Contacts of the helix formed by residues 35 - 49 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27A PHE* 4.7 0.2 - - - -
32A ALA 4.8 1.3 - - - +
33A ASN 3.0 13.7 - - - +
34A TYR* 1.3 89.0 - - + +
36A TYR* 1.3 67.2 + - - +
37A SER* 3.7 14.8 - - - +
38A ALA* 3.0 32.9 + - + +
39A PHE* 3.3 4.2 + - - +
146A ARG* 4.2 6.1 - - - +
219A ASP* 4.4 3.6 - - - +
223A ASN* 6.1 1.1 - - - +
34B TYR* 3.6 17.9 - - + +
42B SER* 5.6 1.1 - - - +
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Residues in contact with TYR 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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27A PHE* 4.3 13.7 - + - -
34A TYR 3.7 2.0 + - - -
35A PRO* 1.3 71.8 - - - +
37A SER* 1.3 61.7 + - - +
39A PHE* 3.1 11.0 + + - +
40A ILE* 3.0 50.8 + - + +
149A MET* 4.7 6.7 - - + -
204A MET* 2.4 41.4 + - + -
205A VAL* 5.5 1.1 - - + -
208A GLY* 3.5 15.9 - - - -
215A SER* 3.6 14.0 - - - -
218A VAL* 3.5 30.0 - - + +
219A ASP* 3.6 30.4 + - + +
222A PHE* 3.7 43.7 - + + -
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Residues in contact with SER 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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35A PRO* 3.7 13.0 - - - +
36A TYR* 1.3 76.7 - - - +
38A ALA* 1.3 59.3 + - - +
40A ILE* 3.7 8.0 - - - +
41A ALA* 2.9 30.3 + - - +
215A SER* 6.4 0.4 - - - -
219A ASP* 2.8 36.2 + - - -
42B SER* 4.7 6.5 + - - -
45B LYS* 5.4 1.7 - - - -
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Residues in contact with ALA 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 TYR* 3.5 16.6 - - + -
35A PRO* 3.0 27.5 + - + +
37A SER* 1.3 79.7 + - - +
39A PHE* 1.3 60.6 + - - +
41A ALA* 3.4 1.7 + - - +
42A SER* 2.8 31.9 + - - -
34B TYR* 3.8 15.9 - - + +
38B ALA* 4.5 6.3 - - + +
42B SER* 4.0 18.4 - - - +
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Residues in contact with PHE 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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25A GLU* 3.8 15.0 - - + -
26A ILE 3.7 18.4 - - - -
27A PHE* 3.6 58.3 - + + -
34A TYR* 3.6 13.6 - - + -
35A PRO 3.3 1.6 + - - -
36A TYR* 3.1 13.6 + + - +
38A ALA* 1.3 79.2 - - - +
40A ILE* 1.3 70.9 + - + +
42A SER* 3.3 2.4 + - - -
43A VAL* 2.8 60.2 + - + +
75A THR* 4.3 18.2 - - + -
77A LEU* 4.8 6.7 - - + -
149A MET* 6.5 0.9 - - + -
205A VAL* 5.1 14.4 - - + -
209A LEU* 6.0 1.3 - - + -
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Residues in contact with ILE 40 (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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36A TYR* 3.0 57.3 + - + +
37A SER* 3.7 8.7 - - - +
38A ALA 3.2 0.2 - - - -
39A PHE* 1.3 85.3 - - + +
41A ALA* 1.3 56.1 + - - +
43A VAL* 3.1 1.4 + - - +
44A ARG* 2.8 75.3 + - + +
204A MET 4.4 4.3 - - - +
205A VAL* 5.0 2.7 - - + +
208A GLY 4.2 6.1 - - - +
209A LEU* 4.3 18.6 - - + -
215A SER* 4.0 8.5 - - - -
45B LYS* 6.0 1.3 - - - -
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Residues in contact with ALA 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 SER 2.9 18.4 + - - +
38A ALA 3.8 3.4 - - - +
40A ILE* 1.3 78.8 - - - +
42A SER* 1.3 60.2 + - - +
44A ARG* 4.3 5.4 - - - +
45A LYS* 3.4 22.5 + - - +
41B ALA* 4.1 8.0 - - - +
42B SER* 4.1 22.4 - - - +
45B LYS* 3.8 33.5 - - + +
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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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25A GLU* 4.2 9.7 + - - -
34A TYR* 4.6 4.5 + - - -
38A ALA 2.8 20.3 + - - -
39A PHE* 3.7 6.9 - - - -
41A ALA* 1.3 74.6 - - - +
43A VAL* 1.3 65.4 + - - +
45A LYS* 3.4 4.2 + - - +
46A ASP* 3.4 28.0 + - - +
35B PRO* 6.1 0.2 - - - +
37B SER* 5.0 5.4 + - - -
38B ALA* 4.4 20.9 - - - +
41B ALA* 4.1 11.7 - - - +
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Residues in contact with VAL 43 (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 GLU* 3.6 28.3 - - + +
39A PHE* 2.8 60.8 + - + +
42A SER* 1.3 70.9 - - - +
44A ARG* 1.3 66.3 + - - +
46A ASP* 3.3 3.0 + - - +
47A VAL* 3.1 29.5 + - + +
73A LEU* 3.8 26.2 - - + -
75A THR* 4.8 2.5 - - + -
209A LEU* 3.6 24.7 - - + -
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Residues in contact with ARG 44 (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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40A ILE* 2.8 35.4 + - - +
41A ALA* 4.3 5.4 - - - +
43A VAL* 1.3 73.9 - - - +
45A LYS* 1.3 52.7 + - - +
47A VAL* 3.2 5.8 + - - +
48A ILE* 2.8 51.3 + - + +
208A GLY 2.8 25.3 + - - -
209A LEU* 3.0 32.9 + - + +
211A PHE 3.4 8.5 + - - -
212A ASN* 3.5 11.9 - - - +
215A SER* 3.0 22.0 + - - -
278A ALA* 3.5 20.9 - - - +
279A LEU* 4.3 13.7 - - + -
45B LYS* 4.7 16.9 - - - +
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Residues in contact with LYS 45 (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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41A ALA 3.4 16.3 + - - +
42A SER 3.5 5.8 - - - +
43A VAL 3.2 0.2 - - - -
44A ARG* 1.3 80.2 - - - +
46A ASP* 1.3 64.2 + - - +
48A ILE* 3.8 9.4 + - - +
49A LYS* 3.5 47.6 + - - +
40B ILE* 6.1 0.9 - - - -
41B ALA* 4.1 22.9 - - + +
44B ARG* 4.2 21.5 - - - +
212B ASN* 6.3 1.1 - - - +
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Residues in contact with ASP 46 (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 PHE* 4.0 12.2 - - + -
25A GLU* 2.7 40.2 - - - +
42A SER* 3.4 15.3 + - - +
43A VAL 3.3 5.7 + - - +
44A ARG 3.2 0.8 - - - -
45A LYS* 1.3 81.9 + - - +
47A VAL* 1.3 63.3 + - - +
49A LYS* 3.2 42.3 + - + +
50A HIS* 3.3 13.5 + - - -
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Residues in contact with VAL 47 (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 PHE* 4.2 5.2 - - + -
43A VAL* 3.1 20.1 + - + +
44A ARG* 3.2 7.2 + - - +
46A ASP* 1.3 74.5 - - - +
48A ILE* 1.3 57.1 + - - +
49A LYS 3.0 4.7 - - - -
50A HIS* 2.9 22.0 + - - +
51A CYS* 3.4 8.6 - - - -
62A LEU* 3.8 26.5 - - + -
73A LEU* 4.1 22.0 - - + -
90A MET* 3.7 30.9 - - - +
93A LEU* 4.3 8.7 - - + -
209A LEU* 5.4 2.2 - - + -
279A LEU* 4.2 13.0 - - + -
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Residues in contact with ILE 48 (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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44A ARG* 2.8 36.8 + - + +
45A LYS* 4.1 8.5 - - - +
46A ASP 3.4 0.2 - - - -
47A VAL* 1.3 73.4 - - - +
49A LYS* 1.3 64.8 + - - +
51A CYS* 3.0 23.2 + - + +
60A PRO* 4.0 28.7 - - + -
279A LEU* 3.9 24.7 - - + -
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Residues in contact with LYS 49 (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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45A LYS* 3.5 36.9 + - - +
46A ASP* 3.2 39.9 + - + +
47A VAL 3.0 0.8 - - - -
48A ILE* 1.3 79.8 - - - +
50A HIS* 1.3 68.0 + - + +
51A CYS 3.4 3.7 + - - +
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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