Contacts of the helix formed by residues 47 - 65 (chain F) in PDB entry 2Q9Q
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 LYS 47 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F ALA* 4.6 11.0 - - + -
44F LEU* 6.5 0.4 - - - -
45F GLU* 3.5 30.8 + - - +
46F SER* 1.3 78.7 + - - +
48F PRO* 1.3 64.3 - - - +
49F GLU* 3.4 19.6 + - - +
50F ILE* 3.2 27.4 + - + +
51F VAL* 3.2 24.7 + - - +
92F TYR* 3.6 26.8 + - + +
96F ARG* 5.2 0.4 - - - +
216F ALA 4.5 11.5 + - - -
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Residues in contact with PRO 48 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F SER* 3.1 24.8 - - - +
47F LYS* 1.3 83.5 - - - +
49F GLU* 1.3 79.1 + - - +
50F ILE 3.1 0.3 + - - -
51F VAL* 3.2 5.9 + - + +
52F GLU* 2.9 44.6 + - + +
123F SER* 5.6 6.5 - - - -
124F PRO* 6.3 1.3 - - + -
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Residues in contact with GLU 49 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46F SER 4.7 0.3 - - - +
47F LYS* 3.7 20.0 + - - +
48F PRO* 1.3 92.6 - - + +
50F ILE* 1.3 81.5 + - + +
52F GLU* 4.1 10.1 + - - +
53F CYS* 3.3 34.3 + - - -
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Residues in contact with ILE 50 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 3.8 14.8 - - + +
29F ARG* 3.9 39.0 - - + +
30F LEU* 4.1 26.5 - - + +
33F ALA* 5.0 3.6 - - + -
47F LYS* 3.2 33.2 + - + +
48F PRO 3.1 0.6 - - - -
49F GLU* 1.3 92.9 - - + +
51F VAL* 1.3 67.7 + - + +
53F CYS 3.4 0.9 + - - -
54F VAL* 2.9 43.6 + - + +
92F TYR* 6.0 1.6 - - + -
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Residues in contact with VAL 51 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47F LYS 3.2 14.3 + - - +
48F PRO* 3.2 9.0 + - + +
50F ILE* 1.3 78.2 - - + +
52F GLU* 1.3 65.6 + - + +
54F VAL* 3.9 0.9 - - - +
55F MET* 3.0 42.7 + - + +
89F LEU* 4.1 30.1 - - + -
92F TYR* 4.2 20.9 - - + -
93F LEU* 4.4 17.3 - - + -
128G LEU* 5.2 11.4 - - + +
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Residues in contact with GLU 52 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48F PRO* 2.9 41.3 + - + +
49F GLU* 4.1 8.1 - - - +
51F VAL* 1.3 78.9 - - + +
53F CYS* 1.3 58.5 + - - +
55F MET* 3.3 6.8 + - - +
56F GLU* 3.0 26.4 + - - +
128G LEU 5.9 4.9 - - - +
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Residues in contact with CYS 53 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21F LEU* 6.4 2.7 - - - -
26F LEU* 3.5 24.9 - - + -
49F GLU* 3.3 24.3 + - - +
52F GLU* 1.3 77.9 - - - +
54F VAL* 1.3 65.1 + - - +
56F GLU* 3.1 28.2 + - - +
57F GLN* 3.1 19.2 + - - +
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Residues in contact with VAL 54 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26F LEU* 3.5 27.8 - - + -
27F ILE* 4.5 6.7 - - + -
30F LEU* 4.2 20.9 - - + -
50F ILE* 2.9 30.9 + - + +
51F VAL* 3.9 5.2 - - - +
53F CYS* 1.3 75.0 - - - +
55F MET* 1.3 62.9 + - - +
57F GLN* 3.3 7.4 + - - +
58F LEU* 3.2 23.6 + - + +
85F ILE* 3.9 27.5 - - + +
89F LEU* 4.2 20.6 - - + -
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Residues in contact with MET 55 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51F VAL* 3.0 24.2 + - + +
52F GLU* 3.7 5.2 - - - +
54F VAL* 1.3 73.7 - - - +
56F GLU* 1.3 65.7 + - - +
58F LEU* 3.4 17.5 + - + +
59F GLU* 3.0 31.4 + - + +
89F LEU* 3.7 26.5 - - + -
93F LEU* 6.0 0.2 - - - -
128G LEU* 4.1 15.7 - - - +
129G GLY* 4.1 29.2 - - - -
133G GLY 4.8 4.0 - - - +
134G LEU* 3.6 31.0 - - + -
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Residues in contact with GLU 56 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52F GLU 3.0 13.2 + - - +
53F CYS* 3.2 25.2 - - - +
55F MET* 1.3 77.7 - - - +
57F GLN* 1.3 63.4 + - + +
59F GLU* 3.1 8.9 + - - +
60F HIS* 2.8 68.1 + - + +
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Residues in contact with GLN 57 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E ILE* 3.8 36.6 - - + +
23F PRO* 4.0 25.2 - - - +
26F LEU* 4.1 17.1 - - + +
27F ILE* 5.7 1.8 - - + -
53F CYS* 3.1 15.6 + - - +
54F VAL* 3.5 7.6 - - - +
56F GLU* 1.3 81.1 + - - +
58F LEU* 1.3 64.9 + - + +
60F HIS* 3.3 12.4 + - - +
61F MET* 2.8 29.8 + - - +
85F ILE* 6.3 0.2 - - + -
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Residues in contact with LEU 58 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E ILE* 4.8 5.2 - - + -
54F VAL* 3.2 23.7 + - + +
55F MET* 3.6 22.9 - - + +
57F GLN* 1.3 80.0 - - + +
59F GLU* 1.3 59.3 + - + +
61F MET* 4.8 2.7 - - - -
62F GLU* 3.1 32.7 + - - +
82F MET* 3.9 44.8 - - + +
85F ILE* 4.0 17.5 - - + -
86F ARG* 4.5 25.6 - - + +
89F LEU* 4.5 9.6 - - + -
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Residues in contact with GLU 59 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55F MET* 3.0 24.9 + - + +
56F GLU* 3.3 10.1 - - - +
57F GLN 3.0 0.2 - - - -
58F LEU* 1.3 79.2 - - + +
60F HIS* 1.3 71.9 + - + +
62F GLU* 3.1 15.5 + - - +
63F GLU* 2.9 23.1 + - - +
130G GLY* 5.2 10.9 + - - -
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Residues in contact with HIS 60 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56F GLU* 2.8 59.1 + - + +
57F GLN* 3.9 12.4 + - - +
59F GLU* 1.3 76.6 - - + +
61F MET* 1.3 62.5 + - - +
63F GLU* 3.0 21.2 - - - +
64F ASN* 2.9 18.4 + - - +
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Residues in contact with MET 61 (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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27E TYR 4.2 6.1 - - - +
29E ILE* 4.1 27.8 - - + +
57F GLN 2.8 17.0 + - - +
58F LEU 4.3 0.2 - - - +
60F HIS* 1.3 71.9 - - - +
62F GLU* 1.3 67.1 + - - +
63F GLU 3.0 2.8 + - - -
64F ASN* 3.0 28.4 + - - +
65F LEU* 3.1 26.1 + - + +
78F HIS* 3.5 44.9 - - + +
82F MET* 3.4 28.0 - - + -
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Residues in contact with GLU 62 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58F LEU* 3.1 22.6 + - - +
59F GLU* 3.6 14.4 - - - +
61F MET* 1.3 76.6 - - - +
63F GLU* 1.3 58.3 + - - +
65F LEU* 2.9 30.0 + - + +
82F MET* 3.6 26.1 - - + +
86F ARG* 4.8 6.1 + - - -
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Residues in contact with GLU 63 (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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59F GLU 2.9 11.9 + - - +
60F HIS* 3.0 15.9 - - - +
62F GLU* 1.3 72.4 - - - +
64F ASN* 1.3 64.2 + - - +
65F LEU 2.6 22.0 - - - +
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Residues in contact with ASN 64 (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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60F HIS* 2.9 22.6 + - - +
61F MET* 3.0 28.6 + - - +
63F GLU* 1.3 78.3 - - - +
65F LEU* 1.3 67.1 + - + +
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Residues in contact with LEU 65 (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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61F MET* 3.1 20.3 + - + +
62F GLU* 2.9 15.5 - - + +
63F GLU 2.6 21.3 + - - +
64F ASN* 1.3 84.1 - - + +
75F VAL* 3.5 30.3 - - + -
78F HIS* 3.9 26.0 - - + -
79F GLN* 3.9 27.1 - - + +
82F MET* 3.8 28.7 - - + -
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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) + - + + + + + -
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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