Contacts of the helix formed by residues 25 - 36 (chain C) in PDB entry 2PYO
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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C SER* 3.5 6.3 - - - +
23C GLN 3.5 1.7 - - - +
24C PHE* 1.3 88.5 - - + +
26C VAL* 1.3 65.6 + - - +
27C GLY 3.3 1.8 - - - +
28C ARG* 3.9 28.9 - - + +
29C ILE* 3.1 26.4 + - + +
34D TYR* 4.4 9.0 - - + -
37D TYR* 3.5 50.7 - - + +
-44I A 5.0 3.6 - - - +
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Residues in contact with VAL 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ARG* 3.7 41.7 - - + +
17C SER* 2.9 33.7 + - - +
20C ALA* 4.5 1.6 - - + -
22C LEU* 4.2 17.9 - - + -
24C PHE 3.2 5.8 + - - +
25C PRO* 1.3 67.9 - - - +
27C GLY* 1.3 67.8 + - - +
29C ILE* 3.3 1.1 + - - -
30C HIS* 3.0 21.7 + - - +
47C PRO* 3.7 6.1 - - + +
48C VAL* 4.1 28.9 - - + +
51C ALA* 4.4 11.0 - - + -
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Residues in contact with GLY 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16C ARG* 3.7 23.0 + - - +
17C SER* 4.7 1.0 + - - +
25C PRO* 3.3 0.8 - - - +
26C VAL* 1.3 79.0 - - - +
28C ARG* 1.3 55.9 + - - +
30C HIS* 3.2 4.3 + - - +
31C ARG* 3.0 24.3 + - - +
-44I A 3.6 21.8 + - - -
-43I G 4.3 11.7 + - - -
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Residues in contact with ARG 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C PRO* 3.4 22.1 + - + +
26C VAL 3.3 0.4 - - - -
27C GLY* 1.3 73.4 - - - +
29C ILE* 1.3 56.4 + - - +
31C ARG* 3.2 10.2 + - - +
32C LEU* 2.8 57.7 + - + +
30D ARG* 5.2 1.4 - - - +
32D GLU* 3.4 37.5 + - - +
33D SER* 2.6 36.8 + - - +
34D TYR* 4.4 11.9 - - + +
37D TYR* 3.9 15.5 + - - -
-45I A 5.5 1.4 + - - -
-44I A 3.2 25.2 + - - +
48J G 3.1 23.2 + - - -
49J G 3.0 19.0 + - - -
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Residues in contact with ILE 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C PHE* 4.7 9.2 - - + -
25C PRO* 3.1 16.5 + - + +
26C VAL 3.8 3.4 - - - +
28C ARG* 1.3 73.2 - - - +
30C HIS* 1.3 60.3 + - - +
32C LEU* 3.7 7.4 - - - +
33C LEU* 2.8 29.7 + - + +
47C PRO* 3.9 23.6 - - + +
50C LEU* 4.1 13.2 - - + -
51C ALA* 3.3 36.1 - - + -
54C MET* 3.6 21.3 - - + -
34D TYR* 4.3 18.8 - - + +
67D PHE* 3.9 15.9 - - + -
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Residues in contact with HIS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C ARG* 2.7 35.4 + - - +
26C VAL 3.0 13.7 + - - +
27C GLY 3.3 10.1 - - - +
29C ILE* 1.3 78.9 - - - +
31C ARG* 1.3 62.5 + - - +
33C LEU* 3.3 3.3 + - - +
34C ARG* 2.8 58.8 + - - +
42C VAL* 3.3 24.8 + - + +
43C GLY 4.3 0.2 + - - -
44C ALA* 4.2 13.5 - - + -
47C PRO* 3.5 22.9 - - + +
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Residues in contact with ARG 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C GLY 3.0 11.1 + - - +
28C ARG* 3.2 18.9 + - - +
30C HIS* 1.3 73.8 - - - +
32C LEU* 1.3 69.0 + - - +
34C ARG* 2.9 13.1 + - + +
35C LYS* 2.8 42.7 + - + +
32D GLU* 2.5 41.0 + - - -
-45I A 3.2 39.7 + - - -
-44I A 2.4 34.1 + - - +
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Residues in contact with LEU 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ARG* 2.8 41.5 + - + +
29C ILE* 3.7 4.5 - - - +
31C ARG* 1.3 83.6 - - - +
33C LEU* 1.3 61.8 + - - +
35C LYS* 3.9 29.8 - - - +
36C GLY* 3.1 21.1 + - - -
38C TYR* 4.0 0.3 - - - -
32D GLU* 4.9 3.8 - - - +
34D TYR* 3.4 26.7 - - + +
64D ASN* 5.4 3.6 - - - +
67D PHE* 3.6 26.7 - - + -
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Residues in contact with LEU 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ILE* 2.8 20.5 + - + +
30C HIS* 3.5 5.6 - - - +
31C ARG 3.1 0.2 - - - -
32C LEU* 1.3 77.9 - - - +
34C ARG* 1.3 60.6 + - - +
36C GLY 3.6 0.5 + - - -
37C ASN 4.1 2.1 + - - -
38C TYR* 3.2 32.1 + - + +
39C ALA 5.6 0.5 - - - +
42C VAL* 3.6 37.2 - - + +
46C ALA* 4.1 7.2 - - + -
47C PRO* 4.1 25.4 - - + -
50C LEU* 4.1 11.7 - - + -
67D PHE* 3.9 12.1 - - + -
71D ALA* 3.8 30.3 - - + -
86D ILE* 5.2 6.5 - - + -
91D ILE* 5.1 6.1 - - + -
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Residues in contact with ARG 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C HIS* 2.8 52.7 + - + +
31C ARG* 2.9 13.8 + - + +
33C LEU* 1.3 77.9 - - - +
35C LYS* 1.3 64.2 + - - +
36C GLY 3.3 0.9 + - - -
37C ASN* 3.5 11.8 + - - -
39C ALA 5.5 3.5 - - - +
40C GLU 5.3 1.2 + - - -
41C ARG* 5.2 0.4 - - - +
42C VAL* 3.6 20.7 + - + +
39J T 2.9 45.3 + - - +
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Residues in contact with LYS 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ARG* 2.8 33.6 + - + +
32C LEU* 3.9 26.3 - - + +
34C ARG* 1.3 73.5 - - - +
36C GLY* 1.3 59.9 + - - +
37C ASN* 3.3 4.6 + - - +
79H HIS* 3.5 17.2 + - + -
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Residues in contact with GLY 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32C LEU 3.1 11.7 + - - -
33C LEU 3.6 0.2 + - - -
34C ARG 3.2 1.4 - - - -
35C LYS* 1.3 76.5 - - - +
37C ASN* 1.3 73.4 + - - +
38C TYR* 3.5 33.3 - - - -
79H HIS* 3.2 17.0 - - - -
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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