Contacts of the helix formed by residues 15 - 25 (chain B) in PDB entry 5AIS
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 ALA 15 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6B LEU* 4.2 7.6 - - + +
8B TYR* 3.4 39.7 - - + -
13B GLY 3.2 1.6 - - - -
14B ARG* 1.3 77.0 - - - +
16B GLU* 1.3 64.9 + - - +
17B ILE 3.3 1.6 - - - -
18B ILE* 3.0 20.6 + - - +
19B ARG* 3.2 25.3 + - - +
52B PRO* 4.1 15.0 - - + +
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Residues in contact with GLU 16 (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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12B ARG* 3.1 40.0 + - + +
13B GLY 3.9 5.6 - - - +
14B ARG 3.4 1.6 - - - -
15B ALA* 1.3 77.2 - - - +
17B ILE* 1.3 57.3 + - - +
19B ARG* 2.9 33.4 + - - +
20B TYR* 2.8 48.2 + - + -
33B ARG* 4.8 1.4 + - - -
155B ILE* 3.8 16.2 - - + -
190B TRP* 2.9 24.1 + - - -
194B ARG* 2.8 29.8 + - - +
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Residues in contact with ILE 17 (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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13B GLY 5.0 0.2 + - - -
14B ARG 3.8 17.2 + - - +
16B GLU* 1.3 77.1 - - - +
18B ILE* 1.3 75.3 + - + +
20B TYR* 3.4 2.4 + - - +
21B ILE* 3.1 38.0 + - + +
64B SER* 4.5 7.9 - - - +
65B LEU* 4.7 2.7 - - + -
68B ALA* 4.2 8.7 - - + -
148B TRP* 3.7 42.4 - - + +
151B PHE* 3.7 19.5 - - + -
152B TYR* 3.8 38.8 - - + +
155B ILE* 3.5 10.8 - - + +
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Residues in contact with ILE 18 (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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6B LEU* 3.9 30.3 - - + -
15B ALA* 3.0 11.0 + - - +
17B ILE* 1.3 78.6 - - + +
19B ARG* 1.3 59.6 + - - +
21B ILE* 3.3 9.0 + - - +
22B PHE* 3.0 54.9 + - + -
52B PRO* 4.3 10.5 - - + -
54B LEU* 5.0 0.2 - - + -
64B SER* 4.0 28.5 - - - +
67B ILE* 3.8 32.5 - - + -
68B ALA* 4.5 4.5 - - - +
71B LEU* 4.0 10.8 - - + -
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Residues in contact with ARG 19 (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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6B LEU* 3.8 10.4 - - + +
8B TYR* 3.9 7.1 - - - +
9B PHE 3.8 12.7 + - - -
11B MET 2.9 28.5 + - - -
12B ARG* 3.3 10.5 + - - +
15B ALA* 3.2 27.8 + - - +
16B GLU* 2.9 30.3 + - - +
18B ILE* 1.3 76.3 - - - +
20B TYR* 1.3 61.7 + - - +
22B PHE* 3.6 2.3 + - - +
23B ALA* 3.1 22.9 + - - +
29B TYR* 3.6 21.8 + - - +
31B ASP* 2.9 26.9 + - - -
32B HIS 5.4 0.6 + - - -
33B ARG* 3.3 20.4 - - - +
190B TRP* 3.5 33.5 - - - +
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Residues in contact with TYR 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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16B GLU* 2.8 48.6 + - + +
17B ILE* 3.6 9.6 - - - +
19B ARG* 1.3 73.5 - - - +
21B ILE* 1.3 58.0 + - - +
23B ALA* 3.2 7.0 + - - +
24B TYR* 2.9 30.1 + - - +
151B PHE* 3.7 31.8 - + + -
154B GLU* 2.6 34.1 + - - -
155B ILE* 3.7 20.7 - - + +
158B THR* 5.3 0.2 + - - -
181B VAL* 4.6 3.4 - - + -
187B VAL* 3.8 33.3 - - + +
190B TRP* 3.8 15.3 - + - -
191B ILE* 3.9 7.6 - - + +
194B ARG* 3.1 18.9 + - - -
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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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17B ILE* 3.1 25.9 + - + +
18B ILE* 3.3 6.7 + - - +
20B TYR* 1.3 74.4 - - - +
22B PHE* 1.3 65.4 + - + +
24B TYR* 3.3 1.4 + - - +
25B LEU* 3.0 46.5 + - + +
68B ALA* 3.6 33.4 - - + -
71B LEU* 3.8 21.5 - - + -
72B THR* 3.6 26.0 - - + -
77B LEU* 4.2 14.4 - - + -
148B TRP* 4.4 6.7 - - + -
151B PHE* 4.5 8.3 - - + -
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Residues in contact with PHE 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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4B TYR* 3.9 25.1 - + + -
6B LEU* 4.8 0.9 - - + -
18B ILE* 3.0 42.7 + - + +
19B ARG 3.9 1.1 - - - +
21B ILE* 1.3 76.0 - - + +
23B ALA* 1.3 57.3 + - - +
25B LEU* 3.6 1.1 + - - -
26B ASP* 2.9 8.0 + - - -
27B ILE* 2.9 57.8 + - + +
29B TYR* 3.5 50.9 - + + -
54B LEU* 3.9 25.6 - - + -
71B LEU* 3.7 30.5 - - + -
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Residues in contact with ALA 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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19B ARG 3.1 15.0 + - - +
20B TYR* 3.4 10.1 - - - +
22B PHE* 1.3 76.9 - - - +
24B TYR* 1.3 63.8 + - - +
26B ASP* 3.2 13.8 + - - +
29B TYR* 5.2 1.3 - - + -
186B ALA* 3.5 31.0 - - - +
187B VAL* 5.4 0.7 - - - -
190B TRP* 4.0 20.0 - - + -
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Residues in contact with TYR 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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20B TYR 2.9 17.0 + - - +
21B ILE 3.8 3.6 - - - +
23B ALA* 1.3 77.0 - - - +
25B LEU* 1.3 66.8 + - + +
26B ASP* 3.4 2.3 + - - +
76B ASP* 2.8 39.4 + - - -
77B LEU* 3.5 28.9 - - + -
146B VAL* 4.0 15.7 - - + +
151B PHE* 3.7 28.9 - + + -
184B ILE* 3.8 27.8 - - + -
186B ALA* 3.7 15.0 - - + +
187B VAL* 4.8 1.8 - - + +
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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 34.4 + - + +
24B TYR* 1.3 91.5 - - + +
26B ASP* 1.3 71.1 + - - +
27B ILE* 3.3 31.1 + - + +
71B LEU* 3.5 24.9 - - + +
75B THR* 4.1 30.1 - - + +
76B ASP* 4.5 5.4 - - - +
77B LEU* 4.4 4.9 - - + -
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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