Contacts of the helix formed by residues 19 - 29 (chain P) in PDB entry 5A0Q
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 VAL 19 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11P THR 4.3 10.0 + - - +
13P SER* 3.9 22.2 - - - +
17P LYS 3.8 11.2 - - - +
18P LEU* 1.3 69.5 - - - +
20P GLN* 1.3 62.0 + - + +
22P GLU* 3.1 17.2 + - - +
23P TYR* 3.0 63.4 + - + +
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Residues in contact with GLN 20 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15O ILE* 3.4 29.0 - - + +
16O PHE* 2.9 58.8 + - - +
9P LEU* 3.4 25.6 - - + +
10P THR* 4.3 9.1 - - + +
11P THR 5.7 0.2 + - - -
18P LEU* 3.3 0.8 - - - +
19P VAL* 1.3 81.8 - - + +
21P ILE* 1.4 55.6 + - - +
23P TYR* 3.4 21.4 + - - +
24P ALA* 3.0 21.3 + - - +
128P PRO* 4.3 18.8 - - + +
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Residues in contact with ILE 21 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10P THR* 4.9 3.8 - - + -
18P LEU* 3.2 44.2 + - + +
20P GLN* 1.4 72.0 - - - +
22P GLU* 1.4 60.8 + - + +
24P ALA* 3.1 9.1 + - - +
25P LEU* 3.0 36.0 + - + +
121P THR* 3.5 26.9 - - + +
128P PRO* 3.9 20.0 - - + -
150P PRO 4.5 2.5 - - - -
151P SER* 3.8 35.7 - - - +
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Residues in contact with GLU 22 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P LYS* 3.6 39.9 - - - +
18P LEU 3.0 15.1 + - - +
19P VAL* 3.1 22.5 + - - +
21P ILE* 1.4 76.6 - - + +
23P TYR* 1.3 65.1 + - + +
25P LEU* 3.2 22.6 + - + +
26P ALA* 3.2 21.1 + - - +
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Residues in contact with TYR 23 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O PHE* 3.4 27.6 - - + -
17O SER 3.3 14.6 - - - +
18O PRO* 3.5 47.4 - - + +
20O GLY* 3.3 9.4 - - - -
19P VAL* 3.0 37.5 + - + +
20P GLN* 3.5 22.0 - - - +
22P GLU* 1.3 82.9 - - + +
24P ALA* 1.3 57.5 + - - +
26P ALA* 3.2 11.2 + - + +
27P ALA 3.1 20.1 + - - -
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Residues in contact with ALA 24 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O PHE* 3.6 28.5 - - + -
20P GLN 3.0 10.9 + - - +
21P ILE* 3.1 14.8 + - - +
23P TYR* 1.3 75.7 - - - +
25P LEU* 1.4 55.0 - - - +
27P ALA* 3.2 8.5 + - - +
28P VAL* 3.1 27.5 + - - +
128P PRO* 4.5 3.8 - - + -
129P PHE 4.0 6.1 - - - +
130P GLY* 3.6 1.8 - - - +
150P PRO* 3.6 21.8 - - + -
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Residues in contact with LEU 25 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21P ILE* 3.0 27.4 + - + +
22P GLU* 3.2 23.3 + - + +
24P ALA* 1.4 72.4 - - - +
26P ALA* 1.3 62.7 + - - +
28P VAL* 3.3 11.4 + - + +
29P ALA* 3.2 19.4 + - - +
149P ASP* 5.0 7.0 - - + -
150P PRO* 4.0 26.2 - - + -
151P SER* 5.3 3.6 - - - +
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Residues in contact with ALA 26 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18O PRO 4.1 10.5 - - - +
19O GLU* 4.0 11.6 - - - +
20O GLY* 3.9 15.5 - - - +
22P GLU 3.2 10.0 + - - +
23P TYR* 3.2 16.6 + - + +
25P LEU* 1.3 74.3 - - - +
27P ALA* 1.4 58.0 + - - +
29P ALA* 3.3 21.7 + - - +
30P GLY* 3.6 4.7 + - - -
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Residues in contact with ALA 27 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O PHE* 4.3 13.7 - - + -
20O GLY* 3.7 24.6 - - - +
23P TYR 3.1 11.1 + - - +
24P ALA* 3.2 14.5 + - - +
26P ALA* 1.4 73.4 - - - +
28P VAL* 1.4 62.1 + - - +
30P GLY* 3.4 12.2 + - - -
77P GLY* 3.5 17.4 - - - -
78P MET* 4.5 11.2 + - + +
130P GLY* 4.4 9.4 - - - -
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Residues in contact with VAL 28 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24P ALA 3.1 8.9 + - - +
25P LEU* 3.3 11.4 + - + +
27P ALA* 1.4 71.9 - - - +
29P ALA* 1.4 55.7 + - - +
30P GLY 2.7 17.6 - - - +
76P SER* 3.6 12.1 + - - +
77P GLY* 4.2 6.7 - - - -
130P GLY 3.0 24.0 - - - +
132P SER* 3.6 29.2 - - - +
149P ASP* 5.9 1.3 - - - -
150P PRO* 3.5 17.0 - - + -
162P MET* 5.4 2.5 - - + -
163P GLY* 3.7 15.1 - - - +
166P TYR* 6.4 3.1 - - + -
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Residues in contact with ALA 29 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25P LEU 3.2 11.9 + - - +
26P ALA* 3.3 16.2 - - + +
27P ALA 3.3 0.4 - - - -
28P VAL* 1.4 70.9 - - - +
30P GLY* 1.3 65.4 + - - +
163P GLY 3.9 5.8 - - - +
164P LYS* 3.7 24.8 + - - +
166P TYR* 5.4 12.1 - - + -
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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