Contacts of the helix formed by residues 10 - 28 (chain A) in PDB entry 1YSD
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 TRP 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A SER* 3.0 16.4 + - - +
9A LYS* 1.3 126.0 - - + +
11A ASP* 1.3 57.7 + - - +
12A GLN 3.4 2.9 - - - -
13A LYS* 3.3 30.3 + - + +
14A GLY* 2.9 24.8 + - - -
38A ILE* 4.1 14.9 - - + +
39A ASN 4.3 3.4 - - - -
40A ASN* 3.4 28.5 + - - -
41A LYS 4.6 2.2 + - - -
42A ASP* 3.3 26.2 - - - -
43A GLY* 3.3 24.4 - - - +
85A TYR* 3.4 12.8 + - - +
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Residues in contact with ASP 11 (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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7A ALA* 3.4 13.9 - - + +
8A SER* 2.6 36.5 + - - +
9A LYS 3.5 0.2 - - - -
10A TRP* 1.3 77.6 - - - +
12A GLN* 1.3 62.8 + - - +
14A GLY 3.5 0.2 + - - -
15A MET* 3.1 24.1 + - - +
85A TYR* 2.8 30.9 + - + -
105A ARG* 3.0 29.8 + - - -
107A VAL* 3.7 11.1 - - + +
130A VAL* 5.6 3.1 - - - +
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Residues in contact with GLN 12 (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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8A SER 4.9 0.6 + - - -
9A LYS 5.0 2.8 + - - +
10A TRP 3.4 0.8 - - - -
11A ASP* 1.3 75.2 - - - +
13A LYS* 1.3 66.8 + - - +
15A MET* 4.7 6.6 - - - +
16A ASP* 3.0 61.1 + - - +
132A VAL* 6.0 3.4 - - - +
136A ARG* 4.0 8.0 + - - -
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Residues in contact with LYS 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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9A LYS 5.4 1.3 + - - +
10A TRP* 3.3 34.4 + - + +
12A GLN* 1.3 79.4 - - - +
14A GLY* 1.3 62.0 + - - +
16A ASP* 3.4 6.2 + - - +
17A ILE* 3.1 35.4 + - + +
38A ILE* 4.3 6.3 - - + -
43A GLY 2.8 29.9 + - - +
44A SER* 4.9 1.4 - - - +
45A VAL* 3.9 21.3 - - - +
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Residues in contact with GLY 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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10A TRP 2.9 11.8 + - - -
12A GLN 3.3 0.2 - - - -
13A LYS* 1.3 78.6 - - - +
15A MET* 1.3 57.0 + - - +
17A ILE 3.4 0.9 + - - -
18A ALA* 3.0 24.8 + - - +
36A CYS* 3.5 12.3 - - - -
38A ILE* 3.6 21.3 - - - +
85A TYR* 3.6 22.1 - - - +
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Residues in contact with MET 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 ASP 3.1 17.1 + - - +
12A GLN* 4.1 9.9 - - - +
13A LYS 3.4 0.2 - - - -
14A GLY* 1.3 72.0 - - - +
16A ASP* 1.3 61.3 + - - +
18A ALA* 3.3 9.2 + - - +
19A TYR* 2.9 28.4 + - - +
85A TYR* 3.7 4.8 - - + -
86A THR 3.8 9.0 - - - +
87A THR* 4.5 0.2 - - - -
107A VAL* 3.6 43.7 - - + +
108A VAL 3.8 1.6 - - - +
109A GLY* 3.6 29.6 - - - +
132A VAL* 4.2 12.6 - - + -
134A ASP* 3.8 24.0 - - + +
136A ARG* 4.7 1.6 - - - +
137A CYS* 4.4 9.2 - - - -
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Residues in contact with ASP 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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12A GLN* 3.0 44.1 + - - +
13A LYS* 3.8 6.1 + - - +
15A MET* 1.3 76.1 - - - +
17A ILE* 1.3 59.6 + - + +
19A TYR* 3.4 7.3 + - - +
20A GLU* 2.9 29.7 + - - +
136A ARG* 3.0 33.2 + - - +
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Residues in contact with ILE 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 LYS* 3.1 34.7 + - + +
14A GLY 3.7 4.0 - - - +
15A MET 3.2 0.2 - - - -
16A ASP* 1.3 74.6 - - + +
18A ALA* 1.3 67.2 + - - +
20A GLU* 3.1 12.8 + - - +
21A GLU* 2.9 22.5 + - + +
36A CYS* 3.7 27.4 - - + -
38A ILE* 4.9 0.7 - - + -
45A VAL* 3.8 29.4 - - + -
48A ARG* 3.5 42.8 - - + +
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Residues in contact with ALA 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 GLY 3.0 17.9 + - - +
15A MET* 3.6 12.8 - - - +
17A ILE* 1.3 78.2 - - - +
19A TYR* 1.3 56.2 + - - +
21A GLU 3.3 1.4 + - - -
22A ALA 3.0 21.8 + - - -
34A GLY* 3.4 11.4 - - - +
35A GLY* 3.6 31.6 - - - +
36A CYS* 4.7 0.2 - - - -
85A TYR* 4.2 9.4 - - + +
87A THR* 3.3 17.9 - - + +
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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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15A MET 2.9 17.9 + - - +
16A ASP* 3.7 6.5 - - - +
18A ALA* 1.3 73.0 - - - +
20A GLU* 1.3 66.3 + - - +
22A ALA* 3.2 2.2 + - + +
23A LEU* 2.9 63.8 + - + +
87A THR* 3.6 8.2 - - - +
136A ARG* 3.6 71.3 + - + +
137A CYS* 4.0 24.9 - - - -
140A LEU* 4.1 10.5 - - + +
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Residues in contact with GLU 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 ASP 2.9 15.4 + - - +
17A ILE* 3.2 13.9 - - - +
19A TYR* 1.3 78.2 - - - +
21A GLU* 1.3 57.0 + - - +
23A LEU* 3.3 12.2 + - + +
24A LEU* 3.0 27.5 + - + +
48A ARG* 2.6 29.0 + - - +
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Residues in contact with GLU 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 ILE 2.9 16.4 + - - +
18A ALA 3.5 8.3 - - - +
19A TYR 3.2 0.2 - - - -
20A GLU* 1.3 75.8 - - - +
22A ALA* 1.3 59.4 + - - +
24A LEU* 3.2 14.8 + - - +
25A GLY 2.9 24.3 + - - -
34A GLY* 3.8 2.5 - - - -
35A GLY 3.8 6.7 - - - +
48A ARG* 2.7 38.4 + - + +
49A GLY* 3.2 41.7 - - - +
50A HIS* 2.8 40.8 + - - +
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Residues in contact with ALA 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 ALA 3.0 10.0 + - - +
19A TYR* 3.2 9.4 + - + +
21A GLU* 1.3 76.0 - - - +
23A LEU* 1.3 57.7 + - - +
25A GLY 3.3 1.0 + - - -
26A TYR* 2.9 27.9 + - - +
32A PRO* 3.5 32.7 - - - +
33A ILE 4.1 1.3 - - - +
34A GLY* 3.6 18.5 - - - +
50A HIS* 4.8 0.4 - - - -
87A THR* 4.0 10.8 - - + -
137A CYS* 6.5 0.2 - - - -
140A LEU* 3.9 12.1 - - + -
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Residues in contact with LEU 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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19A TYR* 2.9 56.9 + - + +
20A GLU* 3.5 12.8 - - + +
21A GLU 3.2 0.2 - - - -
22A ALA* 1.3 77.2 - - - +
24A LEU* 1.3 61.8 + - - +
26A TYR* 3.2 6.6 + - + +
27A LYS* 3.0 31.7 + - + +
140A LEU* 3.6 27.6 - - + -
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Residues in contact with LEU 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 GLU* 3.0 14.2 + - + +
21A GLU* 3.4 22.0 - - - +
23A LEU* 1.3 77.0 - - - +
25A GLY* 1.3 62.6 + - - +
27A LYS* 3.1 18.0 + - + +
28A GLU* 3.0 43.6 + - + +
50A HIS* 3.7 16.8 - - + +
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Residues in contact with GLY 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 GLU 2.9 11.6 + - - -
22A ALA 3.3 3.5 + - - -
24A LEU* 1.3 76.2 - - - +
26A TYR* 1.3 59.9 + - - +
28A GLU* 3.2 10.4 + - - +
29A GLY 3.3 0.2 + - - -
30A GLY* 2.9 30.8 + - - -
31A VAL 4.7 5.8 - - - -
50A HIS* 3.3 29.6 - - - -
55A GLN* 4.0 1.3 - - - -
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Residues in contact with TYR 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 ALA 2.9 13.4 + - - +
23A LEU* 3.4 11.2 - - + +
25A GLY* 1.3 75.4 - - - +
27A LYS* 1.3 73.9 + - + +
29A GLY* 3.0 15.2 + - - -
30A GLY 3.9 6.9 + - - -
32A PRO* 4.0 22.1 - - + +
140A LEU* 3.8 24.2 - - + -
143A GLN* 3.6 15.4 + - + +
144A PHE* 4.2 20.6 - + + -
147A GLU* 2.6 38.4 + - - -
148A ARG* 6.0 1.1 - - - -
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Residues in contact with LYS 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 LEU* 3.0 20.8 + - + +
24A LEU* 3.1 11.4 + - + +
26A TYR* 1.3 88.9 - - + +
28A GLU* 1.3 57.8 + - + +
29A GLY* 3.1 3.5 + - - -
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Residues in contact with GLU 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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24A LEU* 3.0 37.6 + - + +
25A GLY 3.2 1.9 + - - +
27A LYS* 1.3 76.7 - - + +
29A GLY* 1.3 60.7 + - - +
30A GLY 3.4 0.2 - - - -
50A HIS* 2.7 26.6 + - - -
52A MET* 4.5 3.4 - - - +
54A PHE* 5.9 0.3 - - - +
55A GLN* 2.7 42.1 + - + +
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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