Contacts of the helix formed by residues 19 - 29 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR 4.3 9.6 + - - +
12B PHE 5.1 0.2 - - - -
13B SER* 3.9 22.2 - - - +
17B LYS 3.3 11.6 + - - +
18B LEU* 1.3 69.1 - - - +
20B GLN* 1.3 62.6 + - + +
22B GLU* 3.1 17.5 + - - +
23B TYR* 3.0 63.9 + - + +
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Residues in contact with GLN 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A ILE* 3.4 31.4 - - + +
16A PHE* 2.9 58.5 + - - +
9B LEU* 3.4 25.8 - - + +
10B THR* 4.3 8.6 - - + +
18B LEU 3.3 0.4 - - - -
19B VAL* 1.3 83.1 - - + +
21B ILE* 1.4 54.6 + - - +
23B TYR* 3.4 20.9 + - - +
24B ALA* 3.0 21.1 + - - +
127B ARG* 5.3 0.2 - - - +
128B PRO* 4.3 17.6 - - + +
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Residues in contact with ILE 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B THR* 4.9 3.1 - - + -
18B LEU* 3.2 43.1 + - + +
20B GLN* 1.4 73.6 - - - +
22B GLU* 1.4 61.1 + - + +
24B ALA* 3.1 8.8 + - - +
25B LEU* 3.0 35.9 + - + +
121B THR* 3.5 26.9 - - + +
128B PRO* 3.9 20.6 - - + -
150B PRO 4.5 2.7 - - - -
151B SER* 3.8 36.1 - - - +
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Residues in contact with GLU 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS* 3.6 39.7 - - - +
18B LEU 3.0 14.4 + - - +
19B VAL* 3.1 22.7 + - - +
21B ILE* 1.4 76.3 - - + +
23B TYR* 1.3 65.4 + - + +
25B LEU* 3.2 21.6 + - + +
26B ALA* 3.2 21.1 + - - +
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Residues in contact with TYR 23 (chain B).
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* 3.4 27.5 - - + +
17A SER 3.3 14.6 - - - +
18A PRO* 3.5 46.2 - - + +
20A GLY* 3.3 9.4 - - - -
19B VAL* 3.0 39.1 + - + +
20B GLN* 3.5 21.5 - - - +
22B GLU* 1.3 82.1 - - + +
24B ALA* 1.3 56.8 + - - +
26B ALA* 3.2 10.8 + - + +
27B ALA* 3.1 20.4 + - - +
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Residues in contact with ALA 24 (chain B).
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* 3.6 29.4 - - + -
20B GLN 3.0 10.5 + - - +
21B ILE* 3.1 15.7 + - - +
23B TYR* 1.3 75.6 - - - +
25B LEU* 1.4 54.3 + - - +
27B ALA* 3.2 8.8 + - - +
28B VAL* 3.1 27.4 + - - +
128B PRO* 4.5 4.0 - - + -
129B PHE 4.0 5.2 - - - +
130B GLY* 3.6 2.0 - - - +
150B PRO* 3.6 22.7 - - + -
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Residues in contact with LEU 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B ILE* 3.0 28.3 + - + +
22B GLU* 3.2 23.1 + - + +
24B ALA* 1.4 71.5 - - - +
26B ALA* 1.3 63.5 + - - +
28B VAL* 3.3 11.1 + - + +
29B ALA* 3.2 19.2 + - - +
149B ASP* 5.0 6.5 - - + +
150B PRO* 4.0 25.8 - - + -
151B SER* 5.3 2.9 - - - +
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Residues in contact with ALA 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A PRO 4.1 10.8 - - - +
19A GLU* 4.0 11.7 - - - +
20A GLY* 3.9 15.5 - - - +
22B GLU 3.2 9.1 + - - +
23B TYR* 3.2 16.1 + - + +
25B LEU* 1.3 76.2 - - - +
27B ALA* 1.4 58.1 + - - +
29B ALA* 3.3 21.8 + - + +
30B GLY* 3.6 4.9 + - - -
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Residues in contact with ALA 27 (chain B).
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* 4.3 13.9 - - + -
20A GLY* 3.7 23.5 - - - +
23B TYR 3.1 11.7 + - - +
24B ALA* 3.2 14.5 + - - +
26B ALA* 1.4 72.7 - - - +
28B VAL* 1.4 62.9 + - - +
30B GLY* 3.4 11.9 + - - +
31B GLY 4.6 0.2 + - - -
77B GLY* 3.5 17.6 - - - -
78B MET* 4.6 10.8 - - + +
130B GLY* 4.4 9.6 - - - -
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Residues in contact with VAL 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ALA 3.1 9.3 + - - +
25B LEU* 3.4 11.4 - - + +
27B ALA* 1.4 72.2 - - - +
29B ALA* 1.4 56.7 + - - +
30B GLY 2.7 17.6 - - - +
76B SER* 3.6 12.3 + - - +
77B GLY* 4.2 7.0 - - - -
130B GLY 3.0 22.9 - - - +
132B SER* 3.6 29.8 - - - +
149B ASP* 5.5 1.3 - - - +
150B PRO* 3.5 17.3 - - + -
162B MET* 5.4 2.7 - - + -
163B GLY* 3.7 15.9 - - - +
166B TYR* 6.4 2.7 - - + -
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LEU 3.2 11.7 + - - +
26B ALA* 3.3 15.7 - - - +
27B ALA 3.3 0.4 - - - -
28B VAL* 1.4 69.7 - - - +
30B GLY* 1.3 64.7 + - - +
163B GLY 3.9 5.8 - - - +
164B LYS* 3.7 24.6 + - - +
166B 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