Contacts of the helix formed by residues 19 - 33 (chain A) in PDB entry 3QXY
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 LEU 19 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20A ASP* 1.3 65.6 + - + +
21A PRO* 3.8 11.0 - - + +
22A VAL* 3.7 29.8 - - - +
23A ALA* 3.5 19.6 + - - +
75A TYR* 5.0 4.0 + - - -
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Residues in contact with ASP 20 (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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19A LEU* 1.3 77.9 - - + +
21A PRO* 1.3 74.8 - - + +
22A VAL 3.2 0.2 + - - -
23A ALA* 3.2 6.2 + - - +
24A CYS* 3.0 23.7 + - - +
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Residues in contact with PRO 21 (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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19A LEU* 3.8 11.2 - - + +
20A ASP* 1.3 94.9 - - + +
22A VAL* 1.3 56.3 + - - +
24A CYS* 3.4 7.4 + - + +
25A PHE* 2.9 28.1 + - - +
75A TYR* 4.1 13.5 - - - +
142A PRO 5.0 1.7 - - - +
145A ALA* 4.3 22.0 - - + +
146A LEU* 3.9 16.6 - - + +
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Residues in contact with VAL 22 (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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19A LEU* 3.7 19.7 - - - +
20A ASP 3.2 1.0 - - - -
21A PRO* 1.3 77.0 - - - +
23A ALA* 1.3 65.0 + - - +
25A PHE* 3.2 7.5 + - + +
26A LEU* 3.0 36.6 + - + +
66A VAL* 3.9 39.0 - - + +
67A SER* 6.1 0.7 - - - -
75A TYR* 3.7 30.7 - - + -
146A LEU* 4.2 6.5 - - + -
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Residues in contact with ALA 23 (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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19A LEU 3.5 11.1 + - - +
20A ASP* 3.2 9.0 + - - +
22A VAL* 1.3 78.9 - - - +
24A CYS* 1.3 64.4 + - - +
26A LEU* 3.2 12.2 + - - +
27A SER* 3.0 25.7 + - - -
30A ARG* 4.8 1.2 + - - -
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Residues in contact with CYS 24 (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 ASP 3.0 16.4 + - - +
21A PRO* 3.6 8.5 - - + +
23A ALA* 1.3 78.1 - - - +
25A PHE* 1.3 61.4 + - - +
27A SER* 3.3 8.1 + - - +
28A TRP* 3.1 20.6 + - - +
142A PRO* 3.9 27.3 - - - +
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Residues in contact with PHE 25 (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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21A PRO 2.9 18.5 + - - +
22A VAL* 3.2 4.9 + - + +
24A CYS* 1.3 76.9 - - - +
26A LEU* 1.3 71.6 + - + +
28A TRP* 3.1 30.4 + + - +
29A CYS* 2.8 48.5 + - - -
36A LEU* 5.8 1.3 - - + -
66A VAL* 5.0 3.4 - - + -
142A PRO* 3.7 21.7 - - - +
143A TYR* 4.0 20.9 - + - -
146A LEU* 3.5 26.2 - - + -
245A PRO* 4.4 2.0 - - + -
246A ALA* 3.7 27.8 - - + -
249A ILE* 3.8 21.8 - - + -
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Residues in contact with LEU 26 (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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22A VAL* 3.0 32.2 + - + +
23A ALA* 3.6 9.9 - - - +
25A PHE* 1.3 88.8 - - + +
27A SER* 1.3 64.1 + - - +
29A CYS* 3.2 7.8 + - - +
30A ARG* 3.1 40.0 + - - +
36A LEU* 3.7 30.5 - - + -
66A VAL* 4.4 13.2 - - + +
80A ARG* 6.2 1.8 - - - +
479A EDO 3.9 8.8 - - - -
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Residues in contact with SER 27 (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 ALA 3.0 15.1 + - - -
24A CYS* 3.7 10.6 - - - -
25A PHE 3.3 0.2 - - - -
26A LEU* 1.3 75.3 - - - +
28A TRP* 1.3 58.6 + - - +
30A ARG* 3.1 30.7 + - - +
31A ARG* 2.9 26.6 + - - +
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Residues in contact with TRP 28 (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 CYS 3.1 6.5 + - - +
25A PHE* 3.1 27.1 + + - +
27A SER* 1.3 74.4 - - - +
29A CYS* 1.3 71.6 + - - +
31A ARG* 3.0 29.6 + - - +
32A VAL* 2.9 49.3 + - + +
34A LEU* 4.3 7.0 - - + -
96A ALA* 4.2 6.5 - - + -
139A ARG 2.8 22.3 + - - -
140A TRP* 3.5 29.4 - + - -
142A PRO* 3.5 42.7 - - + +
143A TYR* 4.3 4.9 - - + -
245A PRO* 3.6 39.7 - - + -
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Residues in contact with CYS 29 (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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25A PHE* 2.8 51.9 + - - -
26A LEU* 3.2 14.8 - - - +
28A TRP* 1.3 80.9 - - - +
30A ARG* 1.3 62.4 + - - +
32A VAL* 3.2 0.6 + - - -
33A GLY 3.0 4.7 + - - -
34A LEU* 2.9 66.6 + - - +
36A LEU* 4.7 5.6 - - - -
479A EDO 3.9 8.5 - - - -
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Residues in contact with ARG 30 (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 ALA 4.8 1.4 + - - -
26A LEU* 3.1 17.8 + - - +
27A SER* 3.1 35.6 + - - +
29A CYS* 1.3 79.7 - - - +
31A ARG* 1.3 64.3 + - - +
32A VAL 3.3 0.2 + - - -
33A GLY* 3.4 9.2 + - - -
34A LEU 4.9 1.8 - - - -
479A EDO 2.9 42.2 + - - +
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Residues in contact with ARG 31 (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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27A SER 2.9 13.8 + - - +
28A TRP* 3.0 28.2 + - - +
30A ARG* 1.3 78.1 - - - +
32A VAL* 1.3 68.4 + - + +
33A GLY 3.8 0.3 + - - -
139A ARG* 3.3 49.3 + - - +
483A EDO 4.7 6.1 + - - -
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Residues in contact with VAL 32 (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 TRP* 2.9 70.0 + - + +
29A CYS 3.7 5.8 - - - +
31A ARG* 1.3 94.8 - - + +
33A GLY* 1.3 58.8 + - - +
34A LEU* 4.0 7.9 - - + +
93A PRO* 3.6 14.4 - - - +
95A ALA* 6.0 0.2 - - - +
96A ALA* 3.9 18.7 - - + +
483A EDO 4.0 29.8 - - - +
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Residues in contact with GLY 33 (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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29A CYS 3.0 4.7 + - - -
30A ARG* 3.4 9.7 + - - -
31A ARG 3.5 0.8 - - - -
32A VAL* 1.3 77.9 - - - +
34A LEU* 1.3 62.0 + - - +
35A GLU* 3.3 18.7 + - - +
91A VAL* 4.4 1.6 - - - +
93A PRO* 3.3 17.7 - - - +
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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
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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