Contacts of the helix formed by residues 32 - 46 (chain B) in PDB entry 1QAG
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 VAL 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232A ASP* 4.2 39.7 - - + +
239A ASP* 4.5 20.4 - - + +
242A SER* 4.7 1.6 - - - +
31B ASP* 1.3 83.1 - - + +
33B GLN* 1.3 67.9 + - + +
34B LYS 2.9 6.0 + - - -
35B LYS* 2.9 21.4 + - - +
36B THR* 3.0 23.1 + - + +
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Residues in contact with GLN 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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239A ASP* 3.0 39.5 + - - +
241A LYS* 3.9 27.2 + - - +
242A SER* 4.1 1.8 - - - +
31B ASP 4.6 4.0 - - - +
32B VAL* 1.3 80.4 - - - +
34B LYS* 1.3 60.7 + - - +
36B THR* 3.8 9.2 - - - -
37B PHE* 2.9 54.6 + - + -
124B LEU* 3.9 24.6 - - + +
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Residues in contact with LYS 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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31B ASP* 3.6 25.0 - - - +
32B VAL 2.9 1.8 + - - -
33B GLN* 1.3 79.3 - - - +
35B LYS* 1.3 56.6 + - + +
37B PHE* 3.7 0.7 - - - +
38B THR* 2.7 45.2 + - - +
54B ASN 5.8 0.7 - - - -
55B ASP* 3.2 28.5 + - - +
56B MSE 4.2 15.9 - - - +
57B PHE* 3.1 46.3 - - + -
124B LEU* 3.9 13.8 - - + +
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Residues in contact with LYS 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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229A ASP* 3.3 22.0 + - - +
231A GLU* 5.1 2.6 + - - -
232A ASP* 2.5 39.9 + - - +
31B ASP 3.8 11.2 + - - +
32B VAL* 2.9 15.6 + - - +
34B LYS* 1.3 77.2 - - + +
36B THR* 1.3 65.0 + - + +
38B THR* 3.3 6.2 + - - -
39B LYS* 3.0 39.8 + - - +
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Residues in contact with THR 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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227A LEU 3.8 24.2 - - - +
228A LEU* 4.4 10.3 - - + -
232A ASP* 5.1 5.2 - - + +
242A SER* 2.5 35.3 + - - +
245A MSE 3.3 18.9 - - - +
32B VAL* 3.0 21.4 + - + +
33B GLN* 3.4 4.0 + - - -
35B LYS* 1.3 77.6 - - + +
37B PHE* 1.3 72.2 + - - +
39B LYS* 3.0 4.7 + - - +
40B TRP 2.8 25.8 + - - -
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Residues in contact with PHE 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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241A LYS* 4.4 5.6 - - + -
242A SER* 4.2 8.1 - - - -
245A MSE 4.1 19.3 - - - -
33B GLN* 2.9 48.1 + - + +
34B LYS 3.8 1.1 - - - +
36B THR* 1.3 89.8 + - - +
38B THR* 1.3 62.3 + - - +
40B TRP* 3.7 3.6 - - - +
41B ILE* 3.0 25.6 + - - +
56B MSE 4.1 4.5 - - - -
124B LEU* 4.1 17.5 - - + -
127B LEU* 4.1 33.2 - - + +
128B TRP* 3.5 54.5 - + + -
131B ILE* 4.2 5.8 - - + -
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Residues in contact with THR 38 (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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34B LYS* 2.7 32.9 + - - +
35B LYS* 3.5 7.5 - - - -
37B PHE* 1.3 70.6 - - - +
39B LYS* 1.3 62.7 - - + +
41B ILE* 3.0 9.4 - - - +
42B ASN* 2.8 50.2 + - - +
53B ILE* 4.5 9.9 - - + -
54B ASN 4.3 16.7 + - - +
56B MSE 3.5 24.9 + - - +
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Residues in contact with LYS 39 (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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225A GLU* 6.2 0.9 - - + -
226A LYS* 3.5 16.8 + - - +
227A LEU* 3.2 31.2 + - + +
229A ASP* 2.9 38.5 + - - -
35B LYS* 3.0 27.3 + - - +
36B THR* 3.3 7.9 - - - +
38B THR* 1.3 82.5 - - + +
40B TRP* 1.3 52.8 + - - +
42B ASN* 3.0 8.2 + - - +
43B ALA* 2.6 35.5 + - - +
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Residues in contact with TRP 40 (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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227A LEU* 3.7 22.8 - - + +
245A MSE 3.6 30.3 - - + -
249A SER* 4.7 2.0 - - - -
36B THR 2.8 18.5 + - - +
37B PHE* 3.7 4.5 - - - +
39B LYS* 1.3 72.4 - - - +
41B ILE* 1.3 91.2 + - + +
43B ALA* 3.1 6.6 + - + +
44B ARG* 3.0 54.8 + - + +
69B LEU* 4.0 11.9 - - + -
73B LEU* 4.6 12.8 - - + -
127B LEU* 4.1 10.5 - - + -
130B ILE* 4.5 10.8 - - + -
131B ILE* 3.5 41.2 - - + +
134B TRP* 5.9 0.4 - - + -
135B GLN* 2.6 37.1 + - + +
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Residues in contact with ILE 41 (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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37B PHE 3.0 16.2 + - - +
38B THR* 3.0 19.5 - - - +
40B TRP* 1.3 87.7 - - + +
42B ASN* 1.3 73.0 + - - +
44B ARG* 3.1 6.3 + - - +
45B PHE* 2.9 41.9 + - + -
53B ILE* 4.0 19.3 - - + -
60B LEU* 4.4 23.6 - - + -
66B LEU* 5.2 1.6 - - + -
69B LEU* 3.4 40.2 - - + -
127B LEU* 4.0 21.3 - - + -
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Residues in contact with ASN 42 (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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38B THR* 2.8 30.1 + - - +
39B LYS* 3.3 7.3 - - - +
41B ILE* 1.3 79.1 - - - +
43B ALA* 1.3 60.0 + - - +
45B PHE* 3.5 6.7 - - - +
46B SER* 2.9 31.5 + - - -
52B PRO* 2.9 21.2 - - + +
53B ILE* 2.8 48.5 + - - +
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Residues in contact with ALA 43 (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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225A GLU* 3.7 35.9 - - + +
227A LEU* 4.8 2.2 - - + -
39B LYS 2.6 15.3 + - - +
40B TRP* 3.1 15.7 - - + +
42B ASN* 1.3 71.8 - - - +
44B ARG* 1.3 68.8 + - - +
45B PHE 3.0 0.5 + - - -
46B SER* 3.0 8.7 + - - -
47B LYS* 2.9 35.6 + - - +
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Residues in contact with ARG 44 (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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224A ILE* 6.2 1.6 - - - +
249A SER* 4.6 7.7 + - - -
40B TRP* 3.0 45.1 + - + +
41B ILE 3.1 11.0 - - - +
43B ALA* 1.3 83.1 - - - +
45B PHE* 1.3 53.9 + - + +
47B LYS* 3.8 38.2 + - - +
48B SER* 2.6 30.3 + - - -
69B LEU* 4.1 15.5 - - + -
73B LEU* 5.1 12.4 - - + +
135B GLN* 3.9 18.8 + - - -
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Residues in contact with PHE 45 (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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41B ILE* 2.9 32.2 + - + -
42B ASN* 3.5 20.2 - - - +
43B ALA 3.1 0.4 - - - -
44B ARG* 1.3 75.9 - - + +
46B SER* 1.3 60.2 + - - +
48B SER* 2.8 24.0 + - - -
50B LYS* 3.1 44.5 + - + +
51B PRO 3.4 18.4 - - - +
52B PRO* 4.4 0.9 - - + -
53B ILE* 4.2 20.0 - - + -
65B LYS* 3.7 34.8 - - + -
68B ASP* 4.1 8.1 - - + -
69B LEU* 3.7 37.2 - - + -
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Residues in contact with SER 46 (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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225A GLU* 4.0 10.5 + - - -
42B ASN 2.9 16.5 + - - -
43B ALA* 3.0 13.0 + - - -
45B PHE* 1.3 72.0 - - - +
47B LYS* 1.3 67.7 + - - +
48B SER 2.8 10.2 + - - -
49B GLY* 3.1 12.5 + - - +
50B LYS 3.4 8.4 + - - +
52B PRO* 5.8 3.8 - - - -
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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