Contacts of the helix formed by residues 15 - 25 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.3 7.4 - - + +
8A TYR* 3.4 42.6 - - + -
12A ARG 3.3 0.4 + - - -
13A GLY 3.2 1.4 - - - -
14A ARG* 1.3 78.7 - - - +
16A GLU* 1.3 64.6 + - - +
17A ILE 3.2 1.3 - - - -
18A ILE* 2.9 20.6 + - - +
19A ARG* 3.2 25.8 + - - +
52A PRO* 4.2 13.2 - - + +
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Residues in contact with GLU 16 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12A ARG* 3.0 40.0 + - + +
13A GLY 3.9 4.9 - - - +
14A ARG 3.4 1.6 - - - -
15A ALA* 1.3 78.2 - - - +
17A ILE* 1.3 57.5 + - - +
19A ARG* 2.8 32.9 + - - +
20A TYR* 2.9 43.1 + - + -
33A ARG* 4.8 1.2 + - - -
155A ILE* 3.9 16.6 - - + -
190A TRP* 2.8 31.2 + - - -
194A ARG* 2.9 23.2 + - - +
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Residues in contact with ILE 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A GLY 5.0 0.4 + - - -
14A ARG 3.7 18.8 + - - +
16A GLU* 1.3 77.3 - - - +
18A ILE* 1.3 72.2 + - + +
20A TYR* 3.5 0.3 + - - +
21A ILE* 3.2 32.6 + - + +
64A SER* 4.5 2.2 - - - +
65A LEU* 4.5 8.5 - - + -
68A ALA* 4.3 7.9 - - + -
148A TRP* 3.7 46.9 - - + +
151A PHE* 3.8 19.1 - - + -
152A TYR* 3.8 31.6 - - + +
155A ILE* 3.5 15.9 - - + +
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Residues in contact with ILE 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 4.0 27.6 - - + -
15A ALA* 2.9 11.0 + - - +
17A ILE* 1.3 77.0 - - + +
19A ARG* 1.3 60.0 + - - +
21A ILE* 3.3 8.6 + - - +
22A PHE* 3.0 55.5 + - + -
52A PRO* 4.2 13.0 - - + -
54A LEU* 5.2 0.2 - - + -
64A SER* 3.8 35.7 - - - +
67A ILE* 3.9 24.7 - - + -
68A ALA* 4.4 4.5 - - - +
71A LEU* 3.8 11.2 - - + -
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Residues in contact with ARG 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A LEU* 3.7 10.8 - - + +
8A TYR* 3.9 7.1 - - - +
9A PHE 3.7 13.9 + - - -
11A MET 2.9 26.3 + - - -
12A ARG* 3.3 9.9 + - - +
15A ALA* 3.6 28.5 - - - +
16A GLU* 2.8 34.6 + - - +
18A ILE* 1.3 77.9 - - - +
20A TYR* 1.3 61.4 + - - +
22A PHE* 3.5 5.1 + - - +
23A ALA* 3.1 24.3 + - - +
29A TYR* 3.6 20.1 + - - +
31A ASP* 2.9 26.5 + - - -
32A HIS 5.6 0.6 + - - -
33A ARG* 3.3 21.0 - - - +
190A TRP* 3.4 37.7 + - + +
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Residues in contact with TYR 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A GLU* 2.9 44.3 + - + +
17A ILE 3.7 7.4 - - - +
19A ARG* 1.3 76.8 - - - +
21A ILE* 1.3 56.9 + - - +
23A ALA* 3.3 6.4 + - - +
24A TYR* 2.9 30.5 + - - +
151A PHE* 3.8 32.9 - + + -
154A GLU* 2.6 34.3 + - - -
155A ILE* 3.6 21.8 - - + +
158A THR* 5.3 0.3 + - - -
181A VAL* 4.6 3.6 - - + -
187A VAL* 3.9 30.2 - - + +
190A TRP* 3.7 17.3 - + - -
191A ILE* 3.8 7.9 - - + +
194A ARG* 3.2 19.6 + - - -
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Residues in contact with ILE 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ILE* 3.2 24.9 + - + +
18A ILE* 3.3 5.4 + - - +
20A TYR* 1.3 72.1 - - - +
22A PHE* 1.3 67.7 + - + +
24A TYR* 3.9 1.5 - - - -
25A LEU* 3.0 48.6 + - + +
27A ILE* 5.8 0.2 - - + -
68A ALA* 3.6 40.6 - - + +
71A LEU* 3.8 21.5 - - + -
72A THR* 3.8 17.7 - - + -
77A LEU* 4.5 3.1 - - + -
148A TRP* 4.2 14.6 - - + -
151A PHE* 4.5 12.3 - - + -
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Residues in contact with PHE 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A TYR* 4.0 18.2 - + + -
6A LEU* 4.8 1.6 - - + -
18A ILE* 3.0 41.6 + - + +
19A ARG 3.7 1.6 - - - +
21A ILE* 1.3 77.0 - - - +
23A ALA* 1.3 60.6 + - - +
25A LEU 3.8 0.2 - - - -
26A ASP* 3.1 4.2 + - - -
27A ILE* 2.9 66.3 + - + +
29A TYR* 3.4 51.6 - + + -
54A LEU* 3.9 24.7 - - + -
71A LEU* 3.8 30.1 - - + -
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Residues in contact with ALA 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A ARG 3.1 15.8 + - - +
20A TYR* 3.7 5.2 - - - +
22A PHE* 1.3 79.2 - - - +
24A TYR* 1.3 60.7 + - - +
26A ASP* 3.3 12.2 + - - +
29A TYR* 5.2 2.0 - - + -
186A ALA* 3.4 31.0 - - - +
187A VAL* 5.5 1.3 - - - -
190A TRP* 4.1 17.3 - - + -
193A ARG* 4.4 12.8 - - - +
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Residues in contact with TYR 24 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A TYR 2.9 18.1 + - - +
21A ILE 3.9 2.5 - - - +
23A ALA* 1.3 77.7 - - - +
25A LEU* 1.3 69.3 + - + +
26A ASP* 3.2 2.5 + - - +
77A LEU* 3.4 33.4 - - + -
146A VAL* 3.9 22.5 - - + +
151A PHE* 3.7 28.5 - + + -
184A ILE* 3.7 29.2 - - + -
186A ALA* 3.7 14.5 - - + +
187A VAL* 4.9 2.4 - - + +
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.0 34.3 + - + +
24A TYR* 1.3 92.8 - - + +
26A ASP* 1.3 71.3 + - - +
27A ILE* 3.5 27.4 - - + +
71A LEU 3.3 27.1 - - - +
72A THR* 4.6 2.5 - - - -
75A THR* 4.1 27.6 - - + -
77A LEU* 4.1 11.9 - - + -
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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