Contacts of the helix formed by residues 26 - 40 (chain B) in PDB entry 2ETK
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 ASN 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LEU 3.4 13.1 + - - +
18B LEU* 3.6 10.0 + - - +
19B ARG* 4.5 6.3 + - - +
20B ASP 3.2 28.9 + - - +
21B PRO* 4.9 6.4 - - + +
23B SER 3.6 9.6 + - - +
24B GLU 3.5 1.6 - - - -
25B VAL* 1.3 78.7 - - - +
27B SER* 1.3 64.7 + - - +
28B ASP* 3.0 40.0 + - - +
29B CYS* 2.8 34.4 + - - +
30B LEU 3.0 10.6 + - - -
398B THR 4.7 1.0 - - - +
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Residues in contact with SER 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 4.1 32.2 - - - +
27A SER* 4.9 2.1 + - - -
30A LEU* 4.2 1.8 - - - +
18B LEU* 2.8 39.0 + - - +
19B ARG* 5.3 2.1 - - - +
25B VAL 3.8 0.6 + - - -
26B ASN* 1.3 75.8 - - - +
28B ASP* 1.3 59.6 + - - +
30B LEU* 3.5 10.8 + - - +
31B LEU* 3.1 33.9 + - - +
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Residues in contact with ASP 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26B ASN* 3.0 22.1 + - - +
27B SER* 1.3 79.0 - - - +
29B CYS* 1.3 58.9 + - - +
31B LEU* 4.4 7.2 - - - +
32B ASP* 3.3 14.1 + - - +
70B ARG* 2.9 30.8 + - - +
398B THR* 3.8 19.9 - - + +
399B TYR* 4.9 0.2 - - - -
400B TYR* 3.3 52.1 + - - +
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Residues in contact with CYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34A LEU* 6.1 0.9 - - - +
59A TYR* 4.5 2.0 + - - +
21B PRO 5.9 0.9 - - - -
23B SER 3.7 18.8 - - - -
24B GLU* 3.3 25.4 - - - +
26B ASN* 2.8 21.1 + - - +
28B ASP* 1.3 74.5 - - - +
30B LEU* 1.3 65.4 + - - +
32B ASP* 3.3 16.0 - - - +
33B GLY* 3.4 5.2 + - - -
125B ARG* 5.2 5.2 - - - -
395B VAL* 4.0 8.3 - - - +
396B GLY* 3.7 36.8 - - - -
398B THR 4.4 7.0 - - - -
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Residues in contact with LEU 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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30A LEU* 3.5 52.8 - - + +
31A LEU* 3.8 16.4 - - + -
34A LEU* 3.8 34.3 - - + +
18B LEU* 3.7 25.4 - - + -
24B GLU 5.8 0.2 - - - +
25B VAL* 3.3 33.4 - - + +
26B ASN 3.0 6.5 + - - +
27B SER* 3.8 7.0 - - - +
29B CYS* 1.3 75.3 - - - +
31B LEU* 1.3 64.2 + - - +
32B ASP 3.2 0.7 + - - -
33B GLY* 3.4 10.8 + - - +
34B LEU* 3.4 8.8 + - - +
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Residues in contact with LEU 31 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A MET* 4.2 16.6 - - + -
18A LEU* 4.2 18.2 - - + -
25A VAL* 4.9 5.8 - - + -
30A LEU* 3.9 26.9 - - + -
27B SER 3.1 23.3 + - - +
28B ASP* 4.4 7.6 - - - +
30B LEU* 1.3 75.3 - - - +
32B ASP* 1.3 58.1 + - - +
34B LEU* 3.7 3.8 + - + +
35B ASP* 3.0 29.6 + - - +
63B ILE* 5.1 2.5 - - + +
66B ILE* 3.9 34.1 - - + +
70B ARG* 3.5 35.2 + - + +
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Residues in contact with ASP 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 ASP 3.4 8.3 + - - +
29B CYS 3.3 10.3 - - - +
30B LEU 3.2 0.4 - - - -
31B LEU* 1.3 75.8 - - - +
33B GLY* 1.3 55.9 + - - +
35B ASP* 3.0 6.4 + - - +
36B ALA* 2.6 38.4 + - - +
70B ARG* 3.1 17.5 + - - -
144B GLN* 3.0 25.1 + - - +
395B VAL* 4.1 4.0 - - + -
396B GLY* 3.1 23.9 + - - +
397B PHE 3.3 0.2 + - - -
398B THR* 2.7 37.6 + - - -
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Residues in contact with GLY 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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33A GLY 5.6 6.0 - - - +
34A LEU* 5.6 11.4 - - - -
37A LEU* 4.6 12.8 - - - +
55A PHE* 5.9 0.2 - - - -
29B CYS 3.4 5.5 + - - -
30B LEU* 3.4 7.8 + - - -
32B ASP* 1.3 77.8 - - - +
34B LEU* 1.3 56.0 + - - +
36B ALA* 4.0 1.1 - - - +
37B LEU* 3.3 27.4 + - - +
395B VAL* 3.7 22.4 - - - +
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Residues in contact with LEU 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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25A VAL* 3.7 30.1 - - + -
29A CYS* 5.4 3.8 - - + +
30A LEU* 4.0 15.3 - - + -
33A GLY* 4.7 18.6 - - - -
395A VAL* 5.2 1.3 - - + -
30B LEU 3.4 13.4 + - - +
31B LEU* 4.0 5.4 - - + +
32B ASP 3.1 0.4 - - - -
33B GLY* 1.3 75.4 - - - +
35B ASP* 1.3 64.3 + - - +
36B ALA 3.2 1.6 - - - -
37B LEU* 3.4 5.7 + - + +
38B VAL* 3.2 30.6 + - + +
55B PHE* 3.8 30.1 - - + -
59B TYR* 4.0 21.3 - - + -
63B ILE* 3.9 16.4 - - + -
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Residues in contact with ASP 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B LEU 3.0 20.4 + - - +
32B ASP* 3.5 7.7 - - - +
34B LEU* 1.3 76.7 - - - +
36B ALA* 1.3 60.8 + - - +
39B TYR* 3.3 26.5 + - - -
63B ILE* 3.8 13.2 - - + +
66B ILE* 6.0 2.2 - - + -
67B ARG* 2.6 51.8 + - - +
70B ARG* 4.1 13.5 + - - +
144B GLN* 5.2 7.8 - - - +
145B ASP* 5.7 2.8 - - - -
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Residues in contact with ALA 36 (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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32B ASP 2.6 20.2 + - - +
33B GLY 4.2 2.9 - - - +
35B ASP* 1.3 72.0 - - - +
37B LEU* 1.3 58.8 + - - +
38B VAL 3.2 0.2 - - - -
39B TYR* 3.1 5.6 + - - +
40B ASP* 3.0 32.3 + - - +
391B GLN* 3.7 31.6 - - + -
392B LEU* 5.0 4.3 - - + +
395B VAL* 3.7 22.7 - - + -
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Residues in contact with LEU 37 (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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33A GLY 4.6 14.6 - - - +
37A LEU* 3.6 35.2 - - + -
387A PHE* 4.8 5.2 - - + -
392A LEU* 3.8 25.4 - - + -
33B GLY 3.3 18.4 + - - +
34B LEU* 3.4 7.8 + - + +
36B ALA* 1.3 77.3 - - - +
38B VAL* 1.3 61.4 + - - +
40B ASP* 4.0 3.1 - - - +
41B LEU* 3.2 48.5 + - + +
55B PHE* 4.0 18.8 - - + -
387B PHE* 4.7 12.6 - - + -
392B LEU* 6.2 0.9 - - + -
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Residues in contact with VAL 38 (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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34B LEU* 3.2 17.8 + - + +
35B ASP 3.9 0.2 - - - +
36B ALA 3.2 0.6 - - - -
37B LEU* 1.3 75.0 - - - +
39B TYR* 1.3 58.6 + - + +
41B LEU 3.3 0.7 + - - -
42B ASP* 3.0 35.6 + - + +
55B PHE* 4.4 16.4 - - + -
56B LEU* 3.8 20.0 - - + +
59B TYR* 4.9 9.0 - - + +
60B LYS* 6.4 0.4 - - - -
63B ILE* 3.9 32.8 - - + -
67B ARG* 3.4 24.2 - - - +
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Residues in contact with TYR 39 (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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35B ASP* 3.3 29.5 + - - -
36B ALA 3.1 7.2 + - - +
38B VAL* 1.3 80.6 - - - +
40B ASP* 1.3 57.3 + - - +
41B LEU 3.1 4.5 + - - -
42B ASP* 3.7 7.3 + - + +
43B PHE* 3.3 22.2 - - - -
67B ARG* 3.4 43.6 + - - -
145B ASP* 4.9 6.1 - - - +
146B ASP* 3.6 51.3 + - + +
391B GLN* 4.1 18.6 - - + +
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Residues in contact with ASP 40 (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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36B ALA* 3.0 12.7 + - - +
37B LEU* 4.7 2.7 - - - +
38B VAL 3.4 0.2 - - - -
39B TYR* 1.3 75.5 - - - +
41B LEU* 1.3 59.9 + - - +
43B PHE* 4.0 15.5 - - - -
46B LEU* 3.8 5.7 - - - +
387B PHE* 3.2 38.3 - - + -
388B VAL* 5.3 2.8 - - + +
389B GLY* 3.2 8.4 + - - +
390B ASN* 3.0 34.2 + - - +
391B GLN* 3.0 36.3 + - - +
392B LEU* 4.2 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
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Atomic class I II III IV V VI VII VIII
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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