Contacts of the helix formed by residues 24 - 37 (chain D) in PDB entry 1QSW
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 SER 24 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117B GLN* 4.1 16.8 + - - -
118B ASN* 2.6 37.3 + - - -
18D ASP* 4.1 6.7 - - - -
19D GLY* 4.2 2.5 - - - +
22D GLY 3.7 4.8 + - - -
23D ILE* 1.3 75.1 - - - +
25D LEU* 1.4 68.0 + - - +
26D ALA 3.6 1.1 + - - -
27D ASN* 2.9 35.7 + - - +
28D TRP* 3.1 15.0 + - - -
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Residues in contact with LEU 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D ALA* 3.7 16.8 - - + +
12D LEU* 3.5 35.9 - - + -
13D LYS* 3.9 18.4 - - + +
17D MET* 4.4 3.6 - - + -
18D ASP* 3.1 36.6 + - - +
23D ILE 3.9 0.8 + - - -
24D SER* 1.4 72.7 - - - +
26D ALA* 1.3 57.8 + - - +
28D TRP* 3.0 11.1 + - + +
29D MET* 2.9 30.0 + - + +
125D VAL* 4.1 11.9 - - + -
130D VAL* 3.8 33.2 - - + -
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Residues in contact with ALA 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118B ASN* 3.8 20.0 - - - +
24D SER* 3.1 1.2 + - - +
25D LEU* 1.3 78.5 - - - +
27D ASN* 1.3 51.3 + - - +
29D MET* 3.4 3.5 + - - +
30D CYS* 2.8 34.3 + - - +
121D VAL* 3.4 39.1 - - + +
122D ARG* 4.6 0.4 - - - +
124D TYR* 4.1 2.1 - - - +
125D VAL* 4.0 26.5 - - + +
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Residues in contact with ASN 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118B ASN* 3.6 10.5 + - - +
23D ILE* 3.6 16.8 - - + +
24D SER* 2.9 35.0 + - - +
26D ALA* 1.3 72.9 - - - +
28D TRP* 1.3 60.6 + - - +
30D CYS* 3.3 5.2 + - - +
31D LEU* 2.9 28.9 + - - +
106D ILE* 4.1 1.8 - - + -
112D TRP* 2.9 43.5 + - - +
116D CYS* 4.1 9.4 - - - +
121D VAL* 4.3 12.1 - - - +
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Residues in contact with TRP 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12D LEU* 4.1 16.8 - - + -
17D MET* 3.1 67.2 + - + +
20D TYR* 4.5 7.9 + + - -
23D ILE* 3.5 38.1 + - + +
24D SER 3.1 21.6 + - - -
25D LEU* 3.0 9.1 + - + +
27D ASN* 1.3 75.1 - - - +
29D MET* 1.3 63.9 + - - +
31D LEU* 3.3 29.7 + - + +
32D ALA* 3.1 23.2 + - - +
57D PHE* 4.2 10.8 - + + -
96D ALA* 4.2 16.8 - - + -
97D LYS* 5.3 0.2 - - - -
100D VAL* 3.6 34.8 - - + -
106D ILE* 4.8 4.9 - - + -
109D TRP* 4.6 2.7 - + - -
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Residues in contact with MET 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ARG* 3.0 30.5 - - + +
8D LEU* 3.6 24.5 - - + -
9D ALA* 3.6 24.9 - - + +
12D LEU* 3.9 9.2 - - + -
25D LEU* 2.9 15.7 + - + +
26D ALA 3.6 4.5 - - - +
28D TRP* 1.3 72.3 - - - +
30D CYS* 1.3 67.2 + - - +
32D ALA* 3.4 2.6 + - - -
33D LYS* 3.0 25.6 + - - +
38D TYR* 3.7 23.6 + - + +
124D TYR* 3.6 33.4 - - + +
125D VAL* 3.7 18.4 - - + -
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Residues in contact with CYS 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26D ALA 2.8 18.1 + - - +
27D ASN 3.7 4.5 - - - +
28D TRP 3.3 0.2 - - - -
29D MET* 1.3 74.5 - - - +
31D LEU* 1.3 61.6 + - - +
33D LYS 3.4 0.2 + - - -
34D TRP* 3.1 37.4 + - - -
115D ARG 3.7 7.9 - - - -
116D CYS* 2.0 53.8 - - + -
121D VAL* 3.9 7.4 - - + -
124D TYR* 3.5 34.9 - - + -
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Residues in contact with LEU 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27D ASN 2.9 14.4 + - - +
28D TRP* 3.4 26.0 - - + +
29D MET 3.2 0.2 - - - -
30D CYS* 1.3 78.2 - - - +
32D ALA* 1.3 56.4 - - - +
34D TRP* 3.9 1.7 - - - +
35D GLU* 2.9 70.2 + - + +
57D PHE* 3.8 27.6 - - + -
106D ILE* 4.6 3.6 - - + -
109D TRP* 3.7 42.8 - - + -
111D ALA* 5.2 0.9 - - + -
112D TRP* 4.2 19.1 - - + +
116D CYS* 3.9 5.5 - - - -
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Residues in contact with ALA 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D LEU* 4.1 9.6 - - + -
12D LEU* 5.8 0.4 - - + -
28D TRP 3.1 12.8 + - - +
29D MET 4.0 3.4 - - - +
31D LEU* 1.3 76.6 - - - +
33D LYS* 1.3 66.3 + - - +
35D GLU* 4.8 0.2 - - - -
36D SER* 3.0 27.7 + - - -
37D GLY 3.3 2.3 + - - -
38D TYR* 3.5 16.4 + - + -
56D ILE* 3.6 30.3 - - + +
57D PHE* 4.2 12.8 - - + -
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Residues in contact with LYS 33 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29D MET 3.0 18.3 + - - +
30D CYS 3.6 4.3 - - - +
32D ALA* 1.3 75.9 - - - +
34D TRP* 1.3 75.9 + - + +
37D GLY* 2.9 31.4 + - - +
38D TYR* 3.4 38.0 - - + +
124D TYR* 3.6 22.7 - - + -
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Residues in contact with TRP 34 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30D CYS* 3.1 34.2 + - - +
31D LEU* 4.4 0.9 - - - +
33D LYS* 1.3 92.9 - - + +
35D GLU* 1.3 61.9 + - - +
36D SER 3.7 0.2 + - - -
111D ALA* 4.2 22.0 - - + +
115D ARG* 3.3 56.7 + - + +
116D CYS* 4.1 0.9 - - - -
124D TYR* 2.9 28.5 + - - -
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Residues in contact with GLU 35 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D LEU* 2.9 38.6 + - + +
34D TRP* 1.3 73.5 - - - +
36D SER* 1.3 59.5 + - - +
42D ALA* 5.2 0.5 - - - +
56D ILE 4.3 3.4 - - - +
57D PHE 3.6 15.9 - - - +
58D GLN* 3.3 38.7 - - + +
109D TRP* 3.3 31.1 - - - +
110D VAL 4.7 0.2 + - - -
111D ALA* 3.0 28.5 + - + +
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Residues in contact with SER 36 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ALA 3.0 4.4 + - - -
35D GLU* 1.3 78.9 - - - +
37D GLY* 1.3 62.7 + - - +
38D TYR 3.2 12.3 + - - -
39D ASN* 3.2 36.7 + - - +
42D ALA* 3.8 12.9 - - - +
55D GLY 3.8 10.3 - - - -
56D ILE* 2.9 27.1 + - - +
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Residues in contact with GLY 37 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D VAL* 3.8 13.2 - - - +
32D ALA 4.0 0.2 - - - -
33D LYS* 2.9 29.7 + - - -
34D TRP 5.0 0.2 + - - -
36D SER* 1.3 77.6 - - - +
38D TYR* 1.3 75.3 + - - +
39D ASN* 3.3 1.6 + - - +
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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