Contacts of the helix formed by residues 12 - 31 (chain D) in PDB entry 3T79
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 PRO 12 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11D LEU* 1.3 97.2 - - + +
13D THR* 1.3 66.8 + - - +
14D ARG* 4.4 3.4 - - + +
15D THR* 4.0 25.4 - - + +
16D ALA 2.8 19.9 + - - -
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Residues in contact with THR 13 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 3.8 3.2 + - - +
12D PRO* 1.3 69.7 - - - +
14D ARG* 1.3 73.5 + - - +
16D ALA* 3.1 9.0 + - - +
17D HIS* 2.9 24.5 + - - +
20D ARG* 4.9 3.7 + - - +
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Residues in contact with ARG 14 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12D PRO* 3.2 4.1 - - + +
13D THR* 1.3 84.9 + - - +
15D THR* 1.3 61.4 + - - +
17D HIS* 3.1 9.8 + - + +
18D LEU* 2.9 29.2 + - + +
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Residues in contact with THR 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11D LEU* 4.5 6.4 - - + +
12D PRO* 3.3 25.8 + - + +
14D ARG* 1.3 79.4 - - - +
16D ALA* 1.3 62.1 + - - +
18D LEU* 4.2 11.1 - - + +
19D TYR* 3.3 49.8 + - + +
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Residues in contact with ALA 16 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 3.4 17.5 - - + +
11D LEU* 2.9 39.0 - - + +
12D PRO 2.8 5.4 + - - +
13D THR* 3.2 12.3 - - - +
15D THR* 1.3 77.1 - - - +
17D HIS* 1.3 60.1 + - - +
19D TYR* 3.4 4.6 + - - +
20D ARG* 2.9 41.9 + - - +
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Residues in contact with HIS 17 (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 THR 2.9 12.1 + - - +
14D ARG* 3.4 12.3 - - + +
16D ALA* 1.3 76.5 - - - +
18D LEU* 1.3 67.3 + - - +
20D ARG* 2.9 45.3 + - + +
21D SER* 2.9 21.8 + - - -
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Residues in contact with LEU 18 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14D ARG* 2.9 16.8 + - + +
15D THR* 4.3 11.0 - - + +
17D HIS* 1.3 78.1 - - - +
19D TYR* 1.3 90.9 + - + +
21D SER* 2.6 25.1 + - - +
22D ILE* 3.0 31.4 + - + +
66D PRO* 4.6 22.4 - - + +
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Residues in contact with TYR 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8D LEU* 4.4 6.1 - - + -
11D LEU* 5.5 3.8 - - + -
15D THR* 3.3 28.8 + - + +
16D ALA* 3.4 9.5 + - - +
17D HIS 3.2 0.6 - - - -
18D LEU* 1.3 97.0 - - + +
20D ARG* 1.3 68.7 + - - +
22D ILE* 3.2 4.4 + - - +
23D TRP* 2.8 26.2 + - - +
66D PRO 4.5 1.8 - - - -
69D ASP* 4.1 12.4 + - + +
70D ALA* 3.5 34.8 + - + -
73D TRP* 3.7 50.2 - + + +
74D PHE* 3.5 15.8 - + + -
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Residues in contact with ARG 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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5D ASP* 5.8 3.6 - - - -
8D LEU* 4.2 19.2 - - + +
13D THR* 4.9 3.4 + - - +
16D ALA* 2.9 23.5 + - - +
17D HIS* 2.9 55.6 + - + +
19D TYR* 1.3 75.8 - - - +
21D SER* 1.3 56.8 + - - +
23D TRP* 3.2 9.0 - - - +
24D HIS* 2.9 27.3 + - - +
74D PHE* 5.4 0.4 - - - -
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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
----------------------------------------------------------
17D HIS* 2.9 19.6 + - - -
18D LEU* 2.6 30.8 + - - +
20D ARG* 1.3 73.5 - - - +
22D ILE* 1.3 67.0 + - - +
24D HIS* 2.9 17.0 + - - +
25D LYS* 2.9 34.4 + - - +
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Residues in contact with ILE 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D LEU* 3.0 36.3 + - + +
19D TYR* 3.7 9.4 - - - +
21D SER* 1.3 77.2 + - - +
23D TRP* 1.3 64.2 + - - +
25D LYS* 3.5 8.1 + - + +
26D TYR* 2.9 23.1 + - + +
53D TYR* 4.7 5.5 + - + +
60D ILE* 5.5 9.0 - - + -
66D PRO* 5.6 2.7 - - + -
67D THR* 4.1 32.3 - - + +
70D ALA* 4.2 19.3 - - + -
71D MET* 3.8 24.7 - - + -
74D PHE* 4.9 1.1 - - + -
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Residues in contact with TRP 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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1D MET 5.4 10.9 - - - +
4D LEU* 6.1 6.6 - - + +
19D TYR 2.8 12.6 + - - +
20D ARG* 3.2 13.2 - - - +
22D ILE* 1.3 79.4 - - - +
24D HIS* 1.3 70.1 + - + +
26D TYR* 2.9 12.9 + + - +
27D THR* 2.9 54.8 + - + +
44D PHE* 4.8 9.4 - + - -
45D LEU* 4.7 22.0 - - + -
71D MET* 5.1 2.0 - - + -
74D PHE* 4.0 39.0 - + + -
78D LEU* 6.4 1.6 - - + -
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Residues in contact with HIS 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20D ARG 2.9 13.1 + - - +
21D SER* 2.9 14.8 + - - +
23D TRP* 1.3 75.1 - - + +
25D LYS* 1.3 83.3 + - + +
27D THR* 3.3 5.1 + - - -
28D GLU* 2.9 60.3 + - + +
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Residues in contact with LYS 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21D SER* 2.9 26.9 + - - +
22D ILE* 3.5 11.2 - - + +
24D HIS* 1.3 92.1 - - + +
26D TYR* 1.3 67.9 - - - +
28D GLU* 2.9 5.5 + - - +
29D TRP* 2.9 22.2 + - - +
53D TYR* 3.3 21.3 - - + +
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Residues in contact with TYR 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 ILE* 2.9 16.5 + - + +
23D TRP* 2.9 6.7 + + - +
25D LYS* 1.3 78.9 - - - +
27D THR* 1.3 56.1 + - + +
29D TRP* 3.1 3.1 + - - +
30D LEU* 2.7 43.9 + - + +
44D PHE* 2.8 46.1 + + - -
45D LEU* 3.5 15.6 - - + +
49D TYR* 3.5 23.6 - - - +
50D ILE* 3.5 22.9 - - + +
53D TYR* 3.5 52.7 - + + -
71D MET* 3.5 26.5 - - + -
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Residues in contact with THR 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 TRP* 2.9 64.3 + - + +
24D HIS* 3.3 8.1 + - - -
26D TYR* 1.3 67.7 - - + +
28D GLU* 1.3 73.7 + - - +
29D TRP 3.0 4.9 - - - -
30D LEU* 2.6 33.9 + - + +
31D LYS* 3.1 27.1 + - - +
44D PHE* 4.5 3.1 - - + -
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Residues in contact with GLU 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 HIS* 2.9 54.3 + - + +
25D LYS* 2.9 8.9 + - - +
27D THR* 1.3 83.0 + - - +
29D TRP* 1.3 60.3 + - - +
31D LYS* 3.9 24.3 - - - +
32D THR* 4.6 3.5 + - - -
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Residues in contact with TRP 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 LYS 2.9 10.4 + - - +
26D TYR* 3.2 9.6 - + - +
28D GLU* 1.3 74.7 - - - +
30D LEU* 1.3 94.0 + - + +
31D LYS 3.1 2.0 - - - -
32D THR* 2.8 40.5 + - + +
33D MET* 3.7 31.1 - - + +
49D TYR* 3.4 25.1 - + + -
52D LYS* 3.6 25.6 - - + -
53D TYR* 3.4 49.4 - + + -
56D SER* 4.0 5.5 + - - -
57D HIS* 3.4 29.1 - + - +
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Residues in contact with LEU 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 TYR* 2.7 20.0 - - + +
27D THR* 2.6 45.4 + - + +
29D TRP* 1.3 100.6 - - + +
31D LYS* 1.3 70.7 + - + +
32D THR 2.8 2.2 - - - -
33D MET* 2.8 28.3 + - + +
35D ASP 6.0 1.2 - - - -
44D PHE* 2.4 55.0 - - + -
49D TYR* 5.5 0.2 - - + -
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Residues in contact with LYS 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 THR* 3.1 22.4 + - - +
28D GLU* 3.9 22.2 - - + +
29D TRP 3.1 0.6 - - - -
30D LEU* 1.3 79.2 - - + +
32D THR* 1.3 57.3 + - - +
33D MET 2.9 14.6 + - - +
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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
------------------------------------------------------------
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