Contacts of the helix formed by residues 28 - 40 (chain C) in PDB entry 1C3Q
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 28 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30A ASN* 4.4 4.9 - - - +
301A TZE 3.8 14.1 - - + -
24C THR* 3.4 18.2 - - + +
25C ASN* 3.0 31.3 + - - +
27C VAL* 1.3 86.6 - - + +
29C THR* 1.3 60.2 + - - +
30C ASN 3.4 2.5 - - - -
31C PHE* 3.4 5.5 + - + +
32C THR* 2.9 36.8 + - - +
194C THR* 4.4 2.5 - - - +
195C GLY* 3.4 36.1 - - - +
198C CYS* 3.7 11.9 - - + -
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Residues in contact with THR 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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26B ASN* 2.8 38.2 + - - +
27B VAL* 4.0 12.7 - - - +
24C THR* 3.9 17.7 - - + +
25C ASN 3.3 18.7 + - - +
26C ASN* 4.0 10.1 + - - -
27C VAL 3.9 0.8 - - - -
28C VAL* 1.3 74.8 - - - +
30C ASN* 1.3 65.3 + - - +
32C THR* 3.3 1.9 + - - -
33C ALA* 3.1 23.4 + - - +
45C MET* 3.7 5.9 - - + +
47C TYR* 3.2 26.5 - - + +
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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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30A ASN* 6.0 7.2 - - + -
26B ASN 5.2 0.7 - - - +
27B VAL* 2.9 30.8 + - - +
28B VAL* 4.4 1.4 - - - +
30B ASN* 5.9 7.0 - - + +
31B PHE* 4.1 25.8 - - - +
194B THR* 3.2 20.4 + - - +
245B GLN* 4.7 6.2 - - - +
28C VAL 3.4 0.4 - - - -
29C THR* 1.3 82.1 + - - +
31C PHE* 1.3 64.9 + - - +
33C ALA* 3.4 1.7 + - - +
34C ASN* 3.0 41.0 + - - +
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Residues in contact with PHE 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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30A ASN* 4.2 20.2 - - - +
28C VAL* 3.4 9.0 + - + +
29C THR 3.3 0.4 - - - -
30C ASN* 1.3 82.2 + - - +
32C THR* 1.3 58.0 + - - +
34C ASN* 3.4 2.7 + - - +
35C GLY* 2.8 28.2 + - - -
193C VAL* 4.0 16.2 - - + -
194C THR 3.7 20.6 - - - -
195C GLY* 4.0 20.4 - - - -
196C ALA* 4.2 4.3 - - - -
199C LEU* 3.8 25.1 - - + +
225C TYR* 4.8 0.2 - - - -
245C GLN* 3.8 31.6 - - + -
248C LEU* 4.2 16.2 - - + -
249C LEU* 3.7 28.9 - - + -
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Residues in contact with THR 32 (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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22C SER* 4.1 4.5 - - - +
24C THR* 4.7 4.2 + - + +
28C VAL* 2.9 36.7 + - - +
29C THR* 3.7 4.3 - - - -
31C PHE* 1.3 76.9 - - - +
33C ALA* 1.3 64.5 + - - +
35C GLY 3.3 0.5 + - - -
36C LEU* 3.0 30.4 + - + +
45C MET* 3.7 17.5 - - + -
195C GLY 5.4 0.2 + - - -
198C CYS 4.6 1.0 - - - -
199C LEU* 3.6 22.1 + - + +
202C SER* 3.3 33.3 + - - +
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Residues in contact with ALA 33 (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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27B VAL* 3.9 10.5 - - + -
194B THR* 3.7 24.0 - - - +
303B TZE 4.2 11.9 - - + -
29C THR 3.1 14.2 + - - +
30C ASN 3.8 3.6 - - - +
32C THR* 1.3 80.2 - - - +
34C ASN* 1.3 58.0 + - - +
36C LEU 3.4 0.9 + - - -
37C LEU* 3.0 34.4 + - - +
43C PRO* 3.7 16.4 - - + +
45C MET* 4.2 5.8 - - + -
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Residues in contact with ASN 34 (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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31B PHE* 6.3 0.4 - - - -
192B LYS 3.9 4.7 - - - +
193B VAL* 3.6 9.5 - - - +
194B THR* 2.8 41.7 + - - +
245B GLN* 3.5 24.0 - - - +
30C ASN* 3.0 37.0 + - - +
31C PHE* 3.9 4.5 - - + +
33C ALA* 1.3 76.6 - - - +
35C GLY* 1.3 58.7 + - - +
37C LEU* 3.4 5.0 + - - +
38C ALA* 2.9 30.1 + - - +
249C LEU* 4.1 17.8 - - + +
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Residues in contact with GLY 35 (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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31C PHE 2.8 20.3 + - - -
32C THR 3.8 1.3 - - - -
34C ASN* 1.3 72.5 - - - +
36C LEU* 1.3 57.8 + - - +
38C ALA* 3.4 3.6 + - - +
39C LEU* 3.0 27.5 + - - +
199C LEU* 3.9 20.4 - - - -
203C VAL* 5.6 1.2 - - - +
249C LEU* 3.8 16.1 - - - +
252C LEU* 3.9 10.0 - - - +
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Residues in contact with LEU 36 (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 VAL* 4.1 20.6 - - + +
22C SER* 4.5 3.4 - - - +
32C THR* 3.0 26.5 + - + +
33C ALA 3.8 3.1 - - - +
34C ASN 3.3 0.2 - - - -
35C GLY* 1.3 75.6 - - - +
37C LEU* 1.3 64.2 + - - +
39C LEU* 3.3 6.7 + - + +
40C GLY 3.0 4.9 + - - -
41C ALA* 2.9 44.1 + - + -
43C PRO* 3.8 27.1 - - + -
45C MET* 5.5 0.2 - - + -
199C LEU* 4.5 1.3 - - + -
202C SER* 3.9 42.0 - - - +
203C VAL* 4.3 13.9 - - + +
206C ALA* 4.4 6.3 - - + -
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Residues in contact with LEU 37 (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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191B THR 4.1 14.6 - - - +
192B LYS* 3.7 41.7 + - + +
193B VAL 4.0 0.9 - - - -
194B THR* 3.5 37.7 - - - +
303B TZE 6.3 0.2 - - + -
33C ALA 3.0 21.2 + - - +
34C ASN* 3.7 5.4 - - - +
36C LEU* 1.3 75.5 - - - +
38C ALA* 1.3 65.2 + - - +
40C GLY* 3.1 14.0 + - - -
41C ALA 3.9 7.2 - - - +
42C SER* 5.3 0.4 - - - -
43C PRO* 3.6 25.1 - - + -
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Residues in contact with ALA 38 (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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192B LYS* 5.0 4.0 + - - +
241B PRO* 3.9 19.5 - - + -
34C ASN 2.9 18.7 + - - +
35C GLY* 3.6 7.4 - - - +
37C LEU* 1.3 76.9 - - - +
39C LEU* 1.3 62.4 + - - +
40C GLY* 3.3 0.7 + - - -
249C LEU* 3.3 29.6 - - + +
252C LEU* 4.0 5.8 - - + -
253C SER* 3.1 27.8 - - - -
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Residues in contact with LEU 39 (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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10C LEU* 3.8 27.6 - - + -
13C VAL* 4.0 22.1 - - + +
14C ARG* 2.8 31.9 + - - +
35C GLY 3.0 17.7 + - - +
36C LEU* 3.5 9.9 - - + +
37C LEU 3.2 0.2 - - - -
38C ALA* 1.3 77.1 - - - +
40C GLY* 1.3 58.4 + - - +
41C ALA* 4.7 2.0 - - + +
203C VAL* 4.0 32.1 - - + -
206C ALA* 4.3 13.7 - - + -
207C PHE* 4.3 6.3 - - + -
224C SER* 6.1 1.1 - - - -
252C LEU* 3.4 28.9 + - + +
255C VAL* 5.7 1.1 - - + -
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Residues in contact with GLY 40 (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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192B LYS* 5.1 7.6 - - - -
13C VAL* 3.8 8.6 - - - +
14C ARG* 4.5 10.5 - - - +
17C SER* 3.2 28.3 + - - -
36C LEU 3.0 2.4 + - - -
37C LEU 3.1 11.6 + - - -
38C ALA 4.3 0.9 - - - -
39C LEU* 1.3 79.5 - - - +
41C ALA* 1.3 62.4 + - - +
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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