Contacts of the helix formed by residues 12 - 30 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D SER* 3.5 17.2 + - - +
11D VAL* 1.3 77.5 - - - +
13D PRO* 1.3 89.3 - - + +
14D TYR* 2.9 28.2 + - + +
15D TRP* 2.9 22.4 + - + +
16D SER* 3.2 12.9 + - - -
37D VAL* 5.4 0.2 - - - +
191D ALA* 3.4 36.4 + - + +
192D TYR* 3.2 39.7 + + + +
195D PRO* 5.9 0.6 - - - +
218D THR* 4.1 12.8 - - + -
220D ASP* 5.5 4.4 + - - -
501D XYP 5.7 1.3 - - - -
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Residues in contact with PRO 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D HIS* 1.3 107.3 - - + +
14D TYR* 1.3 61.6 + - - +
16D SER* 3.1 13.7 + - - +
17D GLN* 3.1 25.3 + - - +
218D THR* 4.1 15.5 - - + -
219D PRO* 4.9 8.3 - - + -
220D ASP* 5.3 5.2 - - - +
304D LYS* 6.5 2.0 - - + -
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Residues in contact with TYR 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D HIS* 2.9 20.6 + - + +
13D PRO* 1.3 77.5 - - - +
15D TRP* 1.3 91.2 + + - +
17D GLN* 3.1 28.6 - - - +
18D VAL* 3.2 12.7 + - + +
89D ASP* 2.6 29.7 + - - +
191D ALA* 4.0 10.8 - - + -
216D ASP* 3.8 27.8 - - + -
218D THR* 4.1 6.2 - - + +
236D GLN* 3.8 4.9 + - - -
238D PRO* 3.3 34.8 - - + -
241D MET* 3.5 23.7 - - - +
501D XYP 3.7 24.2 + - - -
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Residues in contact with TRP 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D VAL* 6.1 0.4 - - + -
7D ILE 4.9 0.7 - - - -
8D GLY* 3.6 18.2 - - - -
9D LYS* 3.4 20.4 - - + -
10D SER* 3.2 38.4 + - - +
12D HIS* 2.9 14.4 + - + +
14D TYR* 1.3 87.5 - + - +
16D SER* 1.3 55.4 + - - +
18D VAL* 3.0 38.8 + - + +
19D GLU* 2.7 34.7 + - - +
35D PHE* 3.6 8.2 - + + -
37D VAL* 4.0 12.3 - - + -
64D ALA* 3.6 26.2 - - + -
88D LEU* 4.9 7.6 - - + -
89D ASP* 3.6 26.0 - - + -
501D XYP 2.8 29.0 + - - -
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Residues in contact with SER 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D HIS 3.2 11.2 + - - -
13D PRO* 3.1 17.2 + - - +
15D TRP* 1.3 75.8 - - - +
17D GLN* 1.3 57.1 + - - +
19D GLU* 3.5 15.5 + - - +
20D GLN* 2.8 36.2 + - - +
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Residues in contact with GLN 17 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13D PRO* 3.1 16.5 + - - +
14D TYR* 3.1 18.2 - - - +
16D SER* 1.3 76.7 - - - +
18D VAL* 1.3 58.4 + - - +
20D GLN* 3.4 11.8 - - - +
21D GLY 3.2 15.4 + - - -
216D ASP* 6.2 0.2 - - - +
217D THR* 4.6 9.6 + - - -
218D THR* 4.0 28.4 + - - +
219D PRO* 4.9 4.8 - - - +
238D PRO* 3.2 30.3 - - + +
239D TYR* 3.4 18.6 - - + +
302D PRO 5.1 11.1 + - - +
303D ILE* 5.0 12.0 - - - +
304D LYS* 5.5 8.6 - - + +
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Residues in contact with VAL 18 (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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14D TYR* 3.6 16.2 - - + +
15D TRP* 3.0 42.6 + - + +
17D GLN* 1.3 78.0 - - - +
19D GLU* 1.3 56.8 + - - +
21D GLY* 2.9 18.2 + - - -
22D VAL* 2.9 16.1 + - + +
35D PHE* 4.0 11.2 - - + -
88D LEU* 4.3 11.4 - - + -
238D PRO* 3.5 34.1 - - + +
241D MET* 5.2 4.0 - - + -
242D GLY* 3.7 16.9 - - - -
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Residues in contact with GLU 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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15D TRP 2.7 12.8 + - - +
16D SER* 3.2 15.4 + - - +
18D VAL* 1.3 72.2 - - - +
20D GLN* 1.3 52.9 + - - +
22D VAL* 3.0 12.3 + - - +
23D LYS* 2.7 57.4 + - + +
35D PHE* 3.2 50.1 - - + +
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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
----------------------------------------------------------
16D SER* 2.8 18.6 + - - +
17D GLN* 3.4 12.0 - - - +
19D GLU* 1.3 76.6 - - - +
21D GLY* 1.3 59.9 + - - +
23D LYS* 3.8 25.7 + - - +
24D ALA* 3.1 25.9 + - + +
239D TYR* 3.8 13.3 - - + -
302D PRO* 3.4 30.6 + - + +
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Residues in contact with GLY 21 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D GLN 3.2 7.3 + - - -
18D VAL 2.9 10.1 + - - -
20D GLN* 1.3 73.4 - - - +
22D VAL* 1.3 65.5 + - - -
24D ALA* 3.1 2.9 + - - +
25D ALA* 2.8 24.8 + - - +
239D TYR* 3.4 34.2 - - - -
243D TYR* 3.7 11.3 - - - -
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Residues in contact with VAL 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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6D VAL* 3.5 35.0 - - + -
18D VAL* 2.9 24.9 + - + +
19D GLU* 3.2 14.1 - - - +
21D GLY* 1.3 69.0 - - - +
23D LYS* 1.3 64.2 + - + +
25D ALA* 3.6 1.9 - - - +
26D GLY* 3.0 21.7 + - - -
33D THR* 3.7 24.2 - - - +
35D PHE* 3.9 24.2 - - + -
242D GLY* 3.7 15.7 - - - +
246D VAL* 3.8 15.6 - - + +
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Residues in contact with LYS 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 GLU* 2.7 45.2 + - + +
20D GLN* 3.8 31.1 + - - +
22D VAL* 1.3 74.0 - - + +
24D ALA* 1.3 57.6 + - - +
25D ALA 3.2 0.2 + - - -
26D GLY* 3.3 2.1 + - - -
27D LYS* 2.9 31.2 + - - +
33D THR* 4.5 11.2 - - - +
35D PHE* 6.3 0.4 - - + -
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Residues in contact with ALA 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* 3.1 16.2 + - + +
21D GLY 3.1 3.9 + - - +
23D LYS* 1.3 78.5 - - - +
25D ALA* 1.3 64.4 + - - +
27D LYS* 3.5 8.0 + - - +
28D ALA* 3.1 20.4 + - - +
239D TYR* 3.5 23.6 - - + +
243D TYR* 3.9 8.1 - - + -
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Residues in contact with ALA 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 GLY 2.8 16.1 + - - +
22D VAL 3.6 3.6 - - - +
24D ALA* 1.3 75.2 - - - +
26D GLY* 1.3 56.7 + - - +
28D ALA* 2.8 26.0 + - - +
29D LEU* 3.0 15.8 + - + +
243D TYR* 3.4 48.4 - - + +
246D VAL* 3.7 15.7 - - + -
247D THR* 4.4 2.2 - - - +
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Residues in contact with GLY 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 VAL 3.0 11.3 + - - -
23D LYS 3.7 2.7 - - - -
25D ALA* 1.3 78.3 - - - +
27D LYS* 1.3 54.9 + - - +
30D GLY* 3.0 24.9 + - - -
31D VAL* 3.1 40.1 + - - +
33D THR* 4.0 9.2 - - - -
246D VAL* 4.0 1.8 - - - +
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Residues in contact with LYS 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 LYS 2.9 20.9 + - - +
24D ALA* 3.7 8.3 - - - +
26D GLY* 1.3 73.9 - - - +
28D ALA* 1.3 61.8 + - - +
29D LEU 3.3 0.3 + - - -
30D GLY* 3.5 7.4 + - - -
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Residues in contact with ALA 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 ALA 3.1 8.3 + - - +
25D ALA 2.8 15.3 + - - +
27D LYS* 1.3 73.9 - - - +
29D LEU* 1.3 64.2 + - + +
243D TYR* 3.5 23.6 - - - +
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Residues in contact with LEU 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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25D ALA* 3.0 11.9 + - - +
28D ALA* 1.3 82.9 - - + +
30D GLY* 1.3 64.6 - - - +
31D VAL* 3.8 13.5 - - + -
243D TYR* 6.0 2.7 - - + -
246D VAL* 4.4 10.5 - - + -
247D THR* 3.9 32.5 - - + +
250D TYR* 3.5 66.8 + - + -
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Residues in contact with GLY 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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1D MET* 4.3 23.8 - - - +
2D LEU* 5.1 1.0 + - - +
26D GLY 3.0 7.0 + - - -
27D LYS 3.5 5.8 + - - -
28D ALA 3.5 2.2 - - - -
29D LEU* 1.3 80.6 - - - +
31D VAL* 1.3 61.4 + - - +
250D TYR* 4.8 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
------------------------------------------------------------
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