Contacts of the helix formed by residues 19 - 30 (chain C) 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 TYR 19 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9C THR* 6.3 1.1 - - - -
11C ILE* 3.8 30.9 + - + -
13C SER* 3.5 30.3 - - - -
14C PRO* 4.2 12.4 - - + +
15C GLU* 5.4 7.3 - - + +
18C LEU* 1.4 69.9 - - - +
20C GLN* 1.3 76.0 + - + +
22C GLU* 3.2 16.5 + - - +
23C TYR* 3.0 58.2 + + + -
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Residues in contact with GLN 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR* 3.2 29.9 - - - +
12B PHE* 3.3 35.5 + - - -
9C THR* 4.0 29.1 - - - +
18C LEU* 3.5 4.5 - - + +
19C TYR* 1.3 84.2 - - + +
21C VAL* 1.3 61.8 + - + +
23C TYR* 3.8 18.3 - - - -
24C ALA* 2.9 29.6 + - - +
122C THR* 5.8 0.7 - - + -
128C ARG* 4.3 7.3 - - - +
129C PRO* 3.4 30.4 - - + +
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Residues in contact with VAL 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C LEU* 3.7 32.3 + - + +
19C TYR 3.2 0.4 - - - -
20C GLN* 1.3 77.0 - - + +
22C GLU* 1.4 61.9 + - - +
24C ALA* 3.3 5.9 + - - +
25C MET* 3.1 33.7 + - + +
122C THR* 3.9 28.3 - - + -
129C PRO* 5.5 0.7 - - + -
152C PRO 4.6 1.8 - - - +
153C SER* 3.6 30.5 - - - +
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Residues in contact with GLU 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLU* 2.9 30.9 - - - +
17C ARG* 3.1 29.2 + - + +
18C LEU 3.0 17.8 + - - +
19C TYR* 3.2 20.3 + - - +
21C VAL* 1.4 77.1 - - + +
23C TYR* 1.3 77.1 + - + +
25C MET* 3.3 19.4 + - - +
26C GLU* 3.3 19.5 + - + +
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Residues in contact with TYR 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 3.4 43.3 - - + -
13B SER 3.5 15.5 - - - +
14B PRO* 3.5 41.0 - - + +
16B GLY* 3.5 11.5 - - - +
19C TYR* 3.0 46.7 + + + +
20C GLN* 3.5 10.5 + - - +
22C GLU* 1.3 90.9 - - + +
24C ALA* 1.3 58.9 + - - +
26C GLU* 3.3 7.2 + - - +
27C ALA* 3.1 23.0 + - - +
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 3.9 12.3 - - + -
20C GLN 2.9 19.5 + - - +
21C VAL* 3.3 6.7 + - - +
23C TYR* 1.3 72.5 - - - +
25C MET* 1.4 53.4 - - - +
26C GLU 3.3 0.2 + - - -
27C ALA* 3.4 6.9 + - - +
28C ILE* 2.1 34.6 - - - +
129C PRO* 5.3 3.4 - - + -
130C PHE 4.7 1.1 - - - +
131C GLY* 3.4 15.5 - - - +
152C PRO* 3.6 28.7 - - + +
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Residues in contact with MET 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C VAL* 3.1 29.8 + - + +
22C GLU* 3.3 13.9 + - - +
24C ALA* 1.4 77.4 - - - +
26C GLU* 1.4 60.2 + - + +
28C ILE* 3.2 22.3 + - + +
29C GLY* 4.0 3.3 + - - -
133C SER* 5.5 0.4 - - - +
151C ASP* 3.1 27.6 - - + +
152C PRO* 3.5 26.0 - - + -
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Residues in contact with GLU 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B PRO 3.0 22.1 - - - +
15B SER* 3.1 31.9 + - - +
22C GLU* 3.3 17.3 - - + +
23C TYR* 3.3 7.3 + - - +
24C ALA 3.2 0.4 - - - -
25C MET* 1.4 75.5 - - + +
27C ALA* 1.3 64.5 + - - +
28C ILE 3.2 1.6 - - - -
29C GLY* 3.3 10.5 + - - +
30C HIS* 3.2 12.5 + - + -
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Residues in contact with ALA 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B PHE* 4.5 12.3 - - + -
15B SER 3.5 0.6 + - - -
16B GLY* 3.7 24.9 - - - +
23C TYR 3.1 12.4 + - - +
24C ALA* 3.4 14.1 + - - +
26C GLU* 1.3 75.0 - - - +
28C ILE* 1.3 61.6 + - - +
30C HIS* 3.2 20.4 + - - +
31C ALA 3.4 3.6 + - - -
78C GLY 3.9 12.5 - - - +
79C ILE* 5.0 7.8 - - + +
131C GLY 4.4 8.1 - - - +
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Residues in contact with ILE 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C ALA 2.1 40.8 - - - +
25C MET* 3.2 16.4 - - + +
26C GLU 3.2 0.2 - - - -
27C ALA* 1.3 74.0 - - - +
29C GLY* 1.3 60.7 + - - +
30C HIS 3.1 2.0 - - - -
31C ALA* 2.7 38.7 + - + +
77C ALA* 4.4 4.5 - - + -
78C GLY* 4.1 7.2 - - - -
131C GLY 3.3 17.7 - - - +
133C SER* 3.6 15.5 - - - +
152C PRO* 3.8 9.4 - - + -
164C ILE* 3.7 31.6 - - + -
165C GLY* 3.8 16.9 - - - +
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Residues in contact with GLY 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C MET 4.0 3.4 + - - -
26C GLU* 3.3 10.8 + - - -
27C ALA 3.3 1.0 - - - -
28C ILE* 1.3 78.1 - - - +
30C HIS* 1.4 57.7 + - - +
31C ALA 3.4 3.3 - - - +
165C GLY 4.8 2.9 - - - -
166C ASN* 3.0 35.2 + - - +
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Residues in contact with HIS 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B SER* 3.4 34.9 + - - -
16B GLY 4.5 5.1 + - - +
17B LYS* 3.5 27.3 + - + -
26C GLU* 3.2 20.2 + - + -
27C ALA* 3.2 11.0 + - - +
28C ILE 3.1 0.6 - - - -
29C GLY* 1.4 73.2 - - - +
31C ALA* 1.4 63.1 + - - +
32C GLY 3.8 0.5 + - - -
50C ARG* 4.2 18.7 + - - -
166C ASN* 4.9 4.2 + - - +
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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