Contacts of the helix formed by residues 13 - 29 (chain A) in PDB entry 1Y8B
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 ASP 13 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3A GLN 5.1 9.9 - - - +
4A THR* 5.7 0.2 - - - +
5A ILE* 4.8 0.4 - - - -
12A ILE* 1.3 72.7 - - - +
14A ALA* 1.3 60.9 + - - +
15A ASN* 3.4 19.1 - - - +
16A PHE* 3.2 34.4 - - + +
17A LYS* 3.0 22.5 + - - +
280A ALA* 5.5 0.3 - - - +
348A VAL* 3.4 20.7 - - - +
349A ILE* 3.3 30.2 - - - +
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Residues in contact with ALA 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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5A ILE* 4.0 29.1 - - + +
12A ILE 3.6 3.8 + - - -
13A ASP* 1.3 68.5 - - - +
15A ASN* 1.3 72.3 + - - +
16A PHE 3.0 1.8 - - - -
17A LYS* 2.7 20.1 + - + +
18A ARG* 2.9 20.6 + - - +
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Residues in contact with ASN 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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13A ASP* 3.4 17.2 - - - +
14A ALA* 1.3 76.2 + - - +
16A PHE* 1.3 100.9 + - - +
18A ARG* 3.9 4.1 + - - +
19A PHE* 3.7 17.8 + - - +
280A ALA* 4.8 5.7 - - - +
284A ILE* 3.9 18.4 - - + +
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Residues in contact with PHE 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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13A ASP* 3.2 30.0 + - - +
14A ALA 3.0 0.4 - - - -
15A ASN* 1.3 104.4 - - - +
17A LYS* 1.3 61.3 + - - +
19A PHE* 4.7 6.5 - - + +
20A VAL* 2.7 44.1 + - + +
280A ALA* 3.8 23.6 - - + -
283A LYS* 3.9 13.2 - - + -
284A ILE* 3.7 39.3 - - + -
287A TYR* 3.6 43.3 - + + -
348A VAL* 4.5 9.4 - - + -
349A ILE* 5.9 0.9 - - + -
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Residues in contact with LYS 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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5A ILE* 5.2 6.5 - - + -
7A GLN* 6.3 0.4 - - - +
12A ILE* 3.5 43.7 - - + +
13A ASP* 3.0 17.2 + - - +
14A ALA* 2.7 20.2 + - - +
16A PHE* 1.3 72.0 - - - +
18A ARG* 1.3 60.2 + - - +
20A VAL* 5.5 3.1 - - - -
21A ASP* 2.5 67.7 + - + +
36A TRP* 4.0 30.9 - - + +
349A ILE* 5.0 4.2 - - - +
366A MET* 6.2 1.4 - - - +
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Residues in contact with ARG 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 ALA* 2.9 18.6 + - - +
15A ASN* 4.2 4.9 - - - +
17A LYS* 1.3 82.5 + - - +
19A PHE* 1.3 55.6 + - - +
21A ASP* 5.0 9.1 - - - +
22A GLU* 2.6 59.6 + - + +
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Residues in contact with PHE 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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15A ASN 3.7 13.0 + - - +
16A PHE* 3.6 8.6 + - + +
18A ARG* 1.3 79.9 - - - +
20A VAL* 1.3 63.1 + - + +
22A GLU* 4.5 2.7 - - - -
23A GLU* 3.4 44.8 + - - +
287A TYR* 5.8 4.0 - + + -
288A ARG* 4.4 36.8 - - + -
291A LEU* 3.7 23.2 - - + +
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Residues in contact with VAL 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 PHE* 2.7 44.4 + - + +
17A LYS* 3.8 4.5 - - - +
19A PHE* 1.3 73.2 - - + +
21A ASP* 1.3 71.1 + - - +
22A GLU 3.1 1.1 - - - -
24A VAL* 2.9 49.8 + - + +
25A LEU* 3.1 6.2 + - + +
287A TYR* 3.8 39.7 - - + +
366A MET* 5.9 6.1 - - + -
369A ALA* 5.7 2.9 - - + -
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Residues in contact with ASP 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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17A LYS* 2.5 61.3 + - + +
18A ARG* 4.9 8.7 - - - +
20A VAL* 1.3 84.6 - - - +
22A GLU* 1.3 56.3 + - - +
25A LEU* 3.2 32.7 - - + +
26A PRO* 3.0 20.8 - - - +
32A ALA* 5.1 0.7 - - - +
36A TRP* 3.9 15.5 + - - -
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Residues in contact with GLU 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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18A ARG* 2.6 48.2 + - + +
19A PHE* 4.5 1.3 - - - -
21A ASP* 1.3 75.3 - - - +
23A GLU* 1.3 68.7 + - + +
26A PRO* 2.9 17.4 - - - +
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.4 45.2 + - - +
22A GLU* 1.3 90.8 - - + +
24A VAL* 1.3 63.4 + - - +
25A LEU 3.7 0.2 - - - -
26A PRO* 4.0 0.7 - - - -
27A GLY* 2.7 30.6 + - - -
291A LEU* 4.6 15.1 - - + +
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Residues in contact with VAL 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 VAL* 2.9 35.6 + - + +
23A GLU* 1.3 69.2 - - - +
25A LEU* 1.3 61.6 + - + +
28A THR* 2.3 51.4 + - + +
30A LEU* 6.1 0.2 - - + -
287A TYR* 4.7 4.9 - - + +
291A LEU* 3.3 38.1 - - + -
369A ALA* 3.6 34.3 - - + +
370A ILE* 4.2 9.9 - - + -
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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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20A VAL* 3.1 7.0 + - + +
21A ASP* 3.2 45.5 - - + +
24A VAL* 1.3 75.9 - - + +
26A PRO* 1.3 63.9 - - + +
28A THR* 2.9 4.1 + - - -
29A GLY* 2.7 31.4 + - - -
30A LEU* 3.0 38.7 + - + +
31A ASP 3.9 20.0 - - - +
32A ALA* 3.8 23.6 - - + +
35A PHE* 5.2 6.1 - - + -
36A TRP* 5.2 2.5 - - + +
369A ALA* 6.4 1.1 - - + -
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Residues in contact with PRO 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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21A ASP 3.0 19.7 - - - +
22A GLU 2.9 26.9 - - - +
23A GLU* 3.8 1.6 - - - +
24A VAL 3.5 2.7 - - - -
25A LEU* 1.3 88.4 - - + +
27A GLY* 1.3 67.9 + - - +
28A THR 2.9 6.4 + - - -
29A GLY* 3.1 11.9 + - - +
376A LYS* 5.8 1.4 + - - -
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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 GLU 2.7 25.1 + - - -
24A VAL 3.6 0.4 - - - -
26A PRO* 1.3 74.8 - - - +
28A THR* 1.3 62.0 + - - +
373A TYR* 6.1 1.2 - - - -
376A LYS* 4.6 13.3 - - - +
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Residues in contact with THR 28 (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 GLU 4.9 0.2 - - - +
24A VAL* 2.3 46.0 + - + +
25A LEU 2.9 6.2 + - - -
26A PRO 3.9 0.2 - - - -
27A GLY* 1.3 84.0 - - - +
29A GLY* 1.3 58.5 + - - +
30A LEU* 3.1 15.0 + - - +
369A ALA 3.1 27.9 + - - +
370A ILE* 4.3 9.2 - - + +
372A LEU* 3.4 28.4 - - + +
373A TYR 5.6 1.3 - - - +
376A LYS* 5.1 13.7 + - - +
415A MET* 4.2 8.7 - - - +
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Residues in contact with GLY 29 (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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25A LEU 2.7 12.2 + - - -
26A PRO* 3.1 10.1 + - - -
28A THR* 1.3 75.5 - - - +
30A LEU* 1.3 69.8 + - - +
31A ASP* 4.1 8.0 - - - +
376A LYS* 5.6 5.4 - - - -
415A MET* 4.7 10.1 - - - +
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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