Contacts of the helix formed by residues 16 - 34 (chain B) in PDB entry 2DDK
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 TRP 16 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PRO* 1.3 93.6 - - + +
17B GLU* 1.3 96.1 + - + +
18B GLU* 2.9 3.3 + - - +
19B CYS* 2.8 25.5 + - - -
20B PHE* 3.3 7.1 + - - -
129B GLU* 3.1 24.0 - - + -
130B PHE* 5.4 4.9 - - - -
145B ARG* 2.8 23.9 - - - +
146B ARG 4.7 11.4 - - - -
148B ARG* 3.6 31.5 - - + +
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Residues in contact with GLU 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP* 1.3 85.3 - - + +
18B GLU* 1.3 66.6 + - - +
20B PHE* 2.7 19.3 + - + +
21B GLN* 2.8 32.3 + - + +
145B ARG* 2.6 32.6 + - - +
148B ARG* 2.8 21.3 + - - -
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Residues in contact with GLU 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B TRP 2.9 4.5 + - - +
17B GLU* 1.3 76.8 - - - +
19B CYS* 1.3 59.0 + - - +
21B GLN* 3.8 5.5 + - - +
22B ALA 3.5 11.6 + - - -
72B ARG* 2.6 53.4 + - - +
73B PHE* 4.1 14.5 - - + -
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Residues in contact with CYS 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B PRO 3.8 12.1 - - - -
16B TRP* 2.8 48.1 + - - -
18B GLU* 1.3 75.2 - - - +
20B PHE* 1.3 59.7 + - - +
21B GLN 3.3 0.2 - - - -
22B ALA* 3.1 10.5 - - - +
23B ALA 3.0 20.6 + - - -
73B PHE* 3.6 24.7 - - + -
76B HIS* 4.8 2.0 - - - -
98B TRP* 3.2 25.0 - - + -
122B PHE* 4.1 16.4 - - + -
130B PHE* 4.3 6.5 - - - -
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Residues in contact with PHE 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B TRP 3.3 3.6 + - - -
17B GLU* 2.7 25.8 + - + +
19B CYS* 1.3 70.5 - - - +
21B GLN* 1.3 91.4 + - - +
22B ALA 3.0 1.8 - - - -
23B ALA* 3.2 1.6 + - - +
24B VAL* 3.2 31.4 + - + +
130B PHE* 3.6 39.5 - + + -
131B GLY 4.8 0.7 - - - -
132B VAL* 3.5 24.5 - - + -
143B THR* 4.3 16.6 - - + -
145B ARG* 3.4 46.0 - - + +
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Residues in contact with GLN 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B GLU* 2.8 27.9 + - + +
18B GLU* 4.2 4.9 - - - +
20B PHE* 1.3 110.0 - - - +
22B ALA* 1.3 62.6 + - - +
24B VAL* 3.8 8.9 - - - +
25B GLN* 3.2 43.6 + - + +
72B ARG* 5.6 0.7 - - - +
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Residues in contact with ALA 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B GLU 3.5 10.0 + - - +
19B CYS* 3.1 21.7 + - - +
20B PHE 3.0 0.2 - - - -
21B GLN* 1.3 80.4 - - - +
23B ALA* 1.3 54.7 + - - +
25B GLN* 5.1 1.1 - - - -
26B LEU* 2.7 42.2 + - + +
68B GLU* 4.9 1.3 - - - +
69B LEU* 5.1 5.4 - - + -
72B ARG* 4.1 27.8 - - - +
73B PHE* 4.2 11.4 - - + -
98B TRP* 5.0 3.1 - - + -
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Residues in contact with ALA 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B CYS 3.0 5.0 + - - +
20B PHE 3.2 8.9 + - - +
22B ALA* 1.3 75.5 - - - +
24B VAL* 1.3 55.2 + - - +
26B LEU* 3.6 1.6 - - - +
27B ALA* 2.6 38.1 + - - +
69B LEU* 5.8 0.9 - - - -
98B TRP* 3.8 7.4 - - + -
120B ILE* 3.5 36.1 - - + +
130B PHE* 3.6 21.5 - - + -
132B VAL* 4.1 7.9 - - + -
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Residues in contact with VAL 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PHE* 3.2 45.3 + - + +
21B GLN* 3.8 13.7 - - - +
22B ALA 3.4 0.2 - - - -
23B ALA* 1.3 75.5 - - - +
25B GLN* 1.3 62.4 + - - +
27B ALA* 3.2 3.8 + - - +
28B LEU* 2.7 45.8 + - + +
132B VAL* 4.0 13.5 - - + -
141B LEU* 3.5 27.3 - - + +
143B THR* 4.5 4.9 - - + -
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Residues in contact with GLN 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLN* 3.2 31.4 + - + +
22B ALA* 4.3 2.9 - - - +
24B VAL* 1.3 86.3 - - - +
26B LEU* 1.3 58.1 + - + +
28B LEU* 2.9 20.4 + - - +
29B ARG* 2.5 43.1 + - - +
72B ARG* 6.2 0.9 - - - +
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22B ALA* 2.7 29.5 + - - +
23B ALA* 3.7 3.4 - - - +
25B GLN* 1.3 75.5 - - + +
27B ALA* 1.3 67.8 + - - +
29B ARG* 3.8 13.8 - - - +
30B ALA* 2.9 28.2 + - - +
64B LEU* 3.8 19.4 - - + +
65B ILE* 3.7 30.2 - - + +
68B GLU* 3.1 40.2 - - + +
69B LEU* 3.8 15.3 - - + -
72B ARG* 5.5 0.7 - - - +
120B ILE* 4.1 14.6 - - + -
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Residues in contact with ALA 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B ALA 2.6 22.8 + - - +
24B VAL 3.2 5.8 - - - +
26B LEU* 1.3 72.4 - - - +
28B LEU* 1.3 53.9 + - - +
30B ALA* 3.9 1.4 - - - +
31B GLY* 2.7 32.4 + - - -
118B VAL* 4.4 10.5 - - + +
120B ILE* 4.0 11.4 - - + +
132B VAL* 3.3 27.6 - - + +
134B TYR* 3.9 15.6 - - + +
141B LEU* 4.2 7.4 - - + -
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Residues in contact with LEU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B VAL* 2.7 27.8 + - + +
25B GLN* 2.9 30.7 + - - +
27B ALA* 1.3 75.6 - - - +
29B ARG* 1.3 57.0 + - - -
31B GLY* 3.1 1.8 + - - -
32B GLN* 2.8 31.8 + - - +
134B TYR* 3.4 38.5 - - + +
141B LEU* 4.2 13.9 - - + -
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Residues in contact with ARG 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B GLN* 2.5 22.7 + - - +
26B LEU* 3.2 21.0 + - - +
28B LEU* 1.3 68.8 - - - +
30B ALA* 1.3 60.9 + - - +
32B GLN* 2.9 16.4 + - - +
33B ILE* 2.8 41.9 + - + +
64B LEU* 3.2 40.5 - - + +
68B GLU* 2.6 32.8 + - - +
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Residues in contact with ALA 30 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26B LEU 2.9 16.0 + - - +
27B ALA 3.9 2.5 - - - +
29B ARG* 1.3 76.4 - - - +
31B GLY* 1.3 63.7 + - - +
33B ILE* 3.0 16.0 + - - +
34B ILE* 3.0 21.0 + - - +
61B VAL* 3.9 34.3 - - + +
64B LEU* 5.0 4.2 - - + +
65B ILE* 5.8 3.1 - - + -
102B PRO 5.4 0.2 - - - +
118B VAL* 4.0 20.9 - - + -
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Residues in contact with GLY 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B ALA 2.7 20.6 + - - -
28B LEU 3.4 3.4 - - - -
29B ARG 3.1 0.4 - - - -
30B ALA* 1.3 77.9 - - - +
32B GLN* 1.3 54.6 + - - +
34B ILE* 4.0 3.1 - - - +
35B ARG* 3.1 27.9 + - - +
118B VAL* 4.5 1.3 - - - +
134B TYR* 3.4 30.3 - - - -
136B CYS* 4.1 10.7 - - - +
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Residues in contact with GLN 32 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28B LEU 2.8 13.7 + - - +
29B ARG* 2.9 16.3 + - - +
31B GLY* 1.3 77.2 - - - +
33B ILE* 1.3 62.7 + - + +
35B ARG* 3.5 9.8 + - + +
36B LYS* 3.3 27.7 + - + +
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Residues in contact with ILE 33 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B ARG* 2.8 36.7 + - + +
30B ALA* 3.0 11.2 + - - +
32B GLN* 1.3 77.9 - - + +
34B ILE* 1.3 61.9 + - + +
36B LYS* 4.0 10.4 - - + +
37B ALA* 3.0 23.8 + - + +
57B THR* 4.8 5.6 - - + -
60B LEU* 4.9 18.4 - - + +
61B VAL* 3.7 20.4 - - + -
64B LEU* 4.5 18.6 - - + -
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Residues in contact with ILE 34 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30B ALA 3.0 9.4 + - - +
31B GLY 4.0 0.2 - - - +
33B ILE* 1.3 74.7 - - - +
35B ARG* 1.3 63.6 + - - +
36B LYS 3.5 0.2 - - - -
37B ALA* 3.6 8.1 - - - -
38B LEU* 2.9 30.8 + - - +
57B THR* 3.5 17.7 - - + -
61B VAL* 3.4 29.2 - - + -
103B ILE* 3.6 25.1 - - + -
109B PHE* 3.7 9.8 - - + -
116B VAL* 3.4 22.0 - - + -
117B ALA 4.8 0.7 - - - +
118B VAL* 4.6 3.8 - - + -
136B CYS* 2.9 39.9 - - + -
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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