Contacts of the helix formed by residues 18 - 31 (chain D) in PDB entry 3Q37
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 18 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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86C ASP* 3.5 25.6 - - - -
17D GLY* 1.3 73.9 - - - -
19D GLN* 1.3 66.3 + - - +
20D GLN* 3.5 8.5 + - - +
21D SER* 2.9 28.3 + - - -
22D LEU* 2.9 24.2 + - - +
48D HIS* 4.4 4.9 - - - -
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Residues in contact with GLN 19 (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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86C ASP* 2.9 42.7 + - - +
87C TYR* 3.7 34.7 + - + -
18D SER* 1.3 70.7 - - - +
20D GLN* 1.3 63.4 + - - +
22D LEU* 4.0 1.0 - - - +
23D SER* 3.0 25.3 + - - -
48D HIS* 4.5 1.0 + - + -
51D MET* 3.2 34.5 - - + +
55D ARG* 5.4 3.0 - - - +
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Residues in contact with GLN 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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86C ASP* 5.3 1.0 + - - +
18D SER* 3.1 8.1 + - - +
19D GLN* 1.3 77.3 - - - +
21D SER* 1.3 65.9 + - - +
23D SER* 2.6 26.6 + - - -
24D GLU* 2.8 41.6 + - - +
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Residues in contact with SER 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 GLY* 3.7 7.6 - - - -
18D SER* 2.9 36.5 + - - -
20D GLN* 1.3 77.9 - - - +
22D LEU* 1.3 64.1 + - - +
24D GLU* 3.5 15.7 + - - +
25D LEU* 3.3 25.2 + - - +
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Residues in contact with LEU 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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13D TRP* 3.6 47.5 - - + -
16D ASN 4.3 1.6 - - - +
17D GLY* 3.9 16.6 - - - -
18D SER 2.9 16.6 + - - +
19D GLN 4.3 1.6 - - - +
21D SER* 1.3 78.0 - - - +
23D SER* 1.3 66.7 + - - +
25D LEU* 3.2 16.6 + - + +
26D ILE* 2.9 34.0 + - + +
48D HIS* 3.4 47.1 - - + +
51D MET* 4.6 9.0 - - - -
52D THR* 5.2 0.4 - - - +
239D LEU* 4.3 5.6 - - + -
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Residues in contact with SER 23 (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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19D GLN 3.0 16.9 + - - -
20D GLN* 2.6 31.0 + - - -
22D LEU* 1.3 76.4 - - - +
24D GLU* 1.3 58.0 + - - +
26D ILE* 3.4 6.1 + - - +
27D ASP* 3.0 40.1 + - - +
51D MET* 5.4 1.0 - - - -
55D ARG* 3.8 36.5 + - - +
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Residues in contact with GLU 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 GLN* 2.8 46.1 + - - +
21D SER* 3.7 15.9 - - - +
22D LEU 3.2 0.2 - - - -
23D SER* 1.3 81.5 + - - +
25D LEU* 1.3 63.2 + - + +
27D ASP* 3.5 9.9 + - - +
28D LEU* 3.1 20.1 + - - +
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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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13D TRP* 4.0 27.8 - - + +
21D SER* 3.3 9.5 + - - +
22D LEU* 3.2 22.9 + - + +
24D GLU* 1.3 75.9 - - + +
26D ILE* 1.3 61.4 + - - +
28D LEU* 3.1 15.7 + - + +
29D PHE* 2.9 39.6 + - + -
238D SER 4.5 3.1 - - - +
239D LEU* 3.6 46.4 - - + +
240D LYS* 3.9 17.7 - - - +
241D PRO* 4.3 5.8 - - + -
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Residues in contact with ILE 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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13D TRP* 4.3 14.8 - - + -
22D LEU* 2.9 27.3 + - + +
23D SER* 3.8 4.3 - - - +
25D LEU* 1.3 75.0 - - - +
27D ASP* 1.3 60.0 + - - +
29D PHE* 3.1 12.6 + - + +
30D ASN* 2.8 44.6 + - - +
51D MET* 4.4 2.9 - - + +
52D THR* 3.8 39.9 - - + +
55D ARG* 3.8 39.3 - - + -
56D LEU* 3.8 11.9 - - + +
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Residues in contact with ASP 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 SER* 3.0 28.8 + - - +
24D GLU* 3.6 9.7 - - - +
25D LEU 3.2 0.2 - - - -
26D ILE* 1.3 78.0 - - - +
28D LEU* 1.3 59.3 + - - +
30D ASN* 3.3 12.8 + - - +
31D SER* 2.8 28.1 + - - -
55D ARG* 5.6 4.2 + - - +
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Residues in contact with LEU 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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24D GLU 3.1 13.6 + - - +
25D LEU* 3.1 15.8 + - + +
27D ASP* 1.3 75.9 - - - +
29D PHE* 1.3 65.8 + - + +
31D SER* 3.2 10.4 + - - +
32D THR* 2.6 43.0 + - - +
241D PRO* 3.4 45.8 - - + +
244D VAL* 4.1 19.7 - - + -
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Residues in contact with PHE 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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11D ALA* 5.2 0.2 - - + -
13D TRP* 3.9 22.9 - + - -
25D LEU* 2.9 26.9 + - + -
26D ILE* 3.1 14.3 + - + +
28D LEU* 1.3 83.1 - - + +
30D ASN* 1.3 62.8 + - - +
31D SER 3.3 0.7 + - - -
32D THR* 3.3 10.5 + - - -
42D VAL* 3.5 25.6 - - + -
56D LEU* 4.1 15.3 - - + -
58D ASN* 2.8 26.4 + - - -
61D PHE* 3.6 28.3 - + + -
238D SER 4.5 8.7 - - - -
243D PHE* 3.9 32.5 - + + -
244D VAL* 3.9 19.3 - - + -
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Residues in contact with ASN 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 ILE* 2.8 25.1 + - - +
27D ASP* 3.7 12.6 + - - +
28D LEU 3.3 0.4 - - - -
29D PHE* 1.3 75.7 - - - +
31D SER* 1.3 58.3 + - - +
32D THR 3.4 2.1 + - - +
55D ARG* 3.0 24.2 + - - +
56D LEU* 3.6 8.3 - - - +
57D THR* 2.8 39.3 + - - +
58D ASN* 3.2 15.4 + - - +
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Residues in contact with SER 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 ASP 2.8 19.2 + - - -
28D LEU* 3.2 13.8 + - - +
30D ASN* 1.3 76.3 - - - +
32D THR* 1.3 59.3 + - - +
33D SER* 3.8 4.0 + - - -
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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