Contacts of the helix formed by residues 28 - 45 (chain C) in PDB entry 5Y3R
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 ALA 28 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C ALA* 1.3 70.0 - - - +
29C LEU* 1.3 69.6 + - + +
30C ALA 2.9 1.2 + - - -
31C GLY* 2.9 7.6 + - - -
32C HIS* 2.3 36.4 + - - -
77C GLU* 2.3 40.1 + - + +
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Residues in contact with LEU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C ALA 3.5 0.2 + - - -
28C ALA* 1.3 79.7 - - + +
30C ALA* 1.3 64.3 + - - +
32C HIS* 3.0 20.9 + - + +
33C GLN* 3.0 21.8 + - + +
36C ARG* 6.5 0.2 - - - -
80C GLU* 5.9 2.5 - - - +
2390C HIS* 3.3 63.5 - - + +
2391C GLY* 5.3 2.5 - - - +
2393C LEU* 3.6 30.3 - - + -
2426C HIS 4.9 2.7 - - - +
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Residues in contact with ALA 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASP* 4.4 9.4 - - - +
27C ALA* 3.3 19.9 + - - +
28C ALA 2.9 1.2 + - - -
29C LEU* 1.3 79.3 - - - +
31C GLY* 1.3 64.0 + - - +
33C GLN* 3.3 15.6 + - - +
34C LEU* 3.1 19.8 + - - +
2426C HIS* 5.3 8.0 + - + +
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Residues in contact with GLY 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23C ASP* 3.3 22.6 + - - -
27C ALA* 3.5 10.1 - - - +
28C ALA 2.9 10.1 + - - -
30C ALA* 1.3 76.5 - - - +
32C HIS* 1.3 51.3 + - - +
34C LEU* 2.6 8.1 - - - +
35C ILE* 2.5 44.2 + - - +
81C CYS* 4.5 5.2 - - - -
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Residues in contact with HIS 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28C ALA* 2.3 48.8 + - - -
29C LEU* 3.0 11.9 + - + +
31C GLY* 1.3 75.4 - - - +
33C GLN* 1.3 52.5 + - - +
35C ILE* 2.9 13.7 + - - +
36C ARG* 2.4 44.5 + - - +
77C GLU* 2.6 31.5 + - + -
80C GLU* 3.0 26.4 - - + +
81C CYS* 2.8 38.0 + - - -
84C GLU* 3.6 16.6 - - + +
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Residues in contact with GLN 33 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29C LEU* 3.0 19.7 + - + +
30C ALA* 3.3 13.4 + - - +
32C HIS* 1.3 73.0 - - - +
34C LEU* 1.3 58.0 + - - +
36C ARG* 3.0 16.9 - - - +
37C GLY 2.4 35.0 + - - -
2425C ARG 3.8 4.8 + - - -
2426C HIS* 2.8 31.1 + - - +
2427C ARG* 2.9 15.8 - - - +
2428C ASP* 2.6 38.3 + - - +
2429C ASP* 3.0 20.5 - - - +
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Residues in contact with LEU 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15C LEU* 3.6 12.1 - - + +
16C GLN* 4.4 2.2 - - + +
19C LEU* 3.7 21.3 - - + -
20C SER* 3.2 28.5 - - - +
23C ASP* 3.2 26.2 - - - +
30C ALA 3.1 10.8 - - - +
31C GLY* 2.6 14.3 + - - +
33C GLN* 1.3 84.9 - - - +
35C ILE* 1.3 66.2 + - + +
37C GLY 3.0 7.4 + - - -
38C LEU* 3.1 47.3 + - + +
2428C ASP* 3.3 10.1 - - + +
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Residues in contact with ILE 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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20C SER* 6.5 0.2 - - - -
31C GLY* 2.5 25.9 + - - +
32C HIS* 3.1 16.2 - - - +
34C LEU* 1.3 77.1 - - + +
36C ARG* 1.3 64.1 + - - +
38C LEU* 5.6 0.4 - - - -
39C GLY* 2.9 21.0 + - - +
81C CYS* 3.5 40.2 - - + +
84C GLU* 3.3 9.6 - - + +
85C ILE* 3.3 48.0 - - + +
88C PHE* 3.2 5.5 - - + -
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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
----------------------------------------------------------
29C LEU* 5.9 0.6 - - - +
32C HIS* 2.4 27.4 + - - +
33C GLN* 2.9 16.0 + - - +
35C ILE* 1.3 72.5 - - - +
37C GLY* 1.3 57.1 + - - +
40C GLN* 2.1 55.9 + - - +
84C GLU* 3.1 32.8 + - + +
88C PHE* 3.5 11.4 - - + -
2393C LEU* 4.0 24.8 - - - +
2394C LYS* 3.6 42.4 - - - +
2429C ASP* 3.4 28.3 + - - +
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Residues in contact with GLY 37 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLN 2.4 24.2 + - - -
34C LEU 3.0 0.2 + - - -
36C ARG* 1.3 66.5 - - - +
38C LEU* 1.3 58.7 + - - +
40C GLN* 4.7 1.3 - - - -
41C GLU* 2.5 48.4 + - - +
2428C ASP* 3.9 7.4 - - - -
2429C ASP* 4.0 1.8 + - - -
2430C GLU* 4.0 17.0 - - - -
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C SER* 3.2 22.9 - - - +
12C LEU* 3.6 30.3 - - + +
15C LEU* 3.4 22.9 - - + -
16C GLN* 3.3 36.8 - - + +
34C LEU* 3.1 29.4 + - + +
35C ILE* 5.6 0.2 - - - -
37C GLY* 1.3 72.9 - - - +
39C GLY* 1.3 56.9 + - - +
41C GLU* 5.0 2.7 - - - +
42C CYS* 2.8 28.3 + - - +
2428C ASP* 4.7 1.9 + - - +
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Residues in contact with GLY 39 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C ILE* 2.9 23.5 + - - +
38C LEU* 1.3 77.5 - - - +
40C GLN* 1.3 56.7 + - - +
42C CYS* 2.4 31.6 - - - +
88C PHE* 3.6 13.9 - - - -
92C PHE* 3.4 13.9 - - - -
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Residues in contact with GLN 40 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C ARG* 2.1 45.3 + - - +
37C GLY* 4.7 1.3 - - - -
39C GLY 1.3 62.8 - - - +
41C GLU* 1.3 59.2 + - + +
42C CYS 2.8 9.6 + - - -
43C VAL* 3.0 14.7 + - - +
44C LEU* 3.6 19.4 + - + +
88C PHE* 3.2 30.8 - - + -
92C PHE* 5.4 0.6 - - - -
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Residues in contact with GLU 41 (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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12C LEU* 5.0 5.1 - - - +
37C GLY* 2.5 23.9 + - - +
38C LEU* 3.8 2.8 - - - +
40C GLN* 1.3 70.4 - - + +
42C CYS* 1.3 66.6 + - - +
43C VAL 3.4 0.2 - - - -
44C LEU* 4.3 14.8 - - + +
45C SER* 3.4 24.2 + - - +
2430C GLU* 3.1 45.1 - - + +
2464C HIS* 5.6 5.9 - - - +
2465C PRO* 4.6 15.6 - - - +
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Residues in contact with CYS 42 (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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12C LEU* 4.6 12.9 - - + +
38C LEU 2.8 19.2 + - - +
39C GLY* 2.4 28.7 - - - +
40C GLN 2.8 0.4 + - - -
41C GLU* 1.3 79.3 - - - +
43C VAL* 1.3 58.9 + - - +
45C SER* 2.6 29.6 - - - +
46C SER* 3.8 0.3 + - - -
55C THR* 4.5 15.3 - - - +
58C VAL* 5.8 3.6 - - - -
59C PHE* 3.2 42.0 - - - -
92C PHE* 3.6 3.1 - - + -
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Residues in contact with VAL 43 (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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40C GLN 3.0 7.1 + - - +
42C CYS* 1.3 80.1 - - - +
44C LEU* 1.3 63.8 + - - +
45C SER 2.9 5.2 - - - -
46C SER* 2.2 31.3 + - - +
55C THR* 6.2 0.2 - - + -
92C PHE* 3.2 33.2 - - + -
95C LYS* 3.3 40.6 - - + +
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Residues in contact with LEU 44 (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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40C GLN* 3.6 20.8 + - + +
41C GLU* 4.8 10.3 - - + -
42C CYS 3.5 0.6 - - - -
43C VAL* 1.3 77.2 - - - +
45C SER* 1.3 58.7 + - - +
46C SER* 3.7 2.1 + - - -
2431C ARG* 5.7 7.4 - - - +
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Residues in contact with SER 45 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12C LEU* 6.5 0.7 - - - -
41C GLU* 3.4 21.2 + - - +
42C CYS 2.6 20.8 + - - +
43C VAL 2.9 0.8 - - - -
44C LEU* 1.3 76.1 + - - +
46C SER* 1.3 62.3 + - - +
51C LEU* 3.9 16.3 - - - +
55C THR* 5.4 2.8 - - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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