Contacts of the helix formed by residues 19 - 36 (chain C) in PDB entry 1Y8Q
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 TYR 19 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ILE* 5.0 3.6 - - + -
15C GLU* 3.0 46.7 + - + +
18C GLN* 1.3 94.0 - - + +
20C ASP* 1.3 65.5 + - - +
21C ARG 3.3 2.9 - - - -
22C GLN* 3.0 29.7 + - + +
23C ILE* 2.9 38.9 + - + +
31C GLN* 3.8 19.3 - - + -
35C ARG* 5.6 5.2 - - + -
57C LEU 3.7 20.9 - - - -
58C ALA 3.7 5.8 - - - -
59C GLY* 3.3 15.5 - - - -
103C ASN* 3.1 21.2 + - - -
105C MET* 4.0 12.8 - - - +
106C VAL* 4.9 0.2 - - - +
58D ASN* 4.4 4.3 - - + -
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Residues in contact with ASP 20 (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 ALA 3.1 19.9 + - - +
17C ALA* 3.6 12.8 - - - +
18C GLN 3.3 1.4 - - - -
19C TYR* 1.3 77.8 - - - +
21C ARG* 1.3 91.8 + - - +
23C ILE* 3.3 6.9 + - - +
24C ARG* 2.6 67.2 + - - +
55D SER* 4.6 2.2 - - - -
374D PHE* 4.3 7.4 - - - -
377D LYS* 3.4 12.2 + - - -
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Residues in contact with ARG 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C GLN 4.9 1.4 + - - -
19C TYR 3.1 1.2 + - - -
20C ASP* 1.3 110.4 + - - +
22C GLN* 1.3 58.2 + - - +
24C ARG* 3.8 6.6 + - - +
55D SER* 3.6 24.8 + - - +
58D ASN* 4.2 3.4 - - - +
59D ARG* 3.6 31.0 - - - +
346D LYS* 3.4 11.7 - - - +
347D ASP* 3.2 22.2 + - - -
377D LYS* 5.0 4.2 - - - +
383D ILE* 3.6 32.5 - - - +
384D ILE 4.2 7.0 - - - -
385D PRO* 3.4 11.8 - - - +
386D ALA 3.1 34.0 + - - +
801D ATP 2.7 40.3 + - - -
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Residues in contact with GLN 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C TYR* 3.0 26.9 + - - +
21C ARG* 1.3 75.5 - - - +
23C ILE* 1.3 60.8 + - - +
24C ARG 3.0 1.8 - - - -
25C LEU* 2.8 19.5 + - - +
26C TRP* 3.0 34.4 + - + -
31C GLN* 2.9 24.7 + - - +
58C ALA* 2.8 36.9 + - - +
58D ASN* 2.9 30.8 + - - +
386D ALA 3.6 5.6 + - - +
387D ILE* 3.6 26.1 - - + +
388D ALA 5.2 0.7 + - - -
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Residues in contact with ILE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11C ILE* 4.2 22.0 - - + -
16C ALA* 4.1 12.6 - - - +
19C TYR* 2.9 40.8 + - + +
20C ASP* 3.8 5.8 - - - +
22C GLN* 1.3 76.0 - - - +
24C ARG* 1.3 59.9 + - - +
26C TRP* 4.6 1.1 - - - -
27C GLY* 2.8 30.7 + - - +
28C LEU* 4.0 19.7 - - + +
31C GLN* 4.2 19.3 - - + +
307D LEU* 4.4 16.8 - - + -
310D GLN* 5.1 3.4 - - - +
374D PHE* 4.1 22.0 - - + -
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Residues in contact with ARG 24 (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 ASP* 2.6 49.2 + - - +
21C ARG* 3.8 8.3 - - - +
22C GLN 3.0 0.4 - - - -
23C ILE* 1.3 78.0 - - - +
25C LEU* 1.3 57.5 + - - +
374D PHE* 2.9 57.6 + - + +
377D LYS* 3.2 31.5 - - - +
378D SER* 2.8 34.3 + - - +
383D ILE* 3.7 27.2 - - - +
385D PRO* 3.4 21.8 - - + +
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Residues in contact with LEU 25 (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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21C ARG 4.4 0.2 - - - +
22C GLN* 2.8 16.5 + - - +
24C ARG* 1.3 81.5 - - - +
26C TRP* 1.3 62.7 + - + +
27C GLY 3.7 0.4 - - - -
321C ARG* 4.1 11.4 + - - -
143D GLY* 3.7 27.8 - - - -
144D TYR* 3.5 43.6 - - + -
385D PRO* 3.7 17.4 - - + +
386D ALA 5.4 0.2 - - - -
387D ILE* 3.7 31.0 - - + -
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Residues in contact with TRP 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN* 3.0 41.2 + - + -
23C ILE* 4.6 0.2 - - - -
25C LEU* 1.3 85.6 - - + +
27C GLY* 1.3 75.2 + - - +
30C ALA* 3.3 29.7 + - + +
31C GLN* 2.8 26.4 - - - +
34C LEU* 4.2 13.5 - - + -
58C ALA* 4.9 5.8 - - + -
312C GLN* 6.5 0.2 - - + -
315C VAL* 3.8 25.1 - - + -
319C SER* 5.7 3.6 - - - -
321C ARG* 3.4 37.3 + - + +
322C ASP* 5.4 0.4 - - - +
144D TYR* 3.3 32.3 - + + +
387D ILE* 3.8 33.2 - - + -
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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
----------------------------------------------------------
23C ILE* 2.8 24.9 + - - -
25C LEU 3.7 1.0 - - - -
26C TRP* 1.3 86.0 - - - +
28C LEU* 1.3 65.4 + - - -
29C GLU 3.4 2.4 + - - -
31C GLN* 3.2 18.0 + - - +
321C ARG* 5.4 1.6 - - - -
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Residues in contact with LEU 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLY* 3.8 27.1 - - - +
11C ILE* 4.2 24.2 - - + -
23C ILE* 4.0 11.3 - - + +
27C GLY* 1.3 71.1 - - - -
29C GLU* 1.3 59.9 + - + +
31C GLN* 3.1 9.0 + - + +
32C LYS* 2.8 57.8 + - + +
305D LEU 5.0 0.4 - - - +
306D GLY* 3.8 18.4 - - - -
307D LEU* 3.8 26.7 - - + +
310D GLN* 4.0 10.3 - - - +
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Residues in contact with GLU 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27C GLY 3.4 0.6 - - - -
28C LEU* 1.3 78.2 - - + +
30C ALA* 1.3 64.2 + - - +
32C LYS* 3.1 20.4 + - - +
33C ARG* 2.9 57.2 + - - +
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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
----------------------------------------------------------
26C TRP* 3.3 38.0 + - + +
27C GLY 3.5 1.2 + - - -
28C LEU 3.3 0.4 - - - -
29C GLU* 1.3 77.9 - - - +
31C GLN* 1.3 63.2 + - - +
33C ARG* 3.2 11.5 + - - +
34C LEU* 3.0 24.7 + - - +
319C SER* 3.6 25.4 - - - -
321C ARG* 3.9 15.9 - - + -
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Residues in contact with GLN 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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11C ILE* 5.3 7.4 - - + -
19C TYR* 3.8 26.2 - - + -
22C GLN* 2.9 25.7 + - - +
23C ILE* 4.2 17.0 - - + +
26C TRP* 2.8 33.3 - - - +
27C GLY 3.2 11.5 + - - +
28C LEU* 3.1 16.9 + - + +
30C ALA* 1.3 80.4 - - - +
32C LYS* 1.3 56.6 + - - +
34C LEU* 3.4 8.7 + - - +
35C ARG* 2.9 29.0 + - + +
58C ALA 3.0 21.5 - - - +
59C GLY 4.3 4.0 - - - +
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Residues in contact with LYS 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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9C GLY 3.0 16.2 - - - +
10C GLY* 2.7 41.4 - - - +
11C ILE* 4.2 10.8 - - + +
28C LEU* 2.8 46.2 + - + +
29C GLU* 3.6 23.7 + - - +
31C GLN* 1.3 71.8 - - - +
33C ARG* 1.3 65.8 + - - +
35C ARG* 3.2 21.6 + - - +
36C ALA* 3.2 14.4 + - - +
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Residues in contact with ARG 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 GLU* 2.9 43.9 + - - +
30C ALA* 3.3 32.0 - - - +
32C LYS* 1.3 74.1 - - - +
34C LEU* 1.3 61.5 + - - +
36C ALA* 3.0 16.3 + - - +
37C SER* 3.0 18.5 + - - -
175C VAL* 5.2 10.1 - - - +
318C LEU 3.9 14.3 - - - +
319C SER* 3.1 29.0 + - - -
320C GLN* 4.3 22.0 + - - +
321C ARG* 4.9 5.5 - - - +
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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
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26C TRP* 4.2 13.2 - - + -
30C ALA 3.0 17.1 + - - +
31C GLN* 3.5 9.2 - - - +
33C ARG* 1.3 77.6 - - - +
35C ARG* 1.3 56.4 + - - +
37C SER* 3.1 22.0 + - - -
58C ALA* 3.6 33.0 - - + +
59C GLY 3.8 2.0 - - - +
60C VAL* 3.3 28.8 - - + -
315C VAL* 3.7 47.1 - - + +
318C LEU* 3.8 28.0 + - + -
319C SER* 4.7 2.6 - - - +
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Residues in contact with ARG 35 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C GLY* 3.8 20.4 + - - -
11C ILE* 3.5 28.9 - - - +
12C SER 4.8 0.6 - - - +
15C GLU* 3.0 38.5 + - - +
19C TYR* 5.6 6.3 - - + -
31C GLN* 2.9 20.8 + - - +
32C LYS* 3.2 14.4 + - - +
34C LEU* 1.3 74.1 - - - +
36C ALA* 1.3 58.2 + - - +
37C SER 3.5 0.2 - - - -
59C GLY 3.4 16.1 + - - +
60C VAL 5.9 0.2 - - - +
61C LYS* 3.1 24.3 + - - +
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Residues in contact with ALA 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C LYS 3.2 9.3 + - - +
33C ARG* 3.0 12.1 + - - +
35C ARG* 1.3 77.8 - - - +
37C SER* 1.3 60.8 + - - +
38C ARG* 4.0 1.2 + - - +
61C LYS* 3.8 16.9 - - - +
127C ASP* 3.8 6.6 - - - +
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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