Contacts of the helix formed by residues 35 - 50 (chain B) in PDB entry 2PQG
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 35 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26A ILE 6.1 0.2 - - - +
34A TYR* 3.5 19.3 - - + +
42A SER* 6.1 0.2 - - - +
32B ALA 5.3 1.3 - - - +
33B ASN 3.0 14.3 - - - +
34B TYR* 1.3 98.5 - - + +
36B TYR* 1.3 67.1 + - - +
37B SER* 3.8 15.5 - - - +
38B ALA* 3.1 25.9 + - + -
146B ARG* 4.2 6.5 - - - +
219B ASP* 4.7 3.4 - - - +
223B ASN* 5.8 2.0 - - - +
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Residues in contact with TYR 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27B PHE* 4.0 15.0 - + - -
34B TYR 3.6 2.2 + - - -
35B PRO* 1.3 71.3 - - - +
37B SER* 1.3 62.5 + - - +
39B PHE* 3.0 21.0 + + + +
40B ILE* 3.1 40.5 + - + +
146B ARG* 4.3 3.4 - - - +
149B MET* 4.6 8.7 - - + -
204B MET* 2.5 36.4 + - + -
205B VAL* 5.5 1.3 - - + -
208B GLY* 3.7 9.5 - - - -
215B SER* 3.8 14.4 - - - -
218B VAL* 3.3 32.9 - - + +
219B ASP* 3.7 23.8 + - + +
222B PHE* 3.6 43.6 - + + -
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Residues in contact with SER 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A SER* 5.0 4.8 + - - -
35B PRO* 3.8 13.0 - - - +
36B TYR* 1.3 81.6 - - - +
38B ALA* 1.3 58.5 + - - +
40B ILE* 3.2 6.4 + - - +
41B ALA* 2.9 31.2 + - - +
215B SER 5.8 0.4 - - - -
219B ASP* 3.0 34.7 + - - -
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Residues in contact with ALA 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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34A TYR* 3.6 27.6 - - + +
38A ALA* 4.5 5.1 - - + +
42A SER* 4.4 17.7 - - - +
34B TYR* 3.5 16.3 + - + -
35B PRO* 3.1 20.0 + - + +
37B SER* 1.3 82.1 + - - +
39B PHE* 1.3 57.7 + - - +
41B ALA* 4.0 0.9 - - - +
42B SER* 3.0 31.4 + - - -
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Residues in contact with PHE 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLU* 4.1 7.6 - - + -
26B ILE 3.1 31.6 - - - -
27B PHE* 3.5 45.3 - + + -
34B TYR* 3.6 14.6 - - + -
35B PRO 3.5 1.8 + - - -
36B TYR* 3.0 16.0 + + - +
38B ALA* 1.3 78.7 - - - +
40B ILE* 1.3 71.6 + - + +
42B SER* 4.3 1.6 - - - -
43B VAL* 2.9 61.8 + - + +
75B THR* 4.4 25.6 - - + -
76B GLU 5.4 0.2 - - - -
77B LEU* 5.0 7.2 - - + -
149B MET* 6.4 1.1 - - + -
205B VAL* 5.1 13.5 - - + -
209B LEU* 6.1 0.9 - - + -
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Residues in contact with ILE 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A LYS* 6.1 0.9 - - - -
36B TYR* 3.1 53.9 + - + +
37B SER* 3.7 8.5 - - - +
39B PHE* 1.3 80.4 - - + +
41B ALA* 1.3 59.8 + - - +
43B VAL* 4.2 0.2 - - - +
44B ARG* 2.8 79.3 + - + +
204B MET 4.3 3.4 - - - +
205B VAL* 4.8 2.5 - - + +
208B GLY 4.1 9.2 - - - +
209B LEU* 3.9 21.1 - - + -
215B SER* 4.1 8.3 - - - -
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Residues in contact with ALA 41 (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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41A ALA* 4.1 9.2 - - - +
42A SER* 4.1 24.5 - - - +
45A LYS* 4.1 27.4 - - + -
37B SER 2.9 17.1 + - - +
38B ALA* 4.0 4.0 - - - +
40B ILE* 1.3 78.6 - - - +
42B SER* 1.3 62.4 + - - +
44B ARG* 4.2 5.0 - - - +
45B LYS* 3.5 20.3 + - - +
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Residues in contact with SER 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35A PRO* 5.6 1.2 - - - +
37A SER* 4.7 6.8 + - - -
38A ALA* 4.0 25.4 + - - +
41A ALA* 4.1 9.9 - - - +
34B TYR* 4.5 4.4 + - - -
38B ALA 3.0 20.3 + - - -
39B PHE* 3.9 5.8 - - - -
41B ALA* 1.3 76.8 - - - +
43B VAL* 1.3 66.3 + - - +
45B LYS* 3.3 17.5 - - - +
46B ASP* 3.4 13.9 + - - +
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Residues in contact with VAL 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLU* 3.8 15.0 - - + -
39B PHE* 2.9 61.0 + - + +
42B SER* 1.3 73.1 - - - +
44B ARG* 1.3 67.1 + - - +
46B ASP* 3.4 10.0 + - + +
47B VAL* 3.2 19.7 + - + +
73B LEU* 3.8 32.3 - - + -
75B THR* 4.9 3.4 - - + -
209B LEU* 3.8 23.3 - - + -
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Residues in contact with ARG 44 (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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45A LYS* 4.2 21.6 - - - +
40B ILE* 2.8 38.5 + - - +
41B ALA* 4.2 4.4 - - - +
43B VAL* 1.3 73.1 - - - +
45B LYS* 1.3 66.0 + - - +
47B VAL* 2.9 8.8 + - - +
48B ILE* 2.8 36.2 + - + +
208B GLY 2.8 18.0 + - - -
209B LEU* 3.1 25.9 + - + +
211B PHE 3.6 8.1 + - - -
212B ASN* 3.6 11.3 - - - +
215B SER* 2.8 28.5 + - - -
278B ALA* 3.6 21.1 - - - +
279B LEU* 4.0 19.7 - - + -
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Residues in contact with LYS 45 (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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37A SER 5.4 1.8 - - - -
40A ILE* 6.0 1.1 - - - -
41A ALA* 3.8 31.6 - - + +
44A ARG* 4.7 16.2 - - - +
41B ALA 3.5 8.9 + - - +
42B SER 3.3 12.3 + - - +
44B ARG* 1.3 77.0 - - - +
46B ASP* 1.3 67.6 + - - +
48B ILE* 3.0 21.2 + - + +
49B LYS* 3.1 38.5 + - + +
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Residues in contact with ASP 46 (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 PHE* 3.2 33.0 - - + -
24B THR 4.8 3.3 - - - +
25B GLU* 4.4 14.0 - - - +
42B SER* 3.4 16.6 + - - +
43B VAL* 3.4 13.0 + - - +
45B LYS* 1.3 78.3 + - - +
47B VAL* 1.3 63.6 + - - +
49B LYS* 3.2 34.1 + - - +
50B HIS* 3.2 17.2 + - - -
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Residues in contact with VAL 47 (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 PHE* 4.4 2.9 - - + -
43B VAL* 3.2 17.0 - - + +
44B ARG* 2.9 11.4 + - - +
46B ASP* 1.3 75.2 - - - +
48B ILE* 1.3 63.4 + - - +
50B HIS* 3.1 16.5 + - - +
51B CYS* 3.2 10.2 + - - -
62B LEU* 3.5 31.4 - - + -
73B LEU* 3.9 26.7 - - + -
90B MET* 3.7 23.6 - - - -
93B LEU* 4.1 9.6 - - + -
209B LEU* 5.1 3.1 - - + -
279B LEU* 4.1 11.4 - - + -
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Residues in contact with ILE 48 (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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44B ARG* 2.8 30.0 + - + +
45B LYS* 3.0 11.2 + - + +
47B VAL* 1.3 70.5 - - + +
49B LYS* 1.3 57.4 + - - +
50B HIS 2.9 5.4 - - - -
51B CYS* 2.7 30.6 + - + +
60B PRO* 3.8 36.3 - - + -
279B LEU* 3.9 18.8 - - + -
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Residues in contact with LYS 49 (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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45B LYS* 3.1 36.4 + - + +
46B ASP* 3.2 34.0 + - - +
48B ILE* 1.3 75.8 - - - +
50B HIS* 1.3 69.2 + - + +
51B CYS 3.3 3.3 - - - +
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Residues in contact with HIS 50 (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 PHE* 4.2 22.3 - + - +
46B ASP 3.2 25.6 + - - -
47B VAL 3.1 2.3 + - - -
48B ILE 2.9 0.8 - - - -
49B LYS* 1.3 86.8 + - + +
51B CYS* 1.3 60.1 + - - +
52B THR* 5.3 2.8 - - - +
63B PRO* 3.3 20.4 - - + +
71B LEU* 3.7 23.0 - - + +
90B MET* 3.2 33.4 - - + -
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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