Contacts of the helix formed by residues 22 - 40 (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 THR 22 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21F LEU* 1.3 76.0 - - - +
23F PRO* 1.3 75.5 - - - +
24F ALA* 3.4 9.8 + - - +
25F GLU* 2.6 57.5 + - - +
26F LEU* 3.0 10.2 + - - +
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Residues in contact with PRO 23 (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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29E ILE* 3.1 23.8 - - + +
21F LEU 3.6 3.5 - - - +
22F THR* 1.3 86.3 - - - +
24F ALA* 1.3 61.5 + - - +
26F LEU* 3.2 13.9 + - + +
27F ILE* 3.1 27.7 + - - +
57F GLN* 4.0 29.2 - - - +
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Residues in contact with ALA 24 (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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29E ILE 3.7 6.6 + - - +
30E GLY* 4.2 23.6 - - - +
31E GLY* 5.0 1.8 - - - +
22F THR* 3.0 9.5 + - - +
23F PRO* 1.3 79.6 - - - +
25F GLU* 1.3 63.5 + - + +
27F ILE* 3.2 6.7 + - - +
28F GLU* 3.1 20.9 + - - +
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Residues in contact with GLU 25 (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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21F LEU* 2.8 17.8 + - - -
22F THR* 2.6 55.9 + - + +
24F ALA* 1.3 76.0 - - + +
26F LEU* 1.3 57.8 + - - +
28F GLU* 3.0 10.7 + - - +
29F ARG* 2.8 47.2 + - - +
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Residues in contact with LEU 26 (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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21F LEU 5.3 3.6 - - - +
22F THR 3.0 10.6 + - - +
23F PRO* 3.3 13.9 - - + +
24F ALA 3.2 0.2 - - - -
25F GLU* 1.3 76.4 - - - +
27F ILE* 1.3 65.4 + - + +
29F ARG* 3.2 11.7 + - + +
30F LEU* 3.0 21.0 + - - +
49F GLU 5.5 0.2 - - - -
50F ILE* 3.8 24.4 - - + +
53F CYS* 3.5 34.1 - - + +
54F VAL* 3.5 32.3 - - + +
57F GLN* 4.1 17.7 - - + +
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Residues in contact with ILE 27 (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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12E LYS* 5.8 2.0 - - + +
29E ILE* 4.2 15.3 - - + +
30E GLY* 5.0 6.1 - - - -
23F PRO 3.1 16.6 + - - +
24F ALA* 3.7 7.0 - - - +
26F LEU* 1.3 80.3 - - + +
28F GLU* 1.3 62.7 + - - +
30F LEU* 3.4 8.5 + - + +
31F GLU* 3.1 44.5 + - + +
54F VAL* 4.5 14.8 - - + -
57F GLN* 5.7 1.8 - - + -
85F ILE* 3.6 51.6 - - + -
88F VAL* 6.6 0.2 - - + -
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Residues in contact with GLU 28 (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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12E LYS* 4.1 17.6 + - - +
24F ALA 3.1 12.2 + - - +
25F GLU* 3.0 14.5 + - - +
27F ILE* 1.3 78.1 - - - +
29F ARG* 1.3 64.3 + - + +
31F GLU* 3.3 9.9 + - - +
32F GLN* 3.1 24.8 + - + +
176F ARG* 5.6 8.9 + - - +
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Residues in contact with ARG 29 (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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25F GLU* 2.8 29.8 + - - +
26F LEU* 3.2 12.3 + - - +
28F GLU* 1.3 78.9 - - + +
30F LEU* 1.3 61.4 + - - +
32F GLN* 3.4 24.4 + - - +
33F ALA* 3.1 22.5 + - - +
50F ILE* 3.9 28.9 - - + +
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Residues in contact with LEU 30 (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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26F LEU 3.0 12.8 + - - +
27F ILE* 3.5 15.7 - - + +
29F ARG* 1.3 75.1 - - - +
31F GLU* 1.3 59.2 + - + +
33F ALA* 3.2 5.0 + - + +
34F TRP* 2.9 26.3 + - - +
50F ILE* 4.1 21.2 - - + +
54F VAL* 4.2 21.5 - - + -
85F ILE* 4.1 14.8 - - + +
88F VAL* 3.5 28.3 - - + -
89F LEU* 3.9 35.0 - - + +
92F TYR* 4.3 15.3 - - + -
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Residues in contact with GLU 31 (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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8E PHE* 4.3 12.5 - - - -
9E LEU* 4.2 15.2 - - + +
12E LYS* 2.5 48.3 + - - +
27F ILE* 3.1 29.4 + - + +
28F GLU* 3.8 10.5 - - - +
30F LEU* 1.3 75.6 - - + +
32F GLN* 1.3 57.5 + - - +
34F TRP* 3.4 14.7 - - + +
35F MET* 3.0 36.6 + - + +
88F VAL* 4.2 15.8 - - + +
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Residues in contact with GLN 32 (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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28F GLU* 3.1 14.8 + - + +
29F ARG* 3.5 32.4 + - - +
31F GLU* 1.3 77.7 - - - +
33F ALA* 1.3 57.4 + - - +
35F MET 3.5 0.2 + - - -
36F ASN* 3.0 45.0 + - - +
176F ARG* 4.6 21.8 + - - +
215F VAL 5.2 0.5 - - - +
218F GLY* 3.9 22.7 - - - -
220F VAL 5.1 0.3 - - - +
221F GLN* 2.9 29.9 + - - +
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Residues in contact with ALA 33 (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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29F ARG 3.1 10.4 + - - +
30F LEU* 3.7 8.5 - - - +
32F GLN* 1.3 76.6 - - - +
34F TRP* 1.3 67.0 + - - +
36F ASN* 3.8 7.1 - - - +
37F GLU* 2.8 29.1 + - - +
44F LEU* 5.0 1.1 - - - +
47F LYS* 4.6 16.2 - - + -
50F ILE* 5.0 4.7 - - + -
92F TYR* 3.7 29.6 - - + +
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Residues in contact with TRP 34 (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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1E MET* 4.1 16.4 - - + -
5E GLU* 3.4 42.0 - - + -
8E PHE* 4.4 12.6 - + - -
9E LEU* 4.3 17.9 - - + -
30F LEU 2.9 12.8 + - - +
31F GLU* 3.4 19.5 - - + +
33F ALA* 1.3 76.3 - - - +
35F MET* 1.3 72.4 + - + +
37F GLU* 4.0 2.1 - - - +
38F LYS* 3.1 41.7 + - + +
87F TYR* 3.6 17.5 - + - -
88F VAL* 3.7 27.6 - - + -
91F SER* 2.8 24.4 + - - -
92F TYR* 3.5 37.3 - - + -
95F CYS* 5.3 1.6 - - + -
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Residues in contact with MET 35 (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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1E MET* 3.5 42.8 - - + +
9E LEU* 4.2 15.0 - - + -
150E LEU* 4.3 16.4 - - + -
31F GLU* 3.0 20.8 + - + +
32F GLN* 5.1 0.2 - - - -
34F TRP* 1.3 88.5 - - + +
36F ASN* 1.3 62.0 + - - +
38F LYS* 3.2 12.8 + - - +
39F PHE* 3.0 40.3 - - + -
221F GLN* 3.1 27.4 - - + +
222F LEU 3.9 7.6 - - - +
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Residues in contact with ASN 36 (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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32F GLN* 3.0 43.4 + - - +
33F ALA* 3.8 5.3 - - - +
35F MET* 1.3 76.4 - - - +
37F GLU* 1.3 57.8 + - - +
39F PHE 3.5 0.2 + - - -
40F ALA* 2.9 34.1 + - - +
44F LEU* 3.4 17.9 - - + -
215F VAL* 3.9 23.2 + - + +
220F VAL 4.4 3.6 + - - -
221F GLN* 3.5 6.9 + - - -
222F LEU* 2.9 39.4 + - - +
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Residues in contact with GLU 37 (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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33F ALA 2.8 17.7 + - - +
34F TRP 4.0 3.6 - - - +
36F ASN* 1.3 74.1 - - - +
38F LYS* 1.3 66.3 + - - +
39F PHE 3.4 0.5 + - - -
40F ALA 3.7 0.9 + - - -
43F LEU* 3.5 4.3 - - - -
44F LEU* 2.8 35.5 + - + +
45F GLU 4.6 0.3 - - - +
92F TYR* 3.9 14.5 + - + -
95F CYS* 3.5 15.3 - - + -
96F ARG* 2.9 50.4 + - + +
99F LYS* 2.6 53.5 + - - +
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Residues in contact with LYS 38 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1E MET* 3.9 29.8 - - + +
5E GLU* 2.8 39.6 + - - -
34F TRP* 3.1 45.8 + - + +
35F MET* 3.2 17.0 + - - +
37F GLU* 1.3 79.0 - - - +
39F PHE* 1.3 74.7 + - + +
40F ALA 4.7 1.6 - - - +
91F SER* 3.8 10.1 + - - -
95F CYS* 3.8 16.4 - - + +
98F MET* 5.8 2.6 - - - +
99F LYS* 5.2 0.7 - - - -
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Residues in contact with PHE 39 (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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1E MET* 3.8 42.4 - - + -
150E LEU* 5.7 3.1 - - + -
154E ASN* 4.2 12.8 - - - -
35F MET* 3.0 50.5 + - + -
38F LYS* 1.3 88.5 - - + +
40F ALA* 1.3 62.8 + - - +
41F PRO* 3.5 2.9 - - - +
171F VAL* 3.6 23.8 - - + +
172F PHE 5.6 2.0 - - - +
222F LEU* 3.7 34.5 - - + -
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Residues in contact with ALA 40 (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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36F ASN 2.9 19.5 + - - +
37F GLU 3.7 0.5 + - - +
38F LYS 3.6 1.8 - - - +
39F PHE* 1.3 76.6 - - - +
41F PRO* 1.3 67.3 - - + +
42F GLU 3.1 17.3 - - - +
44F LEU* 3.7 21.5 - - + -
99F LYS* 3.0 25.5 + - - +
208F TYR* 4.1 4.9 - - + +
222F LEU* 3.7 12.3 - - + +
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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