Contacts of the helix formed by residues 79 - 97 (chain A) in PDB entry 3QNQ
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 ILE 79 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A SER 3.7 13.9 - - - +
75A ALA 3.6 18.6 - - - +
76A THR 2.8 7.1 + - - +
78A ASN* 1.3 89.3 - - - +
80A MET* 1.3 66.4 + - - +
82A LEU* 3.6 26.9 - - + -
83A ILE* 3.2 25.9 + - + +
141A MET* 3.2 22.0 - - + -
108B LEU* 5.6 1.6 - - + -
109B VAL* 5.3 1.8 - - + -
112B LEU* 3.4 30.7 - - + -
117B PHE* 4.2 7.2 - - + -
136B ILE* 4.0 13.5 - - + -
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Residues in contact with MET 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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32A THR* 3.9 14.7 - - + +
36A LEU* 3.9 36.6 - - + -
76A THR 3.4 1.3 + - - +
77A PHE* 3.3 23.4 + - - +
79A ILE* 1.3 75.4 - - - +
81A ALA* 1.3 53.6 + - - +
83A ILE* 2.8 9.1 + - - +
84A ALA* 2.7 35.2 + - - +
141A MET 3.0 3.6 + - - +
143A SER* 3.0 42.0 - - - +
146A LEU* 3.3 26.5 - - + -
264A LEU* 3.4 17.0 - - + +
267A MET* 5.7 0.9 - - - +
268A ASP* 5.0 4.7 - - - -
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Residues in contact with ALA 81 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A MET* 1.3 78.5 - - - +
82A LEU* 1.3 57.0 + - - +
84A ALA* 3.6 2.0 - - - -
85A VAL* 2.9 35.5 + - - +
111A PHE* 3.5 22.4 - - + -
141A MET 3.0 10.9 + - - +
142A GLY 3.6 5.3 + - - +
145A GLY* 3.6 2.0 - - - -
146A LEU* 3.1 41.6 - - - +
149A ALA* 3.9 2.0 - - + -
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Residues in contact with LEU 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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79A ILE* 3.6 30.7 - - + -
80A MET 3.0 1.0 + - - -
81A ALA* 1.3 78.6 - - - +
83A ILE* 1.3 58.1 + - - +
85A VAL* 3.1 20.1 - - + +
86A PHE* 4.1 1.7 + - - +
108A LEU* 4.1 28.6 - - + +
111A PHE* 4.0 10.7 - - + -
112A LEU* 4.1 29.8 - - + -
141A MET* 3.5 23.4 + - + -
82B LEU* 4.7 12.3 - - + -
108B LEU* 4.5 13.9 - - + +
112B LEU* 3.8 18.2 - - + -
136B ILE* 5.3 3.1 - - + -
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Residues in contact with ILE 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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31A LEU* 4.0 29.7 - - + +
32A THR* 3.7 19.1 - - + -
35A PHE* 3.7 22.0 - - + -
36A LEU* 6.5 0.7 - - + -
75A ALA 5.0 0.9 - - - +
76A THR* 5.1 2.7 - - - +
79A ILE* 3.2 26.1 + - + +
80A MET* 2.8 8.4 + - - +
82A LEU* 1.3 77.1 - - - +
84A ALA* 1.3 62.1 + - - +
85A VAL 3.2 0.4 - - - -
86A PHE* 3.3 8.9 + - - +
87A GLY 3.2 17.2 + - - -
105B ALA* 5.3 5.2 - - + +
108B LEU* 4.7 14.1 - - + -
109B VAL* 3.4 32.8 - - + -
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Residues in contact with ALA 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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28A GLY 4.7 5.6 - - - +
29A LEU* 3.5 30.5 - - + -
32A THR* 3.5 11.2 - - + -
80A MET 2.7 20.0 + - - +
81A ALA* 3.6 8.5 - - - +
83A ILE* 1.3 71.4 - - - +
85A VAL* 1.3 62.7 + - - +
87A GLY 3.9 2.7 - - - +
88A ILE* 3.3 30.5 + - + +
146A LEU* 4.8 6.7 - - + -
149A ALA* 4.6 4.5 - - + -
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Residues in contact with VAL 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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81A ALA 2.9 16.8 + - - +
82A LEU* 3.1 22.4 - - + +
84A ALA* 1.3 76.4 - - - +
86A PHE* 1.3 77.5 + - - +
89A ALA* 3.0 28.8 + - - +
107A SER* 4.2 10.1 - - - +
108A LEU* 3.8 27.1 - - + -
111A PHE* 3.6 24.7 - - + -
149A ALA* 3.3 36.8 - - + +
152A ILE* 5.3 1.3 - - + -
153A ALA* 3.8 4.3 - - + +
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Residues in contact with PHE 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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31A LEU* 4.8 4.9 - - + -
82A LEU 4.6 4.5 - - - +
83A ILE* 3.3 11.6 + - - +
85A VAL* 1.3 83.9 - - + +
87A GLY* 1.3 55.4 + - - +
90A TYR* 2.8 58.2 + + - +
101A LEU* 4.1 12.8 - - + -
104A GLY* 3.1 23.5 - - - -
105A ALA* 3.2 32.8 - - + -
108A LEU* 4.4 13.7 - - + -
86B PHE* 2.9 59.7 - + + -
101B LEU* 4.0 13.2 - - + -
108B LEU* 5.8 2.2 - - + -
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Residues in contact with GLY 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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28A GLY* 3.5 20.1 - - - -
31A LEU* 3.8 21.1 - - - +
83A ILE 3.2 8.6 + - - -
84A ALA 4.3 0.7 - - - -
85A VAL 3.3 0.2 - - - -
86A PHE* 1.3 79.3 - - - +
88A ILE* 1.3 57.3 + - - +
90A TYR* 3.6 3.3 - - - +
91A ARG* 3.0 32.2 + - - +
101B LEU* 5.8 3.1 - - - -
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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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24A ALA* 3.7 34.1 - - + +
25A ILE* 3.7 22.7 - - + +
28A GLY* 3.9 8.3 - - - -
29A LEU* 4.8 9.4 - - + -
84A ALA* 3.3 21.7 + - + +
87A GLY* 1.3 74.9 - - - +
89A ALA* 1.3 57.9 + - - +
91A ARG* 3.8 0.5 - - - +
92A LEU* 2.9 34.9 + - + +
149A ALA* 4.9 0.9 - - + +
150A MET* 3.6 36.3 - - + +
153A ALA* 3.6 19.1 - - + -
154A ILE* 4.5 10.5 - - + +
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Residues in contact with ALA 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 VAL 3.0 13.2 + - - +
86A PHE 4.0 1.3 - - - +
88A ILE* 1.3 74.3 - - - +
90A TYR* 1.3 67.4 + - - +
92A LEU* 3.8 0.6 - - - -
93A GLY 3.0 10.7 + - - -
103A SER* 3.0 21.6 + - - +
104A GLY* 4.0 2.0 - - - -
107A SER* 3.1 41.1 - - - +
153A ALA* 3.6 7.2 - - + +
157A THR* 3.3 18.2 + - - +
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Residues in contact with TYR 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 PHE* 2.8 42.6 + + + +
87A GLY* 3.6 4.7 - - - +
89A ALA* 1.3 73.0 - - - +
91A ARG* 1.3 55.9 + - - +
93A GLY* 2.6 24.1 + - - -
94A GLU* 2.6 46.1 + - + -
100A ALA* 3.3 22.8 - - + +
101A LEU* 3.4 27.0 + - + -
103A SER* 3.8 6.8 + - - -
104A GLY* 4.0 1.5 - - - -
90B TYR* 2.5 32.7 + + - -
101B LEU* 3.5 35.6 - - + +
182B ARG* 5.9 0.7 - - - -
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Residues in contact with ARG 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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23A LEU* 3.5 29.0 - - + +
24A ALA* 3.9 24.5 - - - +
27A ASP* 3.9 5.7 + - + -
28A GLY* 4.8 3.4 - - - +
87A GLY 3.0 14.8 + - - +
88A ILE 3.8 2.9 - - - +
90A TYR* 1.3 80.7 - - + +
92A LEU* 1.3 55.9 + - - +
93A GLY 2.8 1.4 + - - -
94A GLU* 2.9 25.3 + - - +
95A TYR* 2.7 74.3 + - - +
600A ZDM 2.4 50.0 + - - +
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Residues in contact with LEU 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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20A ARG* 4.0 20.4 - - + +
21A HIS* 3.8 31.6 - - + +
23A LEU* 6.5 0.2 - - - -
24A ALA* 3.4 12.3 - - + +
88A ILE* 2.9 22.5 + - + +
89A ALA 4.1 3.6 - - - +
91A ARG* 1.3 71.5 - - - +
93A GLY* 1.3 58.3 + - - +
95A TYR* 3.6 8.7 - - + +
96A TYR* 3.6 31.8 + - + -
153A ALA 4.5 0.2 - - - +
154A ILE* 3.7 38.6 - - + +
157A THR* 3.8 20.0 - - + +
158A GLU* 4.6 4.7 - - - +
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Residues in contact with GLY 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 ALA 3.0 10.2 + - - -
90A TYR 2.6 15.7 + - - -
92A LEU* 1.3 70.5 - - - +
94A GLU* 1.3 65.5 + - - -
95A TYR 2.9 1.8 + - - -
96A TYR* 3.0 11.1 + - - -
97A LYS 3.0 8.7 + - - -
98A VAL* 3.4 32.4 + - - +
100A ALA* 4.7 0.7 - - - -
103A SER* 3.9 6.1 - - - -
157A THR* 4.1 4.9 - - - -
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Residues in contact with GLU 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 TYR* 2.6 35.5 + - + +
91A ARG* 3.2 31.7 + - - +
93A GLY* 1.3 69.4 - - - -
95A TYR* 1.3 64.1 - - - +
97A LYS* 3.0 18.2 + - - +
98A VAL 5.0 2.9 - - - -
100A ALA* 4.0 22.9 - - + +
600A ZDM 4.8 8.1 - - - +
182B ARG* 5.4 8.2 + - - -
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Residues in contact with TYR 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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18A GLU 4.0 11.3 + - - -
20A ARG* 3.3 48.8 + - + +
23A LEU* 3.6 19.1 - - + -
91A ARG* 2.7 42.5 + - - +
92A LEU* 3.6 14.8 - - + +
93A GLY 2.9 0.2 + - - -
94A GLU* 1.3 73.5 - - - +
96A TYR* 1.3 75.5 + + - +
97A LYS* 2.8 13.2 + - - +
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Residues in contact with TYR 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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20A ARG* 3.0 44.7 + - - -
92A LEU* 3.6 18.1 + - + +
93A GLY 3.0 9.7 + - - +
95A TYR* 1.3 87.1 - + - +
97A LYS* 1.3 68.2 + - - +
98A VAL* 3.3 8.8 + - + +
157A THR* 5.0 3.1 - - + -
158A GLU* 3.0 27.9 + - - -
161A ARG* 2.9 71.6 + - + -
165A GLN* 4.1 17.0 + - - +
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Residues in contact with LYS 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 GLY 3.0 0.2 + - - -
94A GLU 3.0 12.9 + - - +
95A TYR 2.8 15.5 + - - +
96A TYR* 1.3 80.5 - - - +
98A VAL* 1.3 62.3 + - - +
444A CIT 4.2 20.6 + - - +
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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