Contacts of the helix formed by residues 17 - 34 (chain D) in PDB entry 2A1T
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 THR 17 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A LEU 3.9 15.9 - - - +
11A GLY* 3.5 25.0 - - - +
16D PHE* 1.3 75.5 - - - +
18D GLU* 1.3 59.4 + - - +
19D GLN* 3.5 10.1 + - - +
20D GLN* 2.8 53.4 + - - +
21D LYS* 2.8 26.3 + - - +
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Residues in contact with GLU 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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10A LEU 5.8 0.2 - - - +
16D PHE 3.8 1.8 + - - -
17D THR* 1.3 71.7 - - - +
19D GLN* 1.3 62.6 + - - +
21D LYS* 3.5 12.3 + - + +
22D GLU* 2.7 69.8 + - - +
72S GLN 5.6 0.2 - - - -
73S GLU* 3.1 39.6 - - + +
76S ARG* 3.3 34.8 + - - +
202S LYS* 5.1 5.9 - - + +
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Residues in contact with GLN 19 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D THR* 3.1 9.7 + - - +
18D GLU* 1.3 80.6 + - - +
20D GLN* 1.3 61.4 + - + +
22D GLU* 3.1 5.9 + - - +
23D PHE* 3.0 51.5 + - + -
75D LEU* 4.8 5.7 - - - +
198S ILE* 3.9 13.7 - - + +
199S MET* 3.1 38.3 + - - +
202S LYS* 3.4 36.0 - - + +
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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
----------------------------------------------------------
11A GLY* 4.4 6.4 - - - -
12A PHE 5.0 1.3 + - - +
16D PHE* 3.3 18.1 - - + +
17D THR* 2.8 59.1 + - - +
19D GLN* 1.3 72.6 - - - +
21D LYS* 1.3 58.7 + - - +
23D PHE* 3.3 12.3 + - + +
24D GLN* 2.8 31.5 + - - +
78D PHE* 3.9 23.1 - - - +
79D ASP* 3.2 28.8 + - - +
82D LEU* 3.6 17.3 - - + +
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Residues in contact with LYS 21 (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 GLU* 2.7 34.2 + - - -
16D PHE* 3.8 28.5 + - + +
17D THR 2.8 19.9 + - - +
18D GLU* 3.5 12.7 - - - +
19D GLN 3.3 0.2 - - - -
20D GLN* 1.3 72.2 - - - +
22D GLU* 1.3 58.2 + - + +
24D GLN* 3.4 12.2 + - - +
25D ALA* 2.8 28.6 + - - +
73S GLU* 3.8 28.1 + - - +
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Residues in contact with GLU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18D GLU* 2.7 38.5 - - - +
19D GLN* 3.1 7.3 + - - +
21D LYS* 1.3 74.6 - - + +
23D PHE* 1.3 61.3 + - - +
25D ALA* 3.3 8.2 + - - +
26D THR* 3.0 31.2 + - - -
73S GLU* 3.2 8.5 - - - +
76S ARG* 3.7 18.6 - - - +
77S THR* 3.0 31.7 + - - +
80S ALA* 5.1 0.4 - - - +
193S ALA* 5.1 3.1 - - + +
198S ILE* 3.5 36.0 - - + +
201S ALA* 5.8 0.3 - - - +
202S LYS* 6.1 0.9 - - - +
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Residues in contact with PHE 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 GLN* 3.0 40.7 + - + -
20D GLN* 3.3 13.2 - - + +
22D GLU* 1.3 72.6 - - - +
24D GLN* 1.3 61.0 + - - +
26D THR* 3.2 2.8 + - - -
27D ALA* 2.8 30.9 + - - +
61D LEU* 4.9 0.3 - - - +
75D LEU* 3.4 32.3 - - + -
79D ASP* 4.5 21.5 - - + -
82D LEU* 4.1 10.1 - - + -
83D ILE* 4.7 6.7 - - + -
195S LEU* 3.8 39.1 - - + +
198S ILE* 3.8 26.7 - - + -
199S MET* 3.8 20.2 - - + -
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Residues in contact with GLN 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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16D PHE* 3.5 32.0 - - + -
20D GLN 2.8 20.1 + - - +
21D LYS* 3.6 9.1 - - - +
23D PHE* 1.3 72.8 - - - +
25D ALA* 1.3 59.7 + - - +
27D ALA* 3.7 5.3 - - - +
28D ARG* 2.8 52.3 + - - +
82D LEU* 3.7 20.9 + - + +
86D GLU* 3.4 25.8 + - + +
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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 LYS 2.8 18.1 + - - +
22D GLU* 3.6 9.0 - - - +
23D PHE 3.2 0.2 - - - -
24D GLN* 1.3 79.5 - - - +
26D THR* 1.3 54.9 - - - +
28D ARG* 3.7 4.9 - - - +
29D LYS* 2.8 29.6 + - - +
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Residues in contact with THR 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 GLU 3.0 14.1 + - - -
23D PHE 3.6 5.8 - - - -
25D ALA* 1.3 70.8 - - - +
27D ALA* 1.3 68.6 + - - +
28D ARG 3.1 1.7 + - - -
29D LYS* 3.1 7.0 + - - +
30D PHE* 2.9 24.4 + - - +
59D LEU* 4.5 18.4 - - + +
61D LEU* 4.6 4.9 - - + -
192S TYR* 4.0 17.2 - - + -
193S ALA* 2.7 41.0 + - - +
195S LEU* 4.2 15.0 - - + -
198S ILE* 4.0 0.2 - - - +
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Residues in contact with ALA 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23D PHE 2.8 19.7 + - - +
24D GLN* 3.7 3.6 - - - +
26D THR* 1.3 73.9 - - - +
28D ARG* 1.3 57.0 + - - +
30D PHE* 3.5 2.9 + - - +
31D ALA* 3.0 27.7 + - - +
61D LEU* 3.8 27.7 - - + +
83D ILE* 4.0 15.9 - - + +
86D GLU* 3.5 25.3 - - + +
87D LEU* 4.3 5.2 - - + +
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Residues in contact with ARG 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 GLN* 2.8 42.9 + - - +
25D ALA* 3.7 4.7 - - - +
27D ALA* 1.3 71.1 - - - +
29D LYS* 1.3 66.0 + - - +
31D ALA* 3.7 3.1 - - - +
32D ARG* 3.0 63.2 + - + +
85D GLU* 5.9 0.4 + - - -
86D GLU* 2.8 37.6 + - - +
35S LYS* 5.2 12.5 - - - +
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Residues in contact with LYS 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 2.8 20.6 + - - +
26D THR* 3.1 2.4 + - - +
28D ARG* 1.3 72.0 - - - +
30D PHE* 1.3 60.4 + - - +
32D ARG* 4.3 1.5 - - - -
33D GLU* 2.9 61.7 + - - +
43S GLU* 5.6 5.8 - - - +
190S PRO 6.0 1.3 - - - +
191S ARG 5.5 3.6 - - - +
192S TYR* 3.2 35.4 - - + -
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Residues in contact with PHE 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 THR 2.9 19.4 + - - +
27D ALA 3.7 2.7 - - - +
29D LYS* 1.3 73.5 - - - +
31D ALA* 1.3 56.2 + - - +
34D GLU* 3.0 61.6 + - + -
35D ILE* 3.3 31.3 + - + -
52D LEU* 3.4 35.2 - - + -
55D ARG* 3.7 12.3 - - + -
56D ALA* 3.8 19.5 - - + -
59D LEU* 3.9 19.3 - - + -
61D LEU* 3.8 16.8 - - + -
87D LEU* 3.9 8.3 - - + -
94D VAL* 5.5 0.9 - - + -
98D ILE* 5.5 2.9 - - + -
192S TYR* 3.2 10.9 - - - +
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Residues in contact with ALA 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 ALA 3.0 18.3 + - - +
28D ARG* 3.2 8.2 + - - +
30D PHE* 1.3 73.8 - - - +
32D ARG* 1.3 74.6 + - - +
35D ILE* 3.4 20.5 + - + +
36D ILE* 3.1 28.7 + - - +
86D GLU* 3.3 28.3 - - - +
87D LEU* 4.5 0.2 - - - -
90D GLY* 4.4 6.5 - - - +
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Residues in contact with ARG 32 (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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28D ARG* 3.0 59.0 + - + +
29D LYS* 4.5 1.8 - - - +
31D ALA* 1.3 77.9 - - - +
33D GLU* 1.3 66.4 + - + +
36D ILE* 3.7 18.2 - - + +
37D PRO* 3.5 15.6 - - - +
86D GLU* 4.6 4.9 + - - -
89D TYR* 3.4 51.6 + - - -
272D ASP* 5.3 1.8 + - - -
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Residues in contact with GLU 33 (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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29D LYS* 2.9 49.5 + - - +
32D ARG* 1.3 84.1 - - - +
34D GLU* 1.3 64.3 + - + +
37D PRO* 3.0 18.3 - - - +
16S TYR* 4.8 9.9 + - - -
189S GLU* 5.6 2.3 - - - +
192S TYR* 4.1 8.9 + - - +
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Residues in contact with GLU 34 (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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30D PHE* 3.0 32.9 + - + +
33D GLU* 1.3 85.7 - - + +
35D ILE* 1.3 63.2 + - - +
37D PRO* 3.6 5.0 - - - +
38D VAL* 3.7 12.0 + - - +
52D LEU* 3.3 17.9 - - + +
55D ARG* 2.8 48.0 + - - +
192S TYR* 2.6 28.0 + - - +
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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
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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