Contacts of the helix formed by residues 19 - 29 (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 PHE 19 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8F MET* 3.5 43.3 - - + -
9F VAL 3.5 26.5 - - - -
10F HIS* 3.5 32.1 - + + -
15F ALA 4.3 5.6 - - - -
16F SER* 3.1 16.6 + - - +
17F PHE 3.0 1.0 - - - -
18F ASN* 1.3 78.3 - - + +
20F ALA* 1.3 64.3 + - - +
21F GLY 3.2 2.9 - - - -
22F ILE* 3.2 21.2 + - + +
23F LYS* 2.8 29.2 + - - +
38F ALA* 4.7 3.8 - - + -
74F VAL* 4.0 19.1 - - + -
76F HIS* 4.1 11.4 - - + -
102F LEU* 4.7 0.9 - - + -
160F LEU* 4.2 17.5 - - + -
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Residues in contact with ALA 20 (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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16F SER 4.2 0.6 + - - -
17F PHE* 3.1 21.2 + - + +
18F ASN 3.3 1.2 - - - +
19F PHE* 1.3 76.6 - - - +
21F GLY* 1.3 58.6 + - - +
23F LYS* 3.5 8.6 + - - +
24F SER* 3.1 33.4 + - - +
33F ARG* 5.0 0.5 + - - -
161F TYR* 5.3 4.7 - - + +
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Residues in contact with GLY 21 (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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18F ASN 4.5 0.4 + - - -
19F PHE 3.2 0.6 - - - -
20F ALA* 1.3 77.7 - - - +
22F ILE* 1.3 59.8 + - - +
24F SER* 3.4 5.7 + - - -
25F TYR* 3.0 28.2 + - - +
160F LEU 4.3 9.9 - - - -
161F TYR* 4.2 19.2 - - - -
166F ASN* 4.9 4.8 + - - -
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Residues in contact with ILE 22 (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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8F MET* 4.1 11.0 - - + -
19F PHE* 3.2 25.6 + - + +
21F GLY* 1.3 73.0 - - - +
23F LYS* 1.3 60.4 + - - +
25F TYR* 3.4 7.3 + - + +
26F LEU* 3.0 47.7 + - + +
74F VAL* 4.5 6.1 - - + -
102F LEU* 3.5 22.7 - - + -
159F LEU 4.4 1.1 - - - +
160F LEU* 3.8 26.8 + - + +
166F ASN* 3.8 15.5 - - - +
169F ILE* 3.5 32.1 - - + -
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Residues in contact with LYS 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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8F MET* 4.0 27.1 - - + +
16F SER* 4.4 10.7 + - - -
19F PHE* 2.8 18.6 + - - +
20F ALA* 3.7 7.6 - - - +
22F ILE* 1.3 77.6 - - - +
24F SER* 1.3 62.9 + - - +
26F LEU* 3.3 2.3 + - - +
27F VAL* 3.0 27.9 + - - +
33F ARG* 3.7 27.1 - - - +
36F LEU* 3.9 36.9 + - + +
38F ALA* 4.1 22.0 - - - +
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Residues in contact with SER 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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20F ALA 3.1 18.3 + - - -
21F GLY* 3.7 6.2 - - - -
22F ILE 3.4 0.2 - - - -
23F LYS* 1.3 76.4 - - - +
25F TYR* 1.3 62.7 + - - +
27F VAL* 3.5 2.6 + - - +
28F SER* 3.0 23.6 + - - -
33F ARG* 3.9 24.4 + - - +
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Residues in contact with TYR 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 GLY 3.0 16.8 + - - +
22F ILE* 3.5 4.9 - - + +
23F LYS 3.2 0.2 - - - -
24F SER* 1.3 77.9 - - - +
26F LEU* 1.3 83.8 + - + +
28F SER* 2.6 26.8 + - - -
29F GLN* 3.0 36.8 + - + +
163F SER 5.6 0.2 - - - -
166F ASN* 3.1 62.6 + - + +
167F SER* 3.7 12.4 + - - -
169F ILE* 5.7 0.7 - - + -
170F LYS* 3.5 25.9 - - + +
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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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6F VAL* 4.8 1.6 - - + -
8F MET* 3.8 28.3 - - + -
22F ILE* 3.0 24.8 + - + +
23F LYS 3.8 3.6 - - - +
25F TYR* 1.3 95.8 - - + +
27F VAL* 1.3 62.7 + - - +
29F GLN* 3.0 10.6 + - - +
30F GLY 3.2 0.9 + - - -
31F TRP* 3.0 52.2 + - + +
36F LEU* 4.0 13.5 - - + -
74F VAL* 5.2 0.4 - - + -
169F ILE* 4.4 8.5 - - + -
170F LYS* 4.9 1.8 - - - -
173F LEU* 3.7 32.1 - - + -
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Residues in contact with VAL 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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23F LYS 3.0 19.2 + - - +
24F SER 3.7 5.2 - - - +
26F LEU* 1.3 74.3 - - - +
28F SER* 1.3 64.9 + - - +
29F GLN 3.2 0.9 + - - -
30F GLY* 3.2 10.7 + - - -
31F TRP 3.3 12.5 - - - +
33F ARG* 3.3 67.1 - - + +
36F LEU* 3.6 8.1 - - + -
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Residues in contact with SER 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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24F SER 3.0 13.5 + - - -
25F TYR* 2.6 26.0 + - - -
27F VAL* 1.3 79.0 - - - +
29F GLN* 1.3 73.4 + - - +
30F GLY 3.4 0.6 + - - -
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Residues in contact with GLN 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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3F HIS* 5.1 1.0 - - - -
25F TYR* 3.0 50.8 + - + +
26F LEU* 3.0 9.2 + - - +
28F SER* 1.3 92.5 + - - +
30F GLY* 1.3 55.8 + - - +
31F TRP* 3.7 23.9 - - + -
170F LYS* 2.6 34.9 + - + -
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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