Contacts of the helix formed by residues 25 - 42 (chain A) in PDB entry 3ZG6
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 25 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23A ASP 3.8 2.2 - - - +
24A PRO* 1.4 84.6 - - + +
26A GLU* 1.3 68.9 + - - +
27A GLU 3.4 0.8 - - - +
28A LEU* 3.5 8.9 - - + +
29A GLU* 3.0 36.5 + - - +
262A ARG* 4.9 6.4 + - - +
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Residues in contact with GLU 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A PRO* 3.4 26.8 - - - +
25A PRO* 1.3 77.6 - - - +
27A GLU* 1.3 74.5 + - + +
29A GLU* 3.4 12.6 - - - +
30A ARG* 2.9 28.5 + - - +
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Residues in contact with GLU 27 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP* 3.6 7.2 - - + +
24A PRO* 2.0 46.1 + - + +
26A GLU* 1.3 85.1 - - + +
28A LEU* 1.3 62.9 + - - +
30A ARG* 3.6 32.7 + - - +
31A LYS* 3.8 25.7 - - + +
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Residues in contact with LEU 28 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP* 4.2 11.2 - - + +
24A PRO 3.5 3.8 - - - +
25A PRO* 3.5 8.7 - - + +
26A GLU 3.5 0.6 + - - -
27A GLU* 1.3 82.4 - - - +
29A GLU* 1.3 55.9 + - - +
31A LYS* 2.9 20.7 + - - +
32A VAL* 2.6 46.6 + - + +
252A ILE* 3.6 30.7 - - + -
253A HIS 4.4 11.4 - - - +
254A GLY* 4.6 5.8 - - - -
258A GLU* 3.5 28.7 - - + +
259A VAL* 4.2 11.2 - - + -
262A ARG* 3.5 20.0 - - + +
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Residues in contact with GLU 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A PRO* 3.0 28.5 + - - +
26A GLU* 3.4 10.1 - - - +
28A LEU* 1.3 80.1 - - - +
30A ARG* 1.3 64.9 + - - +
32A VAL* 3.3 2.6 + - - +
33A TRP* 3.1 23.3 + - - +
262A ARG* 3.2 29.4 + - - +
266A HIS* 4.9 3.3 + - - -
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Residues in contact with ARG 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A GLU 2.9 19.3 + - - +
27A GLU* 3.6 33.4 + - - +
29A GLU* 1.3 73.3 - - - +
31A LYS* 1.3 83.5 + - - +
33A TRP* 3.5 12.7 + - + +
34A GLU* 3.1 32.7 + - - +
250A LEU* 5.6 4.2 - - - +
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Residues in contact with LYS 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A ASP* 3.3 33.4 + - - +
27A GLU* 3.8 21.8 - - + +
28A LEU* 2.9 23.2 + - - +
30A ARG* 1.3 90.9 - - - +
32A VAL* 1.3 59.0 + - - +
34A GLU* 3.2 5.2 + - - +
35A LEU* 2.8 28.1 + - - +
250A LEU* 3.7 22.0 - - + +
251A ARG* 3.0 29.5 + - - +
252A ILE* 3.7 19.5 - - + -
253A HIS* 5.2 2.0 + - - -
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Residues in contact with VAL 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A LEU* 2.6 32.6 + - + +
29A GLU* 4.2 3.6 - - - +
31A LYS* 1.3 70.7 - - - +
33A TRP* 1.3 63.0 + - - +
35A LEU* 3.4 8.1 + - + +
36A ALA* 3.1 21.7 + - - +
252A ILE* 4.4 6.1 - - + -
259A VAL* 3.7 41.5 - - + +
262A ARG* 3.5 30.5 - - + +
263A LEU* 3.5 20.4 - - + +
266A HIS* 4.0 5.5 - - + +
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Residues in contact with TRP 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A GLU 3.1 18.4 + - - +
30A ARG* 3.6 13.2 - - + +
32A VAL* 1.3 78.6 - - - +
34A GLU* 1.3 68.7 + - + +
36A ALA* 3.2 8.5 + - + +
37A ARG* 3.1 44.2 + - + +
266A HIS* 4.0 40.5 + + + +
294A LYS* 3.1 55.2 - - + -
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Residues in contact with GLU 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ARG* 3.1 23.9 + - - +
31A LYS* 3.2 10.7 + - - +
33A TRP* 1.3 77.5 - - + +
35A LEU* 1.3 64.3 + - - +
37A ARG* 3.3 37.9 + - - +
38A LEU* 3.0 46.0 + - + +
250A LEU* 4.2 20.6 - - + -
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Residues in contact with LEU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A LYS 2.8 16.5 + - - +
32A VAL* 3.4 11.4 - - - +
34A GLU* 1.3 72.7 - - - +
36A ALA* 1.3 50.7 + - - +
38A LEU* 3.1 8.6 + - + +
39A VAL* 2.8 39.4 + - + +
47A PHE* 6.6 0.2 - - + -
207A LEU* 4.9 0.4 - - + -
209A ILE* 3.9 26.5 - - + -
211A LEU* 6.2 0.2 - - + -
235A VAL* 3.9 31.9 - - + -
237A VAL* 5.0 4.0 - - + -
250A LEU* 3.9 8.2 - - + +
252A ILE* 4.0 11.2 - - + -
259A VAL* 4.0 26.9 - - + -
260A MET* 5.6 1.8 - - - -
263A LEU* 4.2 24.7 - - + -
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A VAL 3.1 12.3 + - - +
33A TRP* 3.2 14.7 + - + +
35A LEU* 1.3 75.3 - - - +
37A ARG* 1.3 54.6 + - - +
39A VAL* 3.2 3.7 + - - +
40A TRP* 2.8 37.0 + - - +
263A LEU* 3.6 18.8 - - + +
266A HIS* 3.8 28.9 - - + +
267A LEU* 4.1 9.8 - - + +
293A PRO* 6.4 0.9 - - + -
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Residues in contact with ARG 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A TRP* 3.1 45.6 + - + +
34A GLU* 3.3 35.7 + - - +
36A ALA* 1.3 77.6 - - - +
38A LEU* 1.3 57.1 + - + +
40A TRP* 3.3 4.1 + - - -
41A GLN* 2.9 59.1 + - - +
294A LYS* 5.1 10.1 - - + -
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLU* 3.0 36.5 + - + +
35A LEU* 3.3 8.1 - - - +
37A ARG* 1.3 76.7 - - + +
39A VAL* 1.3 62.0 + - - +
41A GLN* 3.9 3.8 - - - +
42A SER* 2.7 34.2 + - - +
207A LEU* 3.8 17.0 - - + -
233A ARG* 3.9 35.4 - - + +
235A VAL* 3.7 29.6 - - + -
249A ASP* 6.2 0.9 - - + -
250A LEU* 4.1 18.4 - - + -
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 2.8 28.7 + - + +
36A ALA* 3.7 6.1 - - - +
38A LEU* 1.3 74.4 - - - +
40A TRP* 1.3 61.3 + - - +
42A SER 3.7 12.5 + - - +
45A VAL* 4.2 8.3 - - + +
47A PHE* 5.2 2.5 - - + -
99A LEU* 5.3 3.4 - - + -
104A LEU* 4.1 41.0 - - + +
207A LEU* 3.8 20.2 - - + -
209A ILE* 3.9 17.9 - - + -
263A LEU* 4.6 10.8 - - + -
267A LEU* 4.2 19.3 - - + -
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Residues in contact with TRP 40 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A ALA 2.8 17.8 + - - +
37A ARG* 4.0 4.7 - - - +
39A VAL* 1.3 79.0 - - - +
41A GLN* 1.3 71.8 + - + +
42A SER 3.6 0.5 + - - +
104A LEU* 4.3 16.4 - - + -
267A LEU* 4.7 8.7 - - + -
289A ARG* 3.6 61.6 + - + +
290A PRO* 3.6 40.8 - - + -
292A THR* 3.0 40.7 - - + +
293A PRO* 3.9 22.2 - - + -
294A LYS* 4.4 12.1 + - + -
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Residues in contact with GLN 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A ARG* 2.9 43.7 + - - +
38A LEU* 4.4 4.8 - - - +
40A TRP* 1.3 89.5 - - + +
42A SER* 1.3 60.1 + - - +
43A SER 4.0 0.7 + - - -
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Residues in contact with SER 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 2.7 24.7 + - - +
39A VAL 3.7 10.0 + - - +
40A TRP 3.4 4.2 - - - +
41A GLN* 1.3 78.5 - - - +
43A SER* 1.3 62.1 + - - +
44A SER 3.5 0.2 - - - -
45A VAL* 3.9 21.0 - - - +
104A LEU* 5.7 0.2 - - - +
206A ASP* 3.0 24.3 + - - -
207A LEU* 3.6 15.3 - - - +
289A ARG* 4.2 8.1 + - - -
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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