Contacts of the helix formed by residues 9 - 27 (chain D) in PDB entry 4QPQ
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 9 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ALA* 4.9 0.2 - - - -
44A GLU* 3.6 15.5 + - - -
8D ILE* 1.3 82.3 - - - +
10D ASN* 1.3 63.5 + - - +
11D ASP* 3.7 10.5 + - - +
12D ALA* 3.1 24.7 + - - +
13D TYR* 3.0 20.0 + - - +
20Q T 5.6 1.1 - - - -
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Residues in contact with ASN 10 (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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2A ALA* 4.1 20.4 + - - +
9D SER* 1.3 74.1 - - - +
11D ASP* 1.3 63.2 + - - +
13D TYR* 3.5 8.3 + - + +
14D GLU* 3.0 39.1 + - + +
19Q C 5.5 4.2 + - - -
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Residues in contact with ASP 11 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D SER* 3.2 9.5 + - - +
10D ASN* 1.3 77.0 - - - +
12D ALA* 1.3 59.7 + - - +
14D GLU* 3.3 11.8 + - - +
15D LYS* 3.0 48.6 + - - +
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Residues in contact with ALA 12 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43A LEU* 5.7 2.2 - - + -
44A GLU* 4.4 13.7 - - + -
47A LEU* 4.0 23.3 - - + +
8D ILE* 4.2 17.7 - - + -
9D SER* 3.1 20.3 + - - +
11D ASP* 1.3 79.2 - - - +
13D TYR* 1.3 62.0 + - - +
15D LYS* 3.4 4.6 + - - +
16D ILE* 3.0 31.2 + - + +
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Residues in contact with TYR 13 (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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2A ALA* 4.3 15.0 - - + -
3A LYS 5.5 2.0 - - - -
4A VAL* 4.1 17.5 - - + -
8D ILE* 3.8 10.5 - - + +
9D SER 3.0 16.0 + - - +
10D ASN* 3.6 9.2 - - - +
11D ASP 3.2 0.2 - - - -
12D ALA* 1.3 77.1 - - - +
14D GLU* 1.3 71.8 + - + +
16D ILE* 3.4 5.6 + - - +
17D ASN* 3.2 44.3 + - - -
35D PHE* 3.6 31.8 - + - -
4P C 4.9 11.2 + - - -
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Residues in contact with GLU 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10D ASN* 3.0 29.0 + - + +
11D ASP* 3.9 11.6 - - - +
13D TYR* 1.3 83.0 - - + +
15D LYS* 1.3 61.9 + - + +
17D ASN* 3.4 8.5 + - - +
18D ALA* 2.8 28.6 + - - +
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Residues in contact with LYS 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.3 21.1 - - + +
48A ARG* 6.4 0.6 - - - +
51A GLU* 3.7 23.8 + - - +
11D ASP* 3.0 33.7 + - - +
12D ALA* 3.7 7.4 - - - +
14D GLU* 1.3 76.3 - - + +
16D ILE* 1.3 63.6 + - - +
18D ALA* 3.3 9.5 + - - +
19D ILE* 3.1 28.7 + - - +
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Residues in contact with ILE 16 (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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43A LEU* 3.8 30.1 - - + -
47A LEU* 4.7 3.4 - - + -
8D ILE* 4.3 8.1 - - + -
12D ALA* 3.0 19.1 + - + +
13D TYR 3.7 4.3 - - - +
15D LYS* 1.3 74.3 - - - +
17D ASN* 1.3 63.5 + - - +
19D ILE* 3.1 19.5 + - + +
20D ILE* 3.1 14.5 + - + +
35D PHE* 3.6 36.8 - - + -
38D THR* 3.7 22.2 - - - +
39D ALA* 4.0 15.9 - - + +
42D LEU* 4.1 15.9 - - + -
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Residues in contact with ASN 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D TYR* 3.2 47.5 + - - -
14D GLU* 3.7 10.7 - - - +
16D ILE* 1.3 78.9 - - - +
18D ALA* 1.3 63.1 + - - +
20D ILE* 3.3 10.9 + - - +
21D GLU* 3.0 38.9 + - + +
35D PHE* 3.4 21.7 - - - -
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Residues in contact with ALA 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D GLU 2.8 19.0 + - - +
15D LYS* 3.3 11.4 - - - +
17D ASN* 1.3 76.8 - - - +
19D ILE* 1.3 63.4 + - + +
21D GLU* 3.6 11.5 + - - +
22D LYS* 3.2 38.5 + - - +
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Residues in contact with ILE 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47A LEU* 4.3 9.4 - - + -
50A HIS* 3.8 32.1 - - + +
15D LYS 3.1 16.2 + - - +
16D ILE* 3.1 9.1 + - + +
18D ALA* 1.3 76.5 - - + +
20D ILE* 1.3 62.1 + - + +
22D LYS* 3.0 19.4 + - + +
23D ARG* 2.9 58.3 + - + +
38D THR* 5.2 9.4 - - - -
41D MET* 5.6 2.7 - - + -
42D LEU* 4.1 27.8 - - + -
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Residues in contact with ILE 20 (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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16D ILE 3.1 14.6 + - - +
17D ASN* 3.3 12.3 + - - +
19D ILE* 1.3 75.6 - - - +
21D GLU* 1.3 58.4 + - + +
23D ARG* 3.2 7.6 + - - +
24D ARG* 2.9 46.7 + - + +
33D VAL* 3.3 21.1 - - + +
34D SER 3.9 2.5 - - - +
35D PHE* 3.7 36.8 - - + +
38D THR* 3.6 31.4 - - + +
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Residues in contact with GLU 21 (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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17D ASN* 3.0 29.4 + - + +
18D ALA* 3.9 9.6 - - - +
20D ILE* 1.3 77.7 - - + +
22D LYS* 1.3 60.2 + - + +
24D ARG* 4.0 6.3 - - - +
25D GLN* 3.2 30.9 + - - +
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Residues in contact with LYS 22 (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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18D ALA* 3.2 26.2 + - - +
19D ILE* 3.0 19.6 + - + +
21D GLU* 1.3 76.9 - - + +
23D ARG* 1.3 60.6 + - + +
25D GLN* 3.1 8.0 + - - +
26D GLU* 2.8 45.2 + - + +
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Residues in contact with ARG 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A HIS* 3.7 27.5 - - - -
19D ILE* 2.9 35.3 + - + +
20D ILE* 3.6 8.3 - - - +
22D LYS* 1.3 77.2 - - - +
24D ARG* 1.3 54.7 + - - +
26D GLU* 4.1 17.2 + - - -
27D GLY 2.7 31.5 + - - -
28D ALA* 3.2 10.1 - - + +
33D VAL* 3.9 27.3 - - + +
38D THR* 5.3 5.5 - - + +
41D MET* 3.9 21.0 - - - +
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Residues in contact with ARG 24 (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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20D ILE* 2.9 29.9 + - + +
21D GLU* 4.4 5.6 - - - +
23D ARG* 1.3 75.5 - - - +
25D GLN* 1.3 57.5 + - - +
27D GLY 3.1 13.6 - - - +
28D ALA* 3.7 13.2 + - + +
30D GLU* 4.2 12.9 - - - +
31D LYS* 3.1 34.1 - - - +
33D VAL* 3.7 27.5 + - + +
34D SER* 5.8 1.4 - - - +
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Residues in contact with GLN 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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21D GLU* 3.2 22.7 + - - +
22D LYS* 3.1 8.4 + - - +
23D ARG 3.0 1.0 - - - -
24D ARG* 1.3 79.1 - - - +
26D GLU* 1.3 67.0 + - + +
27D GLY 3.6 2.6 - - - +
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Residues in contact with GLU 26 (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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22D LYS* 2.8 27.3 + - - +
23D ARG* 3.9 22.1 + - - +
25D GLN* 1.3 76.3 - - + +
27D GLY* 1.3 65.9 + - - +
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Residues in contact with GLY 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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23D ARG 2.7 13.7 + - - -
24D ARG 3.1 13.9 - - - +
25D GLN 3.6 3.3 - - - +
26D GLU* 1.3 80.5 - - - +
28D ALA* 1.3 62.1 + - - -
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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