Contacts of the helix formed by residues 9 - 27 (chain F) in PDB entry 1YIT
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 PRO 9 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7F ASP* 3.1 16.4 - - - +
8F VAL* 1.3 80.7 - - - +
10F ALA* 1.3 69.6 + - - +
11F ASP* 3.2 6.3 - - + +
12F LEU* 2.7 32.6 + - + +
13F GLU 3.1 7.4 + - - -
118F LEU* 3.7 23.1 - - + -
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Residues in contact with ALA 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL 3.3 4.9 + - - -
9F PRO* 1.3 67.6 - - - +
11F ASP* 1.3 68.9 - - - +
13F GLU* 2.9 13.8 + - - +
14F ASP* 2.8 30.7 + - - +
78F GLU* 6.4 0.4 - - - -
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Residues in contact with ASP 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9F PRO* 2.9 7.2 + - + +
10F ALA* 1.3 79.3 - - - +
12F LEU* 1.3 65.1 + - - +
14F ASP* 2.9 15.6 + - - +
15F ASP* 2.9 30.6 + - - +
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Residues in contact with LEU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL* 3.8 14.6 - - + -
9F PRO* 2.7 25.7 + - + +
11F ASP* 1.3 74.5 - - - +
13F GLU* 1.3 56.4 + - - +
15F ASP* 3.2 11.0 + - + +
16F ALA* 2.9 25.1 + - - +
75F ILE* 3.7 20.2 - - + -
111F ILE* 3.8 20.0 - - + -
114F LYS* 4.5 29.8 - - + +
115F VAL* 4.5 13.7 - - + +
118F LEU* 4.1 22.2 - - + -
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Residues in contact with GLU 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL* 3.8 23.0 - - + +
9F PRO 3.1 3.4 + - - +
10F ALA* 2.9 14.2 + - - +
12F LEU* 1.3 80.8 - - - +
14F ASP* 1.3 64.1 + - - +
16F ALA* 3.3 6.8 + - - +
17F LEU* 2.9 40.3 + - + +
75F ILE* 4.7 1.6 - - - -
76F PHE 4.2 6.1 - - - +
77F VAL* 3.2 19.8 - - + +
78F GLU* 2.9 55.5 + - - +
79F GLN 4.4 0.9 + - - -
82F ASP* 5.3 2.8 - - - +
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Residues in contact with ASP 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F ALA* 2.8 32.0 + - - +
11F ASP* 2.9 15.2 + - - +
13F GLU* 1.3 79.0 - - - +
15F ASP* 1.3 62.7 + - - +
17F LEU* 3.4 10.4 + - - +
18F GLU* 3.0 33.3 + - + +
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Residues in contact with ASP 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11F ASP* 2.9 22.1 + - - +
12F LEU* 3.2 12.9 + - + +
14F ASP* 1.3 75.8 - - - +
16F ALA* 1.3 63.4 + - - +
18F GLU* 2.9 32.1 + - - +
19F ALA* 3.0 13.9 + - - +
111F ILE* 4.3 12.5 - - + +
114F LYS* 4.3 17.2 + - + +
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Residues in contact with ALA 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12F LEU 2.9 13.7 + - - +
13F GLU* 3.3 9.2 + - + +
15F ASP* 1.3 76.0 - - - +
17F LEU* 1.3 63.0 + - + +
19F ALA* 3.1 5.5 + - - +
20F LEU 3.0 17.5 + - - -
49F PHE* 3.7 25.3 - - + -
75F ILE* 3.6 25.6 - - + -
77F VAL* 6.2 1.1 - - + -
111F ILE* 3.6 20.8 - - + +
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Residues in contact with LEU 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F GLU* 2.9 38.2 + - + +
14F ASP* 3.8 9.6 - - - +
16F ALA* 1.3 76.2 - - + +
18F GLU* 1.3 62.8 + - - +
20F LEU* 3.1 8.1 + - + +
21F GLU* 3.1 26.8 + - + +
49F PHE* 4.6 2.2 - - + -
77F VAL* 4.2 20.4 - - + -
82F ASP* 4.4 16.2 - - + +
83F LEU* 4.2 24.9 - - + -
86F ALA* 3.9 23.9 - - + +
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Residues in contact with GLU 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14F ASP* 3.0 26.7 + - + +
15F ASP* 2.9 31.2 + - - +
17F LEU* 1.3 75.2 - - - +
19F ALA* 1.3 64.1 + - - +
21F GLU* 3.0 23.3 + - - +
22F VAL* 3.2 17.7 + - + +
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Residues in contact with ALA 19 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15F ASP 3.0 10.5 + - - +
16F ALA 3.1 8.9 + - - +
18F GLU* 1.3 76.4 - - - +
20F LEU* 1.3 52.1 + - - +
22F VAL* 2.8 13.8 - - - +
23F ALA* 2.7 35.7 + - - +
47F LEU* 6.1 0.2 - - + -
49F PHE* 5.6 2.0 - - + -
98F VAL* 6.0 0.7 - - - -
104F ALA* 4.2 6.5 - - + +
107F ASP* 4.5 9.4 - - + -
108F VAL* 4.2 18.2 - - + -
111F ILE* 3.9 20.2 - - + -
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Residues in contact with LEU 20 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16F ALA 3.0 11.3 + - - +
17F LEU* 3.3 10.8 - - + +
18F GLU 3.1 0.2 - - - -
19F ALA* 1.3 78.2 - - - +
21F GLU* 1.3 63.7 + - - +
23F ALA* 2.9 5.5 + - - +
24F ARG* 2.9 24.7 + - - +
29F VAL* 4.1 16.4 - - + -
49F PHE* 3.9 18.5 - - + -
83F LEU* 3.4 33.2 - - + -
86F ALA* 3.5 20.6 - - + -
87F ALA* 4.0 15.9 - - + +
96F ALA* 4.9 7.2 - - + -
98F VAL* 3.7 28.3 - - + +
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Residues in contact with GLU 21 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17F LEU* 3.1 16.6 + - + +
18F GLU* 3.0 14.0 + - - +
20F LEU* 1.3 75.8 - - - +
22F VAL* 1.3 59.9 + - + +
24F ARG* 2.7 56.4 + - - +
25F ASP* 2.8 16.4 - - - +
85F HIS* 4.5 12.9 + - - -
86F ALA* 3.8 19.2 - - + +
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Residues in contact with VAL 22 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18F GLU* 3.5 12.6 - - + +
19F ALA* 2.8 27.6 - - - +
21F GLU* 1.3 75.3 - - + +
23F ALA* 1.3 57.4 + - - +
24F ARG 3.1 2.0 - - - -
25F ASP* 3.0 4.6 + - - +
26F THR* 2.6 46.7 + - - +
102F GLY 4.2 3.1 - - - +
103F GLU* 4.4 5.6 - - + +
104F ALA* 3.4 25.4 - - + -
107F ASP* 5.5 0.9 - - - +
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Residues in contact with ALA 23 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ALA 2.7 19.9 + - - +
20F LEU* 3.2 10.3 - - - +
22F VAL* 1.3 79.9 - - - +
24F ARG* 1.3 56.0 + - - +
27F GLY* 2.8 34.8 + - - +
28F ALA 3.4 2.4 + - - -
29F VAL* 3.9 7.6 - - + +
98F VAL* 3.7 31.2 - - + -
101F ALA* 4.4 13.9 - - + -
102F GLY 4.8 1.3 - - - +
104F ALA* 5.2 0.4 - - + -
108F VAL* 5.8 0.7 - - + -
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Residues in contact with ARG 24 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20F LEU 2.9 11.3 + - - +
21F GLU* 2.7 62.4 + - - +
23F ALA* 1.3 78.3 - - - +
25F ASP* 1.3 77.1 + - - +
27F GLY 3.5 13.8 - - - +
29F VAL* 3.9 27.3 - - + +
85F HIS* 4.1 6.7 + - - -
86F ALA 2.9 21.4 + - - +
87F ALA* 3.7 12.8 - - - +
88F GLY* 3.5 18.0 - - - -
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Residues in contact with ASP 25 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21F GLU* 2.8 21.0 - - - +
22F VAL* 3.0 7.1 + - - +
24F ARG* 1.3 102.9 + - - +
26F THR* 1.3 60.2 + - - +
27F GLY 5.0 0.2 - - - -
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Residues in contact with THR 26 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22F VAL* 2.6 29.5 + - - +
25F ASP* 1.3 77.8 + - - +
27F GLY* 1.3 56.6 + - - +
101F ALA 4.2 0.4 - - - +
102F GLY* 2.9 43.1 + - - +
103F GLU* 3.4 32.5 + - + +
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Residues in contact with GLY 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23F ALA 2.8 13.6 + - - +
24F ARG 3.5 12.5 - - - +
26F THR* 1.3 82.0 - - - +
28F ALA* 1.3 61.8 + - - +
100F ASP 3.8 0.7 - - - -
101F ALA 3.0 19.1 + - - -
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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