Contacts of the helix formed by residues 12 - 30 (chain C) in PDB entry 3C6Q
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 HIS 12 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C SER* 3.5 16.8 + - - +
11C VAL* 1.3 77.3 - - - +
13C PRO* 1.3 90.0 - - + +
14C TYR* 2.9 28.6 + - + +
15C TRP* 2.9 22.6 + - + +
16C SER* 3.2 12.7 + - - -
37C VAL* 5.4 0.2 - - - +
191C ALA* 3.4 36.6 + - + +
192C TYR* 3.2 39.5 + + + +
195C PRO* 5.9 0.6 - - - +
218C THR* 4.1 12.6 - - + -
220C ASP* 5.5 4.4 + - - -
500C XYP 5.8 1.6 - - - -
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Residues in contact with PRO 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C HIS* 1.3 107.1 - - + +
14C TYR* 1.3 61.4 + - - +
16C SER* 3.1 13.7 + - - +
17C GLN* 3.1 25.3 + - - +
218C THR* 4.1 15.3 - - + -
219C PRO* 4.9 8.3 - - + -
220C ASP* 5.3 5.4 - - - +
304C LYS* 6.4 2.5 - - + -
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Residues in contact with TYR 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C HIS* 2.9 20.8 + - + +
13C PRO* 1.3 76.4 - - - +
15C TRP* 1.3 91.6 + + - +
17C GLN* 3.1 28.9 - - - +
18C VAL* 3.2 11.9 + - + +
89C ASP* 2.5 30.6 + - - +
191C ALA* 4.0 10.8 - - + -
216C ASP* 3.8 27.8 - - + -
218C THR* 4.0 6.2 - - + +
236C GLN* 3.8 5.2 + - - -
238C PRO* 3.3 35.7 - - + -
241C MET* 3.5 22.5 - - - +
500C XYP 3.7 24.8 + - - -
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Residues in contact with TRP 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 6.0 0.7 - - + -
7C ILE 4.9 0.4 - - - -
8C GLY* 3.6 17.9 - - - -
9C LYS* 3.4 25.1 - - + -
10C SER* 3.2 38.6 + - - +
12C HIS* 2.9 14.4 + - + +
14C TYR* 1.3 87.2 - + - +
16C SER* 1.3 55.1 + - - +
18C VAL* 3.0 38.2 + - + +
19C GLU* 2.7 35.2 + - - +
35C PHE* 3.6 8.2 - + + -
37C VAL* 4.0 12.1 - - + -
64C ALA* 3.6 26.0 - - + -
88C LEU* 4.9 7.9 - - + -
89C ASP* 3.6 26.9 - - + -
500C XYP 2.6 25.7 + - - -
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Residues in contact with SER 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C HIS 3.2 11.4 + - - -
13C PRO* 3.1 17.2 + - - +
15C TRP* 1.3 76.4 - - - +
17C GLN* 1.3 57.8 + - - +
19C GLU* 3.5 14.4 + - - +
20C GLN* 2.8 36.4 + - - +
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Residues in contact with GLN 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13C PRO* 3.1 16.1 + - - +
14C TYR* 3.1 18.4 - - - +
16C SER* 1.3 77.4 - - - +
18C VAL* 1.3 59.3 + - - +
20C GLN* 3.4 11.9 - - - +
21C GLY 3.1 15.8 + - - -
217C THR* 4.6 9.8 + - - -
218C THR* 4.0 28.0 + - - +
219C PRO* 4.9 4.8 - - - +
238C PRO* 3.1 30.5 - - + +
239C TYR* 3.5 18.6 - - + +
302C PRO 5.0 11.1 + - - +
303C ILE* 5.0 12.0 - - - +
304C LYS* 5.5 8.6 - - + +
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Residues in contact with VAL 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TYR* 3.6 16.6 - - + +
15C TRP* 3.0 42.8 + - + +
17C GLN* 1.3 77.8 - - - +
19C GLU* 1.3 56.1 + - - +
21C GLY* 2.8 18.9 + - - -
22C VAL* 2.9 15.5 + - + +
35C PHE* 4.1 11.0 - - + -
88C LEU* 4.3 11.4 - - + -
238C PRO* 3.5 34.8 - - + +
241C MET* 5.2 3.6 - - + -
242C GLY* 3.7 17.0 - - - -
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Residues in contact with GLU 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C TRP 2.7 13.0 + - - +
16C SER* 3.1 14.9 + - - +
18C VAL* 1.3 72.7 - - - +
20C GLN* 1.3 54.2 + - - +
22C VAL* 3.0 11.9 + - - +
23C LYS* 2.6 57.6 + - + +
35C PHE* 3.2 49.9 - - + +
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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
----------------------------------------------------------
16C SER* 2.8 19.9 + - - +
17C GLN* 3.4 12.2 - - - +
19C GLU* 1.3 76.4 - - - +
21C GLY* 1.3 56.2 + - - +
23C LYS* 3.8 26.2 + - - +
24C ALA* 3.1 30.0 + - + +
239C TYR* 3.8 13.5 - - + -
302C PRO* 3.4 30.8 + - + +
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Residues in contact with GLY 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C GLN 3.1 4.8 + - - -
18C VAL 2.8 10.3 + - - -
20C GLN* 1.3 75.4 - - - +
22C VAL* 1.3 65.3 + - - -
24C ALA* 3.1 2.9 + - - +
25C ALA* 2.9 24.4 + - - +
239C TYR* 3.4 35.1 - - - -
243C TYR* 3.7 11.2 - - - -
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Residues in contact with VAL 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 3.5 35.0 - - + -
18C VAL* 2.9 24.5 + - + +
19C GLU* 3.2 13.5 - - - +
21C GLY* 1.3 69.0 - - - +
23C LYS* 1.3 64.8 + - + +
25C ALA* 3.6 2.1 - - - +
26C GLY* 3.0 21.8 + - - -
33C THR* 3.7 25.7 - - - +
35C PHE* 4.0 23.3 - - + -
242C GLY* 3.7 15.6 - - - +
246C VAL* 3.8 14.1 - - + +
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Residues in contact with LYS 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C GLU* 2.6 44.8 + - + +
20C GLN* 3.8 31.1 + - - +
22C VAL* 1.3 75.8 - - + +
24C ALA* 1.3 63.5 + - - +
26C GLY* 3.3 0.7 + - - -
27C LYS* 2.9 25.1 + - - +
33C THR* 4.5 11.4 - - - +
35C PHE* 6.3 0.4 - - + -
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C GLN* 3.1 16.0 + - + +
21C GLY 3.1 3.9 + - - +
23C LYS* 1.3 78.3 - - - +
25C ALA* 1.3 65.2 + - - +
27C LYS* 3.5 8.6 + - - +
28C ALA* 3.1 21.0 + - - +
239C TYR* 3.5 24.2 - - + +
243C TYR* 3.9 7.3 - - + -
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Residues in contact with ALA 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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21C GLY 2.9 16.4 + - - +
22C VAL 3.6 3.6 - - - +
24C ALA* 1.3 74.7 - - - +
26C GLY* 1.3 55.8 + - - +
28C ALA* 2.8 26.0 + - - +
29C LEU* 3.0 16.3 + - + +
243C TYR* 3.4 48.8 - - + +
246C VAL* 3.7 15.7 - - + -
247C THR* 4.4 2.2 - - - +
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Residues in contact with GLY 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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22C VAL 3.0 11.3 + - - -
23C LYS 3.7 2.7 - - - -
25C ALA* 1.3 78.7 - - - +
27C LYS* 1.3 54.3 + - - +
30C GLY* 3.0 25.3 + - - -
31C VAL* 3.1 38.9 + - - +
33C THR* 4.0 9.6 - - - -
246C VAL* 4.0 1.9 - - - +
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Residues in contact with LYS 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 LYS 2.9 20.8 + - - +
24C ALA* 3.7 7.9 - - - +
26C GLY* 1.3 73.7 - - - +
28C ALA* 1.3 61.8 + - - +
29C LEU 3.3 0.3 + - - -
30C GLY* 3.5 7.6 + - - -
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Residues in contact with ALA 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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254B LYS* 3.6 38.1 + - - +
255B ILE* 4.2 4.0 - - + -
24C ALA 3.1 8.7 + - - +
25C ALA 2.8 15.1 + - - +
27C LYS* 1.3 73.9 - - - +
29C LEU* 1.3 58.7 + - - +
243C TYR* 3.5 23.3 - - - +
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Residues in contact with LEU 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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250B TYR* 5.3 2.0 + - + +
251B LEU* 4.8 8.7 - - + -
254B LYS* 4.2 22.5 + - + -
255B ILE* 4.0 20.9 - - + -
25C ALA 3.0 11.2 + - - +
28C ALA* 1.3 77.9 - - - +
30C GLY* 1.3 64.6 + - - +
31C VAL* 3.8 13.5 - - + -
246C VAL* 4.4 10.8 - - + -
247C THR* 3.9 26.2 - - + +
250C TYR* 3.5 66.4 + - + -
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Residues in contact with GLY 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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1C MET* 4.3 24.4 - - - +
2C LEU* 5.1 1.2 + - - +
26C GLY 3.0 6.8 + - - -
27C LYS 3.5 6.2 + - - -
28C ALA 3.5 2.4 - - - -
29C LEU* 1.3 80.8 - - - +
31C VAL* 1.3 61.3 + - - +
250C TYR* 4.8 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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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