Contacts of the helix formed by residues 20 - 36 (chain C) in PDB entry 5Y7G
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 PHE 20 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18C GLU 3.2 1.0 - - - -
19C PRO* 1.3 91.3 - - + +
21C TYR* 1.3 65.2 + - - +
22C TYR* 3.0 23.1 - + - -
23C LEU* 2.8 27.7 + - + +
24C HIS* 3.2 37.7 + + + +
57C GLU* 5.4 2.5 - - - -
61C ALA* 4.0 16.2 - - + -
83C GLU* 2.9 47.8 - - + -
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Residues in contact with TYR 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 3.4 31.4 + - + +
19C PRO* 4.1 7.6 - - + -
20C PHE* 1.3 75.0 - - - +
22C TYR* 1.3 91.5 + + + +
24C HIS* 3.9 13.5 - - - -
25C ASN* 3.0 47.5 + - + +
65C ARG* 3.6 23.5 + - - -
68C MET* 5.3 3.1 - - + +
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Residues in contact with TYR 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PRO 3.7 11.9 - - - -
20C PHE* 2.9 15.0 + + - -
21C TYR* 1.3 103.7 - + + +
23C LEU* 1.3 78.5 + - + +
25C ASN* 4.3 2.1 - - - +
26C PHE* 3.0 26.9 + - - +
61C ALA* 3.4 27.6 - - - +
64C VAL* 3.4 23.0 - - + +
65C ARG* 3.2 35.1 + - - -
68C MET* 4.0 24.0 - - + +
83C GLU* 2.8 29.3 + - - -
84C ILE* 3.6 21.0 - - - +
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Residues in contact with LEU 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20C PHE* 2.8 20.7 + - + +
22C TYR* 1.3 91.0 - - + +
24C HIS* 1.3 61.2 + - + +
26C PHE* 3.3 6.6 + - + +
27C ARG* 2.8 68.4 + - + +
57C GLU* 4.3 6.5 - - - +
60C GLN* 3.5 37.2 - - + +
61C ALA* 4.1 17.5 - - + -
64C VAL* 3.6 22.9 - - + -
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Residues in contact with HIS 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLU* 5.8 5.2 - - + -
19C PRO* 6.1 0.6 - - - +
20C PHE* 3.2 43.8 + + + +
21C TYR* 4.0 9.6 - - - +
23C LEU* 1.3 76.2 - - + +
25C ASN* 1.3 65.6 + - - +
26C PHE 3.1 0.7 + - - -
27C ARG* 3.2 42.8 + - - +
28C ALA* 3.3 11.3 + - - +
57C GLU* 6.1 0.2 - - - -
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Residues in contact with ASN 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C TYR* 3.0 36.0 + - + +
22C TYR* 4.7 2.0 - - - +
24C HIS* 1.3 77.6 - - - +
26C PHE* 1.3 60.1 + - - +
28C ALA* 3.5 18.1 - - - +
29C VAL* 3.7 11.6 + - - +
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Residues in contact with PHE 26 (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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22C TYR 3.0 23.5 + - - +
23C LEU* 3.6 9.4 - - + +
24C HIS 3.1 0.8 - - - -
25C ASN* 1.3 75.1 - - - +
27C ARG* 1.3 69.5 + - + +
28C ALA 3.0 1.8 - - - -
29C VAL* 3.0 26.5 + - + +
30C LEU* 3.3 49.6 + - + -
64C VAL* 4.4 25.8 - - + -
67C VAL* 6.3 3.4 - - + -
68C MET* 6.4 1.1 - - + -
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Residues in contact with ARG 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C LEU* 2.8 49.7 + - + +
24C HIS* 3.2 37.4 + - - +
26C PHE* 1.3 74.7 - - + +
28C ALA* 1.3 63.8 + - - +
30C LEU* 3.1 23.8 + - + +
31C ALA* 3.1 13.5 + - - +
57C GLU* 3.5 16.0 + - - -
60C GLN* 3.1 30.8 + - - +
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Residues in contact with ALA 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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24C HIS 3.3 10.7 + - - +
25C ASN* 3.5 18.8 - - - +
26C PHE 3.0 1.0 - - - -
27C ARG* 1.3 76.3 - - - +
29C VAL* 1.3 61.4 + - + +
31C ALA* 3.3 8.3 + - - +
32C TRP* 3.2 22.7 + - - +
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Residues in contact with VAL 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C ASN 4.1 10.3 - - - +
26C PHE* 3.0 25.9 + - + +
28C ALA* 1.3 77.4 - - + +
30C LEU* 1.3 65.6 + - + +
32C TRP* 3.9 6.3 - - - +
33C ILE* 3.1 40.9 + - + +
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26C PHE* 3.3 47.3 + - + +
27C ARG* 3.1 17.4 + - + +
29C VAL* 1.3 83.9 - - + +
31C ALA* 1.3 57.1 + - - +
33C ILE* 3.4 7.9 + - + +
34C GLY* 2.9 26.0 + - - -
49C ILE* 5.7 13.2 - - + +
52C PHE* 5.1 28.0 - - + -
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Residues in contact with ALA 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 ARG 3.1 11.7 + - - +
28C ALA* 3.7 9.0 - - - +
30C LEU* 1.3 74.8 - - - +
32C TRP* 1.3 63.7 + - - +
34C GLY* 3.0 3.7 + - - +
35C GLU* 3.0 32.7 + - - +
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Residues in contact with TRP 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 ALA 3.2 13.7 + - - +
29C VAL* 3.9 7.2 - - - +
31C ALA* 1.3 77.7 - - - +
33C ILE* 1.3 63.6 + - + +
35C GLU* 4.1 14.6 - - - -
36C ARG* 2.9 88.9 + - + +
37C TYR* 3.9 23.4 - + - -
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Residues in contact with ILE 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 VAL* 3.1 34.2 + - + +
30C LEU* 4.0 7.6 - - + +
32C TRP* 1.3 80.2 - - + +
34C GLY* 1.3 62.1 + - - +
37C TYR* 3.3 43.8 + - + -
38C ALA* 3.3 7.4 + - - -
41C LEU* 4.3 21.1 - - + +
49C ILE* 4.9 7.9 - - + -
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Residues in contact with GLY 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 LEU 2.9 15.4 + - - -
31C ALA* 3.0 5.1 + - - -
33C ILE* 1.3 78.3 - - - +
35C GLU* 1.3 56.4 + - - +
38C ALA* 3.0 27.8 - - - +
41C LEU* 5.2 5.6 - - - +
49C ILE* 5.4 8.5 - - - -
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Residues in contact with GLU 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 ALA* 3.0 23.2 + - - +
32C TRP* 3.6 24.0 - - - +
34C GLY* 1.3 77.5 - - - +
36C ARG* 1.3 81.3 + - + +
38C ALA* 4.4 6.3 + - - +
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Residues in contact with ARG 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 TRP* 2.9 72.1 + - + +
35C GLU* 1.3 91.6 - - + +
37C TYR* 1.3 75.5 + - + +
38C ALA 3.5 0.6 + - - -
39C ASP* 3.7 10.4 - - - +
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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