Contacts of the helix formed by residues 86 - 104 (chain B) in PDB entry 1QN7
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 86 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25B LEU* 4.6 0.9 - - - -
28B ILE* 3.5 12.9 - - - +
84B ALA* 3.4 1.3 - - - +
85B LYS* 1.3 80.3 - - - +
87B GLU* 1.3 64.7 + - - +
88B ASP* 3.7 6.4 + - - +
89B PHE* 2.9 37.8 + - - -
90B SER* 2.8 34.3 + - - -
178B ARG* 4.3 10.3 - - - -
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Residues in contact with GLU 87 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B LEU* 3.5 12.5 - - - +
28B ILE* 4.3 2.9 - - + -
86B SER* 1.3 69.3 - - - +
88B ASP* 1.3 65.4 + - - +
90B SER* 3.3 2.8 + - - -
91B LYS* 2.9 30.1 + - - +
113B PHE* 4.6 0.3 - - - -
115B ILE* 4.1 34.8 - - + +
118B ILE* 3.9 17.3 - - + +
176B LYS 6.0 0.2 - - - +
178B ARG* 2.9 59.3 + - - +
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Residues in contact with ASP 88 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86B SER* 3.4 6.4 + - - +
87B GLU* 1.3 79.9 - - - +
89B PHE* 1.3 61.6 + - + +
91B LYS* 3.2 7.9 + - - +
92B MET* 2.9 29.0 + - - +
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Residues in contact with PHE 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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66B GLU* 6.1 0.9 - - - -
67B PRO* 3.6 28.6 - - + +
84B ALA* 3.9 13.0 - - + -
85B LYS* 4.5 12.6 - - + +
86B SER* 2.9 33.1 + - - +
87B GLU 3.3 0.2 - - - -
88B ASP* 1.3 79.4 - - + +
90B SER* 1.3 65.0 + - - +
92B MET* 3.2 5.0 + - + -
93B ALA* 2.9 25.8 + - - +
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Residues in contact with SER 90 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28B ILE* 3.6 22.6 + - - +
30B SER* 2.7 32.4 + - - -
81B CYS* 3.9 9.0 - - - -
84B ALA* 3.4 17.2 - - - +
86B SER 2.8 21.0 + - - -
87B GLU* 3.3 4.7 + - - -
89B PHE* 1.3 72.3 - - - +
91B LYS* 1.3 63.2 + - - +
93B ALA* 3.8 4.3 - - - +
94B ALA* 3.0 23.4 + - - +
113B PHE* 4.3 0.9 - - - -
115B ILE* 4.4 2.7 - - - -
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Residues in contact with LYS 91 (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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87B GLU 2.9 16.8 + - - +
88B ASP* 3.6 7.4 - - - +
89B PHE 3.2 0.2 - - - -
90B SER* 1.3 77.5 - - - +
92B MET* 1.3 56.5 + - - +
94B ALA* 3.2 3.1 + - - +
95B ARG* 3.0 66.1 + - - +
110B PHE* 3.8 14.8 - - + -
113B PHE* 3.7 37.6 - - + +
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Residues in contact with MET 92 (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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67B PRO* 4.4 9.0 - - + -
88B ASP 2.9 16.8 + - - +
89B PHE* 3.2 9.2 + - + +
91B LYS* 1.3 71.9 - - - +
93B ALA* 1.3 66.8 + - - +
95B ARG* 3.2 23.3 + - + +
96B LYS* 3.1 53.3 + - + +
99B ARG* 5.6 5.8 - - - +
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Residues in contact with ALA 93 (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 ILE* 4.1 2.4 - - + +
67B PRO* 3.9 11.4 - - + +
69B THR* 3.4 37.9 - - + +
81B CYS* 4.0 4.0 - - - -
89B PHE 2.9 16.2 + - - +
90B SER 3.8 4.0 - - - +
92B MET* 1.3 76.0 - - - +
94B ALA* 1.3 63.2 + - - +
96B LYS* 3.2 22.8 + - - +
97B TYR* 3.0 20.6 + - - -
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Residues in contact with ALA 94 (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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31B THR 6.2 0.4 - - - -
32B VAL* 4.7 1.8 - - + -
79B MET* 3.3 30.3 - - + +
81B CYS* 4.1 8.9 - - + -
90B SER 3.0 18.9 + - - +
91B LYS 3.4 6.3 - - - +
93B ALA* 1.3 77.0 - - - +
95B ARG* 1.3 56.1 + - - +
97B TYR* 3.3 4.2 + - - -
98B ALA* 3.0 21.5 + - - +
110B PHE* 3.6 19.6 - - + -
113B PHE* 4.1 12.8 - - + -
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Residues in contact with ARG 95 (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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91B LYS* 3.0 49.5 + - - +
92B MET* 3.2 25.7 + - + +
94B ALA* 1.3 73.4 - - - +
96B LYS* 1.3 61.6 + - - +
98B ALA* 3.1 5.1 + - - +
99B ARG* 2.9 28.3 + - - +
110B PHE* 3.4 47.4 - - + +
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Residues in contact with LYS 96 (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 ILE* 3.7 27.7 - - + +
66B GLU 2.8 27.3 + - - -
67B PRO* 3.7 7.6 - - + -
92B MET* 3.1 41.2 + - + +
93B ALA* 3.2 8.5 + - - +
95B ARG* 1.3 76.5 - - - +
97B TYR* 1.3 57.5 + - - +
99B ARG* 3.3 34.2 + - - +
100B ILE* 2.9 35.7 + - + +
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Residues in contact with TYR 97 (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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34B LEU* 5.4 0.2 - - - -
62B MET* 3.6 30.9 + - + -
63B ARG* 3.5 2.5 - - - -
64B ILE* 3.2 29.4 + - + +
69B THR* 2.9 48.4 + - - -
70B THR 3.6 0.2 + - - -
71B ALA* 3.5 32.5 - - + -
73B ILE* 5.0 2.6 - - + +
79B MET* 3.5 22.4 - - + -
81B CYS* 4.1 7.6 - - - -
93B ALA 3.0 25.9 + - - -
94B ALA* 3.6 6.7 - - - +
95B ARG 3.2 0.4 - - - -
96B LYS* 1.3 74.6 - - - +
98B ALA* 1.3 66.7 + - - +
100B ILE* 3.3 10.0 + - + +
101B VAL* 3.1 28.9 + - - +
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Residues in contact with ALA 98 (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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34B LEU* 3.6 32.7 - - + +
94B ALA 3.0 13.5 + - - +
95B ARG* 3.1 9.4 + - - +
97B TYR* 1.3 75.4 - - - +
99B ARG* 1.3 57.3 + - - +
101B VAL 3.7 0.2 + - - -
102B GLN* 3.1 38.2 + - - +
108B ALA* 3.7 4.7 - - - +
109B LYS 4.1 6.1 - - - +
110B PHE* 3.9 16.6 - - + -
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Residues in contact with ARG 99 (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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92B MET* 5.6 5.3 - - - +
95B ARG 2.9 12.7 + - - +
96B LYS* 3.4 39.6 + - - +
98B ALA* 1.3 75.6 - - - +
100B ILE* 1.3 55.8 + - - +
102B GLN* 3.1 16.3 + - - +
103B LYS* 2.8 68.3 + - + +
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Residues in contact with ILE 100 (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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62B MET* 3.7 39.5 - - + -
64B ILE* 4.0 27.1 - - + -
96B LYS* 2.9 20.8 + - + +
97B TYR* 3.3 12.1 + - + +
99B ARG* 1.3 74.7 - - - +
101B VAL* 1.3 60.0 + - - +
103B LYS* 3.1 11.1 + - - +
104B LEU* 2.9 35.6 + - + +
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Residues in contact with VAL 101 (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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34B LEU* 4.2 14.8 - - + -
38B LEU* 3.6 30.5 - - + -
43B ILE* 4.6 11.0 - - + -
62B MET* 4.8 6.1 - - + -
73B ILE* 3.9 26.5 - - + -
97B TYR 3.1 16.9 + - - +
98B ALA 3.8 3.6 - - - +
100B ILE* 1.3 72.9 - - - +
102B GLN* 1.3 66.6 + - - +
104B LEU* 3.1 22.9 + - - +
106B PHE* 3.3 21.7 + - + -
108B ALA* 4.0 10.8 - - + -
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Residues in contact with GLN 102 (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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98B ALA* 3.1 27.5 + - - +
99B ARG* 3.1 18.7 + - - +
101B VAL* 1.3 76.3 - - - +
103B LYS* 1.3 56.5 + - + +
105B GLY* 2.7 27.7 + - - -
106B PHE 3.1 15.2 + - - +
107B PRO 4.7 0.4 - - - -
108B ALA* 2.6 38.6 + - + +
109B LYS* 4.7 1.8 + - - +
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Residues in contact with LYS 103 (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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46B GLN* 5.3 2.8 + - - -
99B ARG* 2.8 54.1 + - + +
100B ILE* 3.3 13.2 - - - +
102B GLN* 1.3 74.6 - - + +
104B LEU* 1.3 63.6 + - + +
105B GLY* 3.1 1.9 + - - -
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Residues in contact with LEU 104 (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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43B ILE* 3.7 44.2 - - + +
46B GLN* 3.7 52.4 + - + +
47B ALA* 4.4 9.2 - - + -
62B MET* 4.5 1.3 - - + -
100B ILE* 2.9 27.6 + - + +
101B VAL* 3.3 15.9 - - - +
102B GLN 3.1 0.6 - - - -
103B LYS* 1.3 76.7 - - + +
105B GLY* 1.3 56.8 + - - +
106B PHE* 3.7 16.4 - - + -
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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