Contacts of the helix formed by residues 10 - 26 (chain A) in PDB entry 1IAW
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 GLU 10 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11A PRO* 1.3 79.8 - - + +
12A ASP* 4.4 4.2 - - + +
13A ASP* 2.7 44.8 + - + +
14A ASP* 2.6 61.9 + - - +
134A LYS* 4.2 3.6 - - - +
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Residues in contact with PRO 11 (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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10A GLU* 1.3 96.6 - - + +
12A ASP* 1.3 69.3 + - + +
15A LEU* 2.9 26.9 + - - +
115A ILE* 4.4 0.6 - - + +
134A LYS* 2.9 59.5 - - + +
136A ILE* 5.1 5.6 - - + -
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Residues in contact with ASP 12 (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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10A GLU* 5.1 6.1 - - + +
11A PRO* 1.3 83.2 - - + +
13A ASP* 1.3 63.5 + - - +
15A LEU* 3.6 7.4 - - - +
16A GLU* 3.2 46.8 + - - +
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 2.7 44.8 + - + +
11A PRO 3.2 0.6 - - - -
12A ASP* 1.3 76.9 - - - +
14A ASP* 1.3 64.3 + - - +
15A LEU 3.1 1.6 - - - -
16A GLU* 3.0 9.5 + - - +
17A ARG* 2.9 28.9 + - - +
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Residues in contact with ASP 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A GLU* 2.6 43.9 + - - +
13A ASP* 1.3 76.0 - - - +
15A LEU* 1.3 58.5 + - - +
17A ARG* 2.8 40.6 + - - +
18A VAL* 3.0 28.6 + - - +
92A VAL* 3.8 16.5 - - + +
115A ILE* 3.3 14.8 - - + -
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Residues in contact with LEU 15 (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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11A PRO 2.9 22.6 + - - +
12A ASP* 3.6 6.5 - - - +
14A ASP* 1.3 77.6 - - - +
16A GLU* 1.3 66.7 + - + +
18A VAL* 3.3 3.3 + - - +
19A ARG* 2.9 23.0 + - + -
115A ILE* 3.2 17.0 - - + +
132A LEU* 3.4 44.7 - - + +
133A VAL* 4.3 0.9 - - - +
134A LYS* 4.2 18.2 - - + +
158A GLN 5.2 1.8 - - - +
160A VAL* 3.8 36.3 - - + -
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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 ASP* 3.2 32.7 + - - +
13A ASP* 3.0 8.1 + - - +
15A LEU* 1.3 79.5 - - + +
17A ARG* 1.3 60.8 + - - +
18A VAL 3.0 2.0 - - - -
19A ARG* 2.5 46.0 + - - +
20A ALA* 2.8 32.1 + - - +
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Residues in contact with ARG 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 ASP* 2.9 15.2 + - - +
14A ASP* 2.8 37.3 + - - +
16A GLU* 1.3 78.4 - - - +
18A VAL* 1.3 61.3 + - - +
20A ALA* 3.7 5.2 + - - +
21A THR* 3.3 23.4 + - - -
90A ALA* 3.9 24.9 + - + +
91A GLY 6.2 0.8 - - - -
92A VAL* 4.2 8.8 - - + +
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Residues in contact with VAL 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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14A ASP 3.0 14.5 + - - +
15A LEU* 3.4 8.1 - - - +
17A ARG* 1.3 75.5 - - - +
19A ARG* 1.3 67.1 + - - +
21A THR* 3.0 4.2 + - - -
22A LEU* 2.9 29.7 + - + +
89A ILE* 4.1 24.5 - - + +
90A ALA* 5.0 0.7 - - - -
92A VAL* 3.5 33.7 - - + -
94A VAL* 4.0 21.8 - - + -
115A ILE* 4.3 5.8 - - + -
132A LEU* 3.9 20.4 - - + -
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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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15A LEU* 2.9 17.5 + - + +
16A GLU* 2.5 54.4 + - - +
18A VAL* 1.3 76.2 - - - +
20A ALA* 1.3 61.3 + - - +
22A LEU* 3.0 7.3 + - - +
23A TYR* 2.8 52.3 + - + +
132A LEU* 3.9 12.8 - - + -
160A VAL* 3.9 26.3 - - - +
161A LYS 5.6 1.0 + - - -
162A LEU* 4.0 19.6 - - + +
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Residues in contact with ALA 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 2.8 20.6 + - - +
17A ARG* 3.9 6.7 - - - +
19A ARG* 1.3 76.7 - - - +
21A THR* 1.3 62.2 + - - +
23A TYR* 3.7 6.5 + - - +
24A SER* 3.3 21.0 + - - -
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Residues in contact with THR 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 ARG 3.3 5.6 + - - -
18A VAL 3.0 8.0 + - - -
20A ALA* 1.3 77.3 - - - +
22A LEU* 1.3 67.5 + - + +
24A SER* 3.0 17.3 + - - -
25A LEU* 3.1 28.1 + - + +
79A PHE* 5.9 0.2 - - + -
89A ILE* 3.8 23.8 - - + -
90A ALA* 3.0 27.1 - - + +
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Residues in contact with LEU 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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18A VAL* 2.9 31.5 + - + +
19A ARG* 3.6 7.0 - - - +
21A THR* 1.3 77.4 - - - +
23A TYR* 1.3 64.3 + - + +
24A SER 3.0 0.4 + - - -
25A LEU* 3.1 7.2 + - + +
26A ASP* 3.0 25.3 + - - +
77A PHE* 5.2 13.5 - - + -
79A PHE* 4.0 28.3 - - + -
89A ILE* 5.0 7.0 - - + -
117A LEU* 4.1 22.9 - - + -
132A LEU* 4.2 5.2 - - + -
162A LEU* 3.7 27.6 - - + -
163A TRP* 4.2 19.6 - - + -
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Residues in contact with TYR 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* 2.8 44.0 + - + +
20A ALA* 4.0 6.7 - - - +
22A LEU* 1.3 73.5 - - + +
24A SER* 1.3 59.2 - - - +
26A ASP 4.7 0.7 - - - -
27A PRO* 3.3 31.7 - - + +
161A LYS 4.3 3.6 + - - -
162A LEU* 3.9 21.1 - - + +
163A TRP* 3.0 57.4 + + - -
164A PRO* 3.7 11.4 - - + +
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Residues in contact with SER 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 ALA 3.3 14.2 + - - -
21A THR* 3.0 18.3 + - - -
22A LEU 3.0 0.4 - - - -
23A TYR* 1.3 80.6 - - - +
25A LEU* 1.3 66.1 + - - +
27A PRO* 4.1 5.0 - - - +
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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 THR* 3.1 23.1 + - + +
22A LEU* 3.1 9.0 + - + +
24A SER* 1.3 86.4 - - - +
26A ASP* 1.3 58.8 + - - +
27A PRO* 3.4 7.2 - - - +
31A ARG* 3.2 25.9 + - - +
77A PHE* 3.6 48.5 - - + +
79A PHE* 4.2 14.4 - - + -
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Residues in contact with ASP 26 (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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22A LEU* 3.0 9.1 + - + +
25A LEU* 1.3 78.0 - - - +
27A PRO* 1.3 54.5 - - - +
28A ASP 4.1 1.4 + - - -
29A GLY* 2.9 12.5 + - - -
30A ASP* 3.0 10.9 + - - +
31A ARG* 2.9 29.1 + - - +
32A THR* 2.7 34.7 + - - -
77A PHE* 3.6 20.9 - - + -
163A TRP* 2.6 38.7 + - + -
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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