Contacts of the helix formed by residues 78 - 90 (chain F) in PDB entry 2QXU
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 MET 78 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11F GLY* 3.9 1.3 - - - -
12F ILE* 3.4 57.7 - - + +
45F THR 4.2 6.3 - - - +
46F GLY* 3.2 28.0 - - - +
47F THR* 5.7 1.6 - - - -
48F ASN* 5.5 1.8 - - - +
76F HIS 3.2 0.2 + - - -
77F SER* 1.3 81.7 + - - +
79F GLY* 1.3 63.1 + - - +
80F GLY 3.0 0.2 - - - -
81F ALA* 3.0 20.9 + - - +
82F ASN* 3.1 13.9 + - - +
105F ALA* 4.4 7.1 - - + +
108F LEU* 3.6 31.9 - - + -
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Residues in contact with GLY 79 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 3.8 15.2 - - - +
10F HIS 3.4 20.0 + - - -
75F ALA* 3.6 6.9 - - - +
76F HIS 2.7 14.6 + - - -
78F MET* 1.3 78.8 - - - +
80F GLY* 1.3 55.9 + - - +
82F ASN* 3.4 6.5 + - - +
83F THR* 2.9 32.7 + - - -
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Residues in contact with GLY 80 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F ALA* 3.7 15.3 - - - +
76F HIS 3.9 1.0 + - - -
77F SER 2.8 11.8 + - - -
79F GLY* 1.3 75.9 - - - +
81F ALA* 1.3 64.2 + - - +
83F THR* 3.4 2.8 + - - -
84F LEU* 3.1 28.2 + - - +
101F THR* 4.3 7.2 - - - +
104F GLY* 4.6 1.8 - - - -
106F ASN* 3.3 21.7 - - - +
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Residues in contact with ALA 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F ASN* 3.2 11.4 - - - +
78F MET* 3.0 25.1 + - - +
80F GLY* 1.3 75.7 - - - +
82F ASN* 1.3 58.0 + - - +
84F LEU* 3.3 1.8 + - - +
85F TYR 2.9 20.1 + - - -
105F ALA 3.2 26.4 + - - +
106F ASN* 4.5 2.2 - - - +
108F LEU* 4.2 7.6 - - + -
109F THR* 2.9 30.2 + - - +
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Residues in contact with ASN 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 4.8 2.9 - - + -
10F HIS 4.5 1.8 + - - -
11F GLY 6.1 0.2 - - - -
41F PHE* 4.1 7.4 - - + -
46F GLY* 3.1 19.5 + - - +
48F ASN* 2.8 31.6 + - - +
51F ASN* 2.9 40.7 - - + +
52F GLY* 4.7 4.3 - - - +
55F LEU* 3.9 10.6 - - + +
78F MET* 3.1 16.7 + - - +
79F GLY* 3.7 14.9 - - - +
80F GLY 3.3 0.2 - - - -
81F ALA* 1.3 76.2 - - - +
83F THR* 1.3 57.7 + - - +
85F TYR* 3.3 5.3 + - - +
86F TYR* 2.9 29.3 + - - +
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Residues in contact with THR 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F VAL* 3.8 8.7 - - - +
55F LEU* 3.7 13.0 - - + +
73F ILE* 3.7 31.4 - - + +
75F ALA* 3.6 13.1 - - - +
79F GLY 2.9 20.6 + - - -
80F GLY* 3.7 7.4 - - - -
82F ASN* 1.3 74.9 - - - +
84F LEU* 1.3 64.7 + - + +
86F TYR* 3.2 5.9 + - + +
87F ILE* 3.0 40.6 + - + +
99F VAL* 4.4 14.1 - - + -
101F THR* 5.9 0.4 - - - -
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Residues in contact with LEU 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80F GLY 3.1 15.8 + - - +
81F ALA 3.3 3.8 + - - +
83F THR* 1.3 81.3 - - + +
85F TYR* 1.3 58.4 + - - +
87F ILE* 3.3 5.9 + - + +
88F LYS* 2.8 31.7 + - - +
106F ASN* 3.3 48.7 - - + +
109F THR* 3.9 11.2 - - + -
110F THR* 3.9 21.5 - - + -
112F LYS 4.4 3.8 - - - +
114F LEU* 4.0 6.4 - - + +
125F TYR* 3.7 35.7 - - + +
143F LEU* 4.1 11.2 - - + -
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Residues in contact with TYR 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48F ASN* 3.4 53.2 - - + +
49F TYR* 4.4 14.0 + - - -
52F GLY* 3.9 16.6 - - - -
53F PRO* 4.8 3.9 - - + +
81F ALA 2.9 16.6 + - - +
82F ASN 3.4 4.7 - - - +
83F THR 3.2 0.2 - - - -
84F LEU* 1.3 75.6 - - - +
86F TYR* 1.3 60.6 + - - +
88F LYS* 4.5 2.0 - - - +
89F ASN* 3.0 56.2 + - + +
90F LEU* 3.7 19.3 + - + +
109F THR* 3.6 12.9 - - + +
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Residues in contact with TYR 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F GLY* 4.6 5.4 - - - +
55F LEU* 3.7 22.2 - - + -
56F SER* 3.5 28.1 + - - -
59F VAL* 3.2 40.9 - - + +
73F ILE* 5.9 1.3 - - + -
82F ASN 2.9 14.2 + - - +
83F THR* 3.4 12.1 - - + +
85F TYR* 1.3 76.9 - - - +
87F ILE* 1.3 66.5 + - + +
90F LEU* 3.2 27.0 + - + -
91F ASP* 3.4 16.2 + - - -
92F GLY* 3.2 48.9 + - - -
95F LYS* 3.7 14.6 - - - +
96F VAL* 3.8 18.4 - - + -
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Residues in contact with ILE 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83F THR* 3.0 35.3 + - + +
84F LEU* 3.7 6.3 - - - +
86F TYR* 1.3 81.8 - - + +
88F LYS* 1.3 61.9 + - - +
90F LEU 4.5 3.5 - - - +
92F GLY 4.1 9.6 - - - +
93F GLY* 3.7 22.6 + - - +
96F VAL* 4.2 12.3 - - + -
99F VAL* 4.2 13.5 - - + -
114F LEU* 4.2 15.0 - - + -
116F GLY* 4.6 3.9 - - - -
117F THR* 5.7 1.6 - - - +
123F ILE* 3.6 31.2 - - + -
125F TYR* 3.6 25.8 - - + +
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Residues in contact with LYS 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84F LEU 2.8 17.7 + - - +
85F TYR* 4.1 1.8 - - - +
87F ILE* 1.3 80.0 - - - +
89F ASN* 1.3 85.1 + - - +
90F LEU 4.9 0.9 - - - +
109F THR* 4.1 27.3 + - + +
110F THR* 5.0 3.9 - - - -
114F LEU* 3.3 27.1 - - + -
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Residues in contact with ASN 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F TYR* 3.0 46.3 + - + +
88F LYS* 1.3 111.5 + - - +
90F LEU* 1.3 73.3 + - + +
109F THR* 5.6 0.2 - - - +
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Residues in contact with LEU 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52F GLY* 3.3 42.0 - - - +
53F PRO* 3.6 13.9 - - + -
56F SER* 4.3 6.1 - - - -
85F TYR* 4.2 18.4 - - + +
86F TYR* 3.2 24.6 + - + +
87F ILE 4.5 5.0 - - - +
88F LYS 4.9 0.9 - - - +
89F ASN* 1.3 89.9 - - + +
91F ASP* 1.3 70.4 + - - +
92F GLY 3.4 3.2 + - - -
93F GLY 4.6 1.2 + - - -
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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