Contacts of the helix formed by residues 12 - 27 (chain A) 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 SER 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10A GLY 3.9 1.6 + - - -
11A ILE* 1.3 76.7 - - - +
13A GLU* 1.3 65.6 + - - +
14A GLU* 3.8 7.5 + - - +
15A GLU* 2.9 38.8 + - - +
16A ALA* 3.1 22.0 + - - +
105A MET* 4.7 3.5 - - - +
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Residues in contact with GLU 13 (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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12A SER* 1.3 75.2 - - - +
14A GLU* 1.3 64.0 - - - +
16A ALA* 3.3 8.0 + - - +
17A ALA* 3.1 23.3 + - + +
308B LYS* 5.7 5.7 + - - +
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Residues in contact with GLU 14 (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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12A SER* 3.3 8.4 + - - +
13A GLU* 1.3 81.4 - - - +
15A GLU* 1.3 56.4 + - - +
17A ALA* 3.4 7.0 + - - +
18A GLN* 3.0 37.8 + - + +
104A PRO* 5.8 4.0 - - - +
105A MET* 3.2 32.4 - - + +
54B VAL* 4.8 1.1 - - + +
65B LYS* 3.8 37.5 - - - +
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Residues in contact with GLU 15 (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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11A ILE* 3.6 12.9 - - + -
12A SER* 2.9 40.2 + - - +
13A GLU 3.3 0.4 - - - -
14A GLU* 1.3 73.7 - - - +
16A ALA* 1.3 61.0 + - - +
18A GLN* 4.1 5.2 - - - -
19A TYR* 2.8 57.1 + - + +
35A ARG* 3.0 37.7 + - - -
105A MET* 3.6 33.1 - - + +
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Residues in contact with ALA 16 (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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11A ILE* 3.8 18.3 - - + +
12A SER 3.1 13.5 + - - +
13A GLU* 3.3 11.6 + - - +
15A GLU* 1.3 75.7 - - - +
17A ALA* 1.3 62.4 + - - +
19A TYR 4.0 0.3 - - - -
20A ASP* 3.1 27.0 + - - +
23A ILE* 4.4 5.2 - - - +
307B LEU* 4.1 19.6 - - + +
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Residues in contact with ALA 17 (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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13A GLU* 3.1 18.1 + - + +
14A GLU* 3.7 6.7 - - - +
16A ALA* 1.3 80.1 - - - +
18A GLN* 1.3 60.7 + - - +
20A ASP* 3.6 15.0 - - - +
54B VAL* 3.9 26.8 - - + +
55B SER* 3.6 17.2 + - - -
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Residues in contact with GLN 18 (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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14A GLU* 3.0 29.7 + - + +
15A GLU* 3.6 5.2 - - - +
17A ALA* 1.3 80.4 - - - +
19A TYR* 1.3 76.1 + - + +
20A ASP 3.8 0.2 + - - -
21A ARG 5.2 0.2 + - - -
57A LEU 4.9 1.0 + - - -
102A LEU 5.5 0.2 + - - -
103A ASN* 3.1 40.4 + - - +
104A PRO* 5.5 3.5 - - - +
105A MET* 3.6 18.3 - - - +
54B VAL* 4.0 13.6 - - + +
55B SER 4.3 5.2 - - - +
57B LEU* 4.3 30.4 + - + +
58B ASN* 3.3 23.5 + - + +
65B LYS* 6.0 1.0 - - - +
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Residues in contact with TYR 19 (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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11A ILE* 5.2 2.2 - - + -
15A GLU* 2.8 58.5 + - + +
18A GLN* 1.3 96.2 + - + +
20A ASP* 1.3 66.0 + - - +
21A ARG 3.3 2.5 - - - -
22A GLN* 2.9 42.6 + - + +
23A ILE* 2.9 28.8 + - + +
31A GLN* 3.8 18.6 - - + -
35A ARG* 5.5 3.8 - - + -
57A LEU 3.7 12.3 - - - -
58A ALA 3.6 13.9 - - - -
59A GLY* 3.2 16.7 + - - -
103A ASN* 3.2 17.3 + - - -
105A MET* 4.0 12.1 - - - +
58B ASN* 4.5 2.5 - - + -
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Residues in contact with ASP 20 (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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16A ALA 3.1 18.2 + - - +
17A ALA* 3.6 13.1 - - - +
18A GLN 3.4 2.2 - - - -
19A TYR* 1.3 76.6 - - - +
21A ARG* 1.3 89.1 + - - +
23A ILE* 3.3 6.9 + - - +
24A ARG* 2.6 71.9 + - - +
55B SER* 4.7 2.2 - - - -
374B PHE* 4.4 8.0 - - - -
377B LYS* 4.0 8.9 - - - +
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Residues in contact with ARG 21 (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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18A GLN 5.2 0.6 + - - -
19A TYR 3.1 0.8 + - - -
20A ASP* 1.3 98.6 + - - +
22A GLN* 1.3 58.1 + - - +
24A ARG* 4.1 4.1 + - - +
25A LEU 4.0 0.9 + - - -
55B SER* 3.4 27.0 + - - +
58B ASN* 4.4 3.5 - - - +
59B ARG* 3.6 28.5 - - - +
346B LYS* 3.3 12.9 - - - +
347B ASP* 3.0 26.1 + - - -
377B LYS* 4.4 4.4 - - - +
383B ILE* 3.5 33.3 - - - +
384B ILE 4.3 5.2 - - - -
385B PRO* 3.3 12.2 - - - +
386B ALA 2.8 39.7 + - - +
802B ATP 2.9 36.9 + - - -
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Residues in contact with GLN 22 (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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19A TYR* 2.9 33.7 + - + +
21A ARG* 1.3 76.9 - - - +
23A ILE* 1.3 61.0 + - - +
24A ARG 3.1 1.6 - - - -
25A LEU* 2.9 20.1 + - - +
26A TRP* 3.0 36.6 + - + -
31A GLN* 2.8 26.4 + - - +
58A ALA* 3.0 31.5 + - - -
58B ASN* 2.8 33.4 + - - +
386B ALA 3.7 1.5 + - - -
387B ILE* 3.6 22.4 - - + +
388B ALA 5.2 0.5 + - - -
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Residues in contact with ILE 23 (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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11A ILE* 4.1 24.5 - - + -
16A ALA 4.4 6.1 - - - +
19A TYR* 2.9 40.5 + - + +
20A ASP* 3.8 7.0 - - - +
22A GLN* 1.3 72.8 - - - +
24A ARG* 1.3 58.9 + - - +
25A LEU 2.9 5.6 - - - -
26A TRP* 4.6 0.7 - - - -
27A GLY* 2.9 29.7 + - - +
28A LEU* 3.8 27.8 - - + +
31A GLN* 4.1 19.5 - - + +
307B LEU* 4.2 22.4 - - + -
310B GLN* 5.0 3.1 - - - +
374B PHE* 4.3 12.7 - - + -
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Residues in contact with ARG 24 (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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20A ASP* 2.6 43.2 + - - +
21A ARG* 4.1 8.3 - - - +
22A GLN 3.1 0.4 - - - -
23A ILE* 1.3 76.6 - - - +
25A LEU* 1.3 59.9 + - - +
309B ASP* 5.9 0.2 + - - -
374B PHE* 3.0 57.4 + - + +
377B LYS* 3.1 33.1 - - - +
378B SER* 2.6 33.3 + - - +
383B ILE* 3.7 32.1 - - - +
385B PRO* 3.7 20.9 - - + +
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Residues in contact with LEU 25 (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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21A ARG 4.1 0.4 - - - +
22A GLN* 2.9 18.3 + - - +
24A ARG* 1.3 83.0 - - - +
26A TRP* 1.3 76.8 + - + +
27A GLY 3.6 0.2 - - - -
321A ARG* 4.3 9.4 + - - -
143B GLY* 4.0 18.6 - - - -
144B TYR* 3.1 51.0 - - + +
385B PRO* 3.6 24.5 - - + -
387B ILE* 4.4 10.1 - - + -
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Residues in contact with TRP 26 (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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22A GLN* 3.0 47.3 + - + -
23A ILE* 4.6 0.2 - - - -
25A LEU* 1.3 93.4 - - + +
27A GLY* 1.3 72.2 + - - +
30A ALA* 3.2 21.1 + - + +
31A GLN* 2.9 23.8 + - - +
34A LEU* 4.2 13.2 - - + +
58A ALA* 5.2 4.3 - - + -
312A GLN* 6.3 0.9 - - + -
315A VAL* 3.9 28.7 - - + -
319A SER* 5.7 4.3 - - - +
321A ARG* 3.1 47.4 + - + +
144B TYR* 3.5 15.0 - + - +
387B ILE* 3.6 35.9 - - + -
389B THR* 5.8 1.8 - - + -
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Residues in contact with GLY 27 (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 ILE* 2.9 24.0 + - - -
25A LEU 3.6 1.2 - - - -
26A TRP* 1.3 89.3 - - - +
28A LEU* 1.3 64.7 + - - -
29A GLU 3.5 2.5 - - - -
30A ALA 3.6 0.4 + - - -
31A GLN* 3.3 16.8 + - - +
321A ARG* 5.4 0.9 - - - -
310B GLN* 6.2 0.7 - - - -
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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