Contacts of the helix formed by residues 13 - 26 (chain A) in PDB entry 2IAI
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 THR 13 (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 3.9 1.5 + - - +
12A GLU* 1.4 76.8 - - - +
14A LEU* 1.3 66.0 + - - +
15A LEU* 3.5 8.6 + - - +
16A SER* 2.9 29.5 + - - -
17A VAL* 3.0 22.2 + - - +
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Residues in contact with LEU 14 (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 THR* 1.3 74.1 - - - +
15A LEU* 1.3 64.2 + - - +
17A VAL* 3.3 6.3 + - + +
18A ALA* 2.9 27.0 + - + +
35A LEU* 5.2 6.1 - - + +
39A ALA* 3.8 28.0 - - + -
41A ILE* 4.8 4.9 - - + -
46A ILE* 4.4 20.6 - - + -
49A HIS* 3.6 42.2 - - + +
50A VAL* 4.4 9.6 - - + -
56A LEU* 4.2 24.9 - - + -
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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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13A THR* 3.2 7.8 + - - +
14A LEU* 1.3 79.8 - - - +
16A SER* 1.3 57.0 + - - +
18A ALA* 3.3 1.8 + - + +
19A VAL* 2.9 38.3 + - + +
56A LEU* 3.5 43.6 - - + +
59A ARG* 4.1 28.5 - - + +
60A ALA 4.1 4.0 - - - +
63A ARG* 5.5 4.0 - - - -
103A TYR* 4.2 24.2 - - + +
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Residues in contact with SER 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 GLU* 3.2 14.7 - - - +
13A THR* 2.9 37.4 + - - -
15A LEU* 1.3 77.3 - - - +
17A VAL* 1.3 61.5 + - - +
19A VAL* 3.5 5.1 + - - +
20A GLN* 3.2 21.1 + - - +
103A TYR* 4.4 13.7 + - - -
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Residues in contact with VAL 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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10A THR* 4.0 20.0 - - + -
12A GLU* 3.9 18.8 - - + +
13A THR 3.0 18.1 + - - +
14A LEU* 3.6 11.2 - - + +
16A SER* 1.3 73.4 + - - +
18A ALA* 1.3 67.0 + - - +
20A GLN* 3.1 9.1 + - - +
21A VAL* 3.0 22.8 + - + +
35A LEU* 4.6 3.4 - - + +
38A ALA* 3.7 18.8 - - + +
39A ALA* 3.7 32.5 - - + +
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Residues in contact with ALA 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 LEU* 2.9 19.4 + - + +
15A LEU* 3.7 5.2 - - + +
17A VAL* 1.3 77.7 - - - +
19A VAL* 1.3 57.9 + - - +
21A VAL* 3.2 2.1 + - - +
22A PHE* 2.8 46.0 + - + -
35A LEU* 3.7 24.9 - - + -
56A LEU* 3.9 26.0 - - + -
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Residues in contact with VAL 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 26.1 + - + +
16A SER* 3.8 6.7 - - - +
17A VAL 3.3 0.2 - - - -
18A ALA* 1.3 76.4 - - - +
20A GLN* 1.3 63.8 + - - +
22A PHE* 3.3 3.8 + - + +
23A ILE* 3.0 30.5 + - + +
60A ALA* 3.7 20.2 - - + -
102A PRO* 3.6 34.1 - - + -
103A TYR* 3.7 28.5 - - + -
106A LEU* 3.9 16.2 - - + -
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Residues in contact with GLN 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 SER 3.2 12.8 + - - +
17A VAL* 3.1 13.1 + - - +
19A VAL* 1.3 79.0 - - - +
21A VAL* 1.3 61.9 + - + +
23A ILE* 3.4 7.5 + - - +
24A GLU* 3.1 51.0 + - + +
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Residues in contact with VAL 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 VAL* 3.0 15.3 + - + +
18A ALA 3.7 5.2 - - - +
20A GLN* 1.3 73.7 - - + +
22A PHE* 1.3 60.6 + - - +
24A GLU* 3.1 8.7 + - - +
25A ARG* 2.8 48.5 + - - +
30A THR* 3.6 26.7 - - + +
34A HIS* 4.1 10.8 - - + +
35A LEU* 3.9 12.1 - - + -
38A ALA* 3.5 31.0 - - + -
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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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18A ALA* 2.8 29.5 + - + +
19A VAL* 3.7 6.1 - - + +
21A VAL* 1.3 77.2 - - - +
23A ILE* 1.3 57.2 + - - +
26A GLY* 2.8 30.9 + - - -
27A TYR* 3.7 29.9 + + - +
30A THR* 3.6 35.9 - - + -
35A LEU* 4.3 4.3 - - + -
53A LYS* 3.6 31.0 - - + -
56A LEU* 4.1 12.8 - - + -
57A LEU* 3.8 27.6 - - + -
60A ALA* 5.6 0.2 - - + -
106A LEU* 3.7 32.4 - - + +
109A ARG* 4.7 0.9 + - - -
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Residues in contact with ILE 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 VAL* 3.0 24.5 + - + +
20A GLN* 3.9 6.7 - - - +
21A VAL 3.3 0.2 - - - -
22A PHE* 1.3 77.0 - - - +
24A GLU* 1.3 68.4 + - + +
26A GLY 3.9 2.3 + - - -
102A PRO* 3.6 43.1 - - + +
105A THR* 4.6 9.4 - - + -
106A LEU* 3.7 16.4 - - + -
109A ARG* 3.1 38.9 + - - +
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Residues in contact with GLU 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 GLN* 3.1 39.9 + - + +
21A VAL* 3.1 8.0 + - - +
23A ILE* 1.3 82.2 - - + +
25A ARG* 1.3 64.8 + - + +
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Residues in contact with ARG 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 VAL* 2.8 29.2 + - + +
24A GLU* 1.3 78.1 - - + +
26A GLY* 1.3 61.3 + - - +
29A GLY* 4.0 18.3 + - - +
30A THR* 3.5 8.5 - - - +
34A HIS* 3.4 59.7 + - - +
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Residues in contact with GLY 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 PHE 2.8 17.2 + - - -
23A ILE 3.9 2.9 + - - -
24A GLU 3.5 1.8 - - - -
25A ARG* 1.3 80.7 - - - +
27A TYR* 1.3 68.0 + - - -
28A ASP 3.3 2.9 - - - -
29A GLY 4.0 0.7 - - - -
30A THR* 2.9 21.8 + - - -
109A ARG* 5.7 4.3 - - - -
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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