Contacts of the helix formed by residues 24 - 37 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B ASP* 4.2 5.6 - - - -
19B GLY* 4.3 2.0 - - - +
22B GLY 3.9 2.8 + - - -
23B ILE* 1.3 74.7 - - - +
25B LEU* 1.3 66.8 + - - +
26B ALA 3.7 0.8 + - - -
27B ASN* 3.0 34.5 + - - +
28B TRP* 3.1 15.0 + - - -
117D GLN* 3.8 18.9 + - - -
118D ASN* 2.7 36.8 + - - -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B ALA 3.8 13.0 - - - +
12B LEU* 3.7 37.7 - - + -
13B LYS* 4.1 14.6 - - + +
17B MET* 5.1 2.7 - - + -
18B ASP* 3.2 34.7 + - + +
23B ILE 3.9 0.2 + - - -
24B SER* 1.3 73.4 - - - +
26B ALA* 1.3 57.4 + - - +
28B TRP* 3.1 9.9 + - + +
29B MET* 2.9 33.3 + - + +
125B VAL* 4.2 8.1 - - + -
130B VAL* 3.6 38.8 - - + +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B SER* 3.1 1.4 + - - -
25B LEU* 1.3 77.9 - - - +
27B ASN* 1.3 55.5 + - - +
29B MET* 3.4 3.7 + - - +
30B CYS* 3.0 29.1 + - - +
121B VAL* 3.5 40.7 - - + +
122B ARG* 4.8 0.4 - - - -
124B TYR* 4.2 2.1 - - - +
125B VAL* 3.7 26.4 - - + +
118D ASN* 3.9 18.8 - - - +
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Residues in contact with ASN 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ILE* 3.9 15.6 - - + +
24B SER* 3.0 30.6 + - - +
26B ALA* 1.3 75.6 - - - +
28B TRP* 1.3 64.4 - - - +
30B CYS* 3.4 4.6 + - - +
31B LEU* 3.1 23.4 + - - +
106B ILE* 4.1 2.6 - - + +
112B TRP* 2.9 42.4 + - + +
116B CYS* 4.2 9.2 - - - +
117B GLN* 5.3 0.2 - - - -
121B VAL* 4.2 12.0 - - - +
117D GLN* 5.9 1.0 - - - +
118D ASN* 3.8 9.9 + - - +
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Residues in contact with TRP 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LEU* 4.2 17.9 - - + +
17B MET* 3.2 62.4 + - + +
20B TYR* 4.3 5.0 - + - +
23B ILE* 3.2 36.6 + - + +
24B SER 3.1 25.0 + - - -
25B LEU* 3.1 9.0 + - + +
27B ASN* 1.3 75.7 - - - +
29B MET* 1.3 63.1 + - - +
31B LEU* 3.4 30.1 + - + +
32B ALA* 3.1 22.3 + - - +
57B PHE* 4.1 13.8 - + + -
96B ALA* 4.1 21.3 - - + -
100B VAL* 3.4 37.2 - - + -
106B ILE* 4.7 3.6 - - + -
109B TRP* 4.6 2.7 - + - -
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Residues in contact with MET 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ARG* 3.3 26.2 - - + +
8B LEU* 3.6 28.3 - - + -
9B ALA* 3.7 20.4 - - + +
12B LEU* 3.8 8.3 - - - -
25B LEU* 2.9 21.0 + - + +
26B ALA 3.6 4.0 - - - +
28B TRP* 1.3 74.7 - - - +
30B CYS* 1.3 59.8 + - - +
32B ALA* 3.3 1.8 + - - +
33B LYS* 2.9 29.8 + - - +
38B TYR* 3.6 28.4 - - + +
124B TYR* 3.6 29.4 - - + +
125B VAL* 3.8 19.5 - - + -
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Residues in contact with CYS 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B ALA 3.0 18.1 + - - +
27B ASN* 3.7 5.2 - - - +
28B TRP 3.3 0.2 - - - -
29B MET* 1.3 76.3 - - - +
31B LEU* 1.3 59.5 + - - +
33B LYS 3.2 0.7 + - - -
34B TRP* 3.0 36.0 + - - -
115B ARG 3.7 7.4 - - - -
116B CYS* 2.0 51.3 - - + -
121B VAL* 3.8 7.9 - - + -
124B TYR* 3.5 37.0 - - + -
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ASN 3.1 16.7 + - - +
28B TRP* 3.5 29.4 - - + +
30B CYS* 1.3 76.3 - - - +
32B ALA* 1.3 57.4 + - - +
34B TRP* 3.8 1.6 - - - +
35B GLU* 2.9 61.1 + - + +
57B PHE* 4.0 15.9 - - + -
106B ILE* 4.3 5.4 - - + -
109B TRP* 3.6 50.7 - - + -
111B ALA 5.3 0.4 - - - -
112B TRP* 4.0 20.0 - - + +
116B CYS* 3.8 5.8 - - - -
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Residues in contact with ALA 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LEU* 4.3 8.1 - - + -
12B LEU* 5.8 0.4 - - + -
28B TRP 3.1 9.0 + - - +
29B MET 4.1 2.5 - - - +
31B LEU* 1.3 77.6 - - - +
33B LYS* 1.3 63.0 + - - +
35B GLU* 4.5 0.2 - - - -
36B SER* 3.0 27.4 + - - -
37B GLY 3.2 3.1 + - - -
38B TYR* 3.4 17.6 + - + -
56B ILE* 3.6 29.2 - - + +
57B PHE* 3.9 21.7 - - + -
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Residues in contact with LYS 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B MET 2.9 18.2 + - - +
30B CYS 3.6 4.0 - - - +
31B LEU 3.1 0.2 - - - -
32B ALA* 1.3 76.7 - - - +
34B TRP* 1.3 116.7 - - + +
37B GLY* 3.0 29.7 + - - +
38B TYR* 3.6 30.9 - - + +
124B TYR* 4.0 16.4 - - + -
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Residues in contact with TRP 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B CYS* 3.0 36.1 + - - +
31B LEU* 4.3 1.3 - - - +
33B LYS* 1.3 115.9 - - + +
35B GLU* 1.3 62.6 + - - +
37B GLY 5.0 0.2 + - - -
111B ALA* 4.2 17.6 - - + +
115B ARG* 3.6 66.0 + - + +
116B CYS* 4.1 0.7 - - - -
124B TYR* 2.9 24.6 + - - -
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Residues in contact with GLU 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B LEU* 2.9 38.9 + - + +
34B TRP* 1.3 79.2 - - - +
36B SER* 1.3 58.1 + - - +
42B ALA* 5.2 0.3 - - - +
56B ILE 4.1 9.9 - - - +
57B PHE 3.9 9.4 - - - +
58B GLN* 3.5 39.2 - - + +
109B TRP* 3.2 30.7 - - - +
110B VAL 4.7 0.3 + - - -
111B ALA* 3.2 28.4 + - + +
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Residues in contact with SER 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32B ALA 3.0 9.7 + - - -
35B GLU* 1.3 77.0 - - - +
37B GLY* 1.3 63.8 + - - +
38B TYR* 3.1 9.9 + - - -
39B ASN* 3.3 38.3 + - - +
42B ALA* 3.9 10.9 - - - +
55B GLY 3.6 10.3 - - - -
56B ILE* 2.9 26.8 + - - -
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Residues in contact with GLY 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B VAL* 3.9 12.6 - - - +
32B ALA 3.2 0.4 + - - -
33B LYS* 3.0 27.1 + - - -
35B GLU 4.0 0.2 - - - -
36B SER* 1.3 77.0 - - - +
38B TYR* 1.3 73.4 + - - +
39B ASN* 3.3 2.6 + - - +
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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