Contacts of the helix formed by residues 18 - 31 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C GLY* 1.3 73.9 - - - -
19C GLN* 1.3 66.0 + - - +
20C GLN* 2.9 33.4 + - - -
21C SER* 2.9 15.6 + - - -
22C LEU* 3.0 24.8 + - - +
48C HIS* 4.4 5.4 - - - -
86D ASP* 3.5 24.9 - - - -
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Residues in contact with GLN 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C SER* 1.3 71.4 - - - +
20C GLN* 1.3 63.1 + - - +
23C SER* 2.9 31.7 + - - +
48C HIS* 4.6 1.2 + - + -
51C MET* 3.6 18.0 - - + +
86D ASP* 2.9 36.0 + - - +
87D TYR* 3.5 52.0 + - + -
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Residues in contact with GLN 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C SER* 2.9 24.9 + - - +
19C GLN* 1.3 81.9 - - + +
21C SER* 1.3 78.8 + - - +
23C SER* 3.5 4.7 + - - -
24C GLU* 3.2 31.5 + - - +
86D ASP* 4.7 5.5 - - - +
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Residues in contact with SER 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C GLY* 3.8 6.4 - - - -
18C SER* 2.9 37.3 + - - -
20C GLN* 1.3 87.7 - - - +
22C LEU* 1.3 66.2 + - - +
24C GLU* 3.4 11.8 + - - +
25C LEU* 3.2 19.8 + - - +
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Residues in contact with LEU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C TRP* 3.8 41.9 - - + -
16C ASN 4.2 1.1 - - - +
17C GLY* 3.8 19.3 - - - -
18C SER 3.0 14.5 + - - +
21C SER* 1.3 82.2 + - - +
23C SER* 1.3 61.1 + - - +
25C LEU* 3.2 8.2 + - + +
26C ILE* 2.8 36.2 + - + +
48C HIS* 3.3 50.0 - - + +
51C MET* 4.1 11.0 - - + -
52C THR* 5.5 0.2 - - - +
239C LEU* 4.2 13.7 - - + -
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Residues in contact with SER 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C GLN* 2.9 23.0 + - - +
20C GLN* 3.8 5.4 - - - -
22C LEU* 1.3 74.5 - - - +
24C GLU* 1.3 59.8 + - - +
26C ILE* 3.3 1.3 + - - -
27C ASP* 2.9 29.5 + - - -
51C MET* 3.2 16.5 - - - +
55C ARG* 3.2 34.3 + - - +
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Residues in contact with GLU 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20C GLN* 3.2 18.6 + - - +
21C SER* 3.6 12.4 - - - +
23C SER* 1.3 77.4 - - - +
25C LEU* 1.3 62.9 + - - +
27C ASP* 3.3 12.7 + - - +
28C LEU* 3.2 20.1 + - - +
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Residues in contact with LEU 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C TRP* 3.4 31.6 - - + +
21C SER 3.2 9.8 + - - +
22C LEU* 3.2 13.5 + - + +
24C GLU* 1.3 78.0 - - - +
26C ILE* 1.3 63.8 + - - +
28C LEU* 3.1 10.9 + - + +
29C PHE* 3.0 41.8 + - + -
238C SER 3.5 18.4 - - - +
239C LEU* 3.7 32.1 - - + +
240C LYS* 3.9 17.3 - - - +
241C PRO* 4.3 7.2 - - + -
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Residues in contact with ILE 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13C TRP* 4.2 14.8 - - + -
22C LEU* 2.8 23.0 + - + +
23C SER* 3.3 6.3 + - - +
25C LEU* 1.3 73.1 - - - +
27C ASP* 1.3 61.0 + - - +
29C PHE* 3.3 10.0 + - + +
30C ASN* 2.9 30.8 + - - +
51C MET* 4.0 17.7 - - + -
52C THR* 3.9 39.3 - - + +
55C ARG* 3.9 21.5 - - + +
56C LEU* 3.9 36.1 - - + +
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Residues in contact with ASP 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C SER* 2.9 18.9 + - - +
24C GLU* 3.4 13.9 - - - +
25C LEU 3.2 0.2 - - - -
26C ILE* 1.3 79.0 - - - +
28C LEU* 1.3 60.8 + - - +
30C ASN* 3.4 10.1 + - - +
31C SER* 3.3 22.7 + - - -
55C ARG* 2.5 33.9 + - - -
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C GLU 3.2 8.5 + - - +
25C LEU* 3.1 12.9 + - + +
27C ASP* 1.3 78.8 - - - +
29C PHE* 1.3 66.0 + - + +
31C SER* 3.1 19.0 + - - +
32C THR* 2.7 33.9 + - - +
241C PRO* 3.6 40.2 - - + -
244C VAL* 4.1 16.4 - - + -
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Residues in contact with PHE 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ALA* 5.4 0.2 - - + -
13C TRP* 4.0 15.5 - + - -
25C LEU* 3.0 45.0 + - + -
26C ILE* 3.7 11.0 - - + +
28C LEU* 1.3 82.8 - - + +
30C ASN* 1.3 61.9 + - - +
32C THR* 3.2 11.0 + - - +
42C VAL* 3.6 24.9 - - + -
56C LEU* 4.0 18.2 - - + -
58C ASN* 2.8 27.3 + - - +
61C PHE* 3.6 29.2 - + + -
238C SER 4.4 5.8 - - - -
240C LYS 5.1 0.7 - - - -
243C PHE* 3.8 32.3 - + + -
244C VAL* 4.8 12.8 - - + -
247C ILE* 5.7 1.1 - - + -
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Residues in contact with ASN 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C ILE* 2.9 23.8 + - - +
27C ASP* 3.6 14.6 + - - +
28C LEU 3.2 0.4 - - - -
29C PHE* 1.3 77.1 - - - +
31C SER* 1.3 58.7 + - - +
32C THR 3.4 1.9 + - - +
55C ARG* 2.9 26.8 + - - +
56C LEU* 3.5 8.3 - - - +
57C THR* 2.7 42.6 + - - +
58C ASN* 3.4 13.8 + - - +
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Residues in contact with SER 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ASP 3.3 11.5 + - - -
28C LEU* 3.1 20.6 + - - +
30C ASN* 1.3 77.6 - - - +
32C THR* 1.3 60.1 + - - +
33C SER* 3.6 6.6 + - - -
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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