
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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 PHE* 4.1 19.5 - - + -
40A PHE* 3.7 29.6 - - + -
41A MET* 4.1 6.5 - - + -
45A LEU* 4.4 2.2 - - + -
61A MET* 3.4 31.6 - - + -
65A LEU* 4.0 22.2 - - + +
73A LEU* 5.4 1.6 - - + -
77A GLU 3.4 3.1 + - - +
78A PHE* 3.1 18.6 + - + +
80A ASN* 1.3 76.2 - - - +
82A ILE* 1.3 71.0 + - + +
84A GLY* 3.4 0.9 + - - -
85A LEU* 3.2 47.0 + - + +
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Residues in contact with ILE 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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15A LEU* 4.2 28.3 - - + -
40A PHE* 4.3 13.7 - - + -
45A LEU* 5.2 7.2 - - + -
78A PHE* 3.1 48.8 + - + +
79A LEU* 3.2 10.7 + - + +
81A LEU* 1.3 81.9 - - + +
83A GLY* 1.3 57.0 + - - +
85A LEU* 3.4 7.2 + - + +
86A ALA* 2.9 30.2 + - + +
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Residues in contact with GLY 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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79A LEU 2.9 16.0 + - - -
80A ASN* 3.9 1.6 - - - -
82A ILE* 1.3 74.2 - - - +
84A GLY* 1.3 58.2 + - - +
86A ALA* 3.2 6.4 + - - +
87A ILE* 2.8 43.9 + - - +
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Residues in contact with GLY 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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80A ASN 2.8 21.0 + - - -
81A LEU* 3.4 1.5 + - - -
83A GLY* 1.3 70.7 - - - +
85A LEU* 1.3 58.2 + - - +
87A ILE* 3.4 8.9 + - - +
88A ALA* 3.1 28.1 + - - +
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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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41A MET* 5.9 0.2 - - + -
45A LEU* 3.4 39.7 - - + -
48A PHE* 4.3 27.1 - - + -
61A MET* 5.9 0.7 - - + -
81A LEU* 3.2 27.8 + - + +
82A ILE* 3.6 11.2 - - + +
84A GLY* 1.3 75.3 - - - +
86A ALA* 1.3 66.0 + - - +
88A ALA* 4.0 5.3 - - + +
89A CYS* 3.0 30.2 + - - -
3D VAL* 6.5 0.2 - - + -
6D PHE* 4.3 2.2 - - + -
7D LEU* 4.3 21.3 - - + -
11D TRP* 6.0 0.4 - - + -
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Residues in contact with ALA 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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82A ILE* 2.9 19.8 + - + +
83A GLY* 3.8 7.0 - - - +
85A LEU* 1.3 76.3 - - - +
87A ILE* 1.3 58.8 + - + +
89A CYS* 3.3 7.2 + - - +
90A HIS* 2.9 30.7 + - - +
3D VAL* 6.5 0.2 - - - -
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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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83A GLY* 2.8 25.9 + - - +
84A GLY* 3.8 6.7 - - - +
85A LEU 3.2 0.2 - - - -
86A ALA* 1.3 76.8 - - + +
88A ALA* 1.3 63.0 + - - +
90A HIS* 3.1 6.9 + - - +
91A ASP* 2.9 36.8 + - - +
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Residues in contact with ALA 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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84A GLY 3.1 17.7 + - - +
85A LEU* 4.0 5.4 - - + +
87A ILE* 1.3 76.4 - - - +
89A CYS* 1.3 64.0 + - - +
91A ASP* 3.3 8.1 + - - +
92A SER* 3.0 24.9 + - - -
6D PHE* 3.5 20.8 - - + -
10D ALA* 5.6 0.2 - - + -
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Residues in contact with CYS 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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85A LEU* 3.0 21.0 + - - +
86A ALA* 3.6 7.0 - - - +
88A ALA* 1.3 76.8 - - - +
90A HIS* 1.3 58.9 + - - +
92A SER* 3.5 2.8 + - - -
93A PHE* 3.0 26.7 + - - +
2D MET* 4.5 10.1 - - - +
3D VAL* 3.9 37.0 - - + -
6D PHE* 2.7 51.4 - - + -
7D LEU* 4.3 3.4 - - - -
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Residues in contact with HIS 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 ALA 2.9 16.8 + - - +
87A ILE* 3.7 6.0 - - - +
89A CYS* 1.3 75.7 - - - +
91A ASP* 1.3 72.6 + - - +
93A PHE* 3.1 18.4 + + - +
94A ILE* 3.0 50.1 + - + +
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Residues in contact with ASP 91 (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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87A ILE* 2.9 28.0 + - - +
88A ALA* 3.5 11.1 - - - +
90A HIS* 1.3 81.9 + - - +
92A SER* 1.3 56.4 + - - +
94A ILE* 3.2 7.8 + - - +
95A LYS* 3.0 49.7 + - - +
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Residues in contact with SER 92 (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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88A ALA 3.0 6.4 + - - -
89A CYS 3.7 4.9 - - - -
91A ASP* 1.3 71.5 - - - +
93A PHE* 1.3 66.8 + - - +
95A LYS* 3.7 7.8 - - - +
96A SER* 3.0 27.0 + - - -
2D MET* 5.5 3.8 - - - -
6D PHE* 2.9 41.4 - - - -
9D GLN* 5.9 0.9 - - - -
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Residues in contact with PHE 93 (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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89A CYS 3.0 17.4 + - - +
90A HIS* 3.1 18.1 + + - +
92A SER* 1.3 78.4 - - - +
94A ILE* 1.3 80.4 + - + +
96A SER* 3.4 7.3 + - - -
97A THR* 2.9 52.4 + - + +
98A GLN* 6.2 0.2 - - - -
2D MET* 4.2 22.4 - - + +
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Residues in contact with ILE 94 (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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90A HIS* 3.0 46.2 + - + +
91A ASP* 3.6 9.0 - - - +
93A PHE* 1.3 92.4 - - + +
95A LYS* 1.3 60.8 + - + +
97A THR* 3.0 2.9 + - - -
98A GLN* 2.7 70.6 + - + +
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Residues in contact with LYS 95 (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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91A ASP* 3.0 37.8 + - - +
92A SER* 3.7 9.0 - - - +
94A ILE* 1.3 81.6 - - + +
96A SER* 1.3 60.1 + - - +
98A GLN 4.1 3.2 - - - +
99A LYS* 3.5 22.5 - - - +
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Residues in contact with SER 96 (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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92A SER 3.0 17.1 + - - -
93A PHE* 3.4 10.2 + - - -
95A LYS* 1.3 76.7 - - - +
97A THR* 1.3 70.4 + - - +
99A LYS* 3.3 29.3 - - - +
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Residues in contact with THR 97 (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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93A PHE* 2.9 46.7 + - + +
94A ILE* 3.0 7.4 + - - -
96A SER* 1.3 89.1 + - - +
98A GLN* 1.3 68.3 + - - +
99A LYS* 3.4 8.0 + - - +
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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