Contacts of the helix formed by residues 7 - 24 (chain A) in PDB entry 2IAF
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 7 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4A SER* 3.1 19.7 + - - +
6A HIS* 1.3 86.5 - - + +
8A VAL* 1.3 72.4 + - - +
10A PRO* 3.4 4.2 - - - +
11A MSE 3.0 28.3 + - - +
48A HIS 5.4 1.3 - - - +
49A GLY* 4.3 21.3 - - - -
52A LYS* 5.7 4.7 - - - -
53A ALA* 3.3 22.8 - - - +
71A MSE 6.4 0.9 - - - -
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Residues in contact with VAL 8 (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 SER 4.3 12.6 - - - +
5A SER* 3.3 10.6 - - - +
7A THR* 1.3 83.2 + - - +
9A GLY* 1.3 67.4 + - - +
11A MSE 3.2 6.6 + - + +
12A LEU* 3.0 27.3 + - + +
63A PRO* 3.9 30.0 - - + +
138A GLY* 4.0 21.1 - - - +
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Residues in contact with GLY 9 (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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5A SER* 2.6 20.6 - - - -
8A VAL* 1.3 71.1 - - - +
10A PRO* 1.4 59.8 - - - +
12A LEU* 3.1 4.2 + - - -
13A ALA* 2.9 26.0 + - - +
134A SER* 3.4 15.9 - - - -
138A GLY* 4.4 8.7 - - - -
140A ILE* 3.1 21.8 - - - +
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Residues in contact with PRO 10 (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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5A SER 3.6 13.5 - - - +
6A HIS 3.7 16.2 - - - +
7A THR 3.4 15.9 - - - +
9A GLY* 1.4 85.6 - - - +
11A MSE 1.3 63.0 + - - +
13A ALA* 3.2 4.3 + - - +
14A ALA* 3.0 21.3 + - - +
41A LEU* 4.0 13.5 - - + -
50A THR* 3.7 17.3 - - + -
53A ALA* 4.5 2.9 - - + -
54A ILE* 3.6 28.9 - - + +
115A MSE 3.8 17.0 - - - -
117A PHE* 4.4 0.2 - - - -
134A SER* 3.7 4.2 - - - +
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Residues in contact with MSE 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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7A THR* 3.0 30.3 + - - +
8A VAL* 3.6 5.4 - - + +
10A PRO* 1.3 75.1 - - - +
12A LEU* 1.3 57.8 + - - +
14A ALA* 3.2 6.8 + - - +
15A ASN* 3.1 30.4 + - - -
53A ALA* 3.5 27.7 - - + +
57A GLY* 3.8 2.9 - - - -
61A LYS* 3.6 21.5 - - - +
62A ALA 3.8 8.3 - - - +
63A PRO* 3.7 34.5 - - + -
71A MSE 3.2 38.8 - - + -
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Residues in contact with LEU 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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8A VAL* 3.0 24.2 + - + +
9A GLY* 3.1 7.6 + - - +
11A MSE 1.3 72.6 - - - +
13A ALA* 1.3 61.5 + - - +
15A ASN* 3.4 11.3 + - + +
16A ALA* 2.9 29.5 + - - +
62A ALA* 5.8 0.2 - - + -
63A PRO* 3.6 26.5 - - + -
64A GLU* 4.0 12.8 - - - +
138A GLY 3.3 27.1 - - - +
139A PHE* 5.1 3.4 - - + -
140A ILE* 3.7 16.5 - - + +
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Residues in contact with ALA 13 (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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9A GLY 2.9 13.1 + - - +
10A PRO 3.2 8.7 + - - +
12A LEU* 1.3 77.5 - - - +
14A ALA* 1.3 56.5 + - - +
16A ALA* 3.4 2.9 + - - +
17A PHE* 2.8 29.3 + - - +
115A MSE 3.8 28.5 - - + -
117A PHE* 3.9 10.3 - - + -
132A TYR* 3.8 18.8 - - + -
140A ILE* 3.8 14.0 - - + +
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Residues in contact with ALA 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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10A PRO 3.0 11.8 + - - +
11A MSE 3.4 10.1 - - - +
13A ALA* 1.3 75.9 - - - +
15A ASN* 1.3 61.6 + - - +
17A PHE* 3.3 3.2 + - - +
18A LEU* 3.0 27.4 + - - +
54A ILE* 3.7 12.8 - - - +
57A GLY* 3.5 24.7 - - - -
58A LEU* 3.6 13.2 - - + +
117A PHE* 3.7 18.3 - - + -
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Residues in contact with ASN 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 MSE 3.1 16.9 + - - +
12A LEU* 3.5 14.9 - - + +
13A ALA 3.3 0.2 - - - -
14A ALA* 1.3 75.4 - - - +
16A ALA* 1.3 62.7 + - - +
18A LEU* 3.2 9.9 + - - +
19A GLN* 3.1 21.1 + - - +
57A GLY 2.9 23.1 + - - -
60A ASN* 4.1 14.4 + - - +
61A LYS 2.9 25.9 + - - +
62A ALA* 3.7 17.6 - - - +
63A PRO* 3.9 7.4 - - - +
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Residues in contact with ALA 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 LEU 2.9 17.9 + - - +
13A ALA 3.5 5.2 - - - +
15A ASN* 1.3 73.7 - - - +
17A PHE* 1.3 59.8 + - - +
19A GLN* 3.1 8.5 + - - +
20A LEU* 2.9 28.4 + - - +
132A TYR* 3.5 15.1 + - + +
140A ILE* 3.9 18.4 - - + -
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Residues in contact with PHE 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 ALA 2.8 19.5 + - - +
14A ALA 3.3 5.1 + - - +
16A ALA* 1.3 71.2 - - - +
18A LEU* 1.3 65.8 + - - +
20A LEU* 3.1 10.0 + - + +
21A LEU* 3.0 41.9 + - + +
33A VAL* 4.6 8.1 - - + -
58A LEU* 4.3 10.5 - - + -
117A PHE* 3.4 51.6 - + + -
118A SER* 3.8 30.7 - - - -
119A ALA* 3.9 11.4 - - + -
128A ILE* 4.1 17.7 - - + -
130A GLN* 4.1 22.2 - - + -
132A TYR* 3.4 9.1 + + + +
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Residues in contact with LEU 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 ALA 3.0 15.8 + - - +
15A ASN* 3.2 8.0 + - - +
17A PHE* 1.3 76.7 - - - +
19A GLN* 1.3 60.3 + - - +
21A LEU* 3.2 22.9 + - + +
22A GLU* 3.3 18.4 + - - +
27A PHE* 4.9 1.7 - - + -
57A GLY 3.4 21.1 - - - +
58A LEU* 3.4 32.1 - - + +
60A ASN* 3.4 35.2 - - - +
86A LEU* 3.5 25.8 - - + -
87A ALA* 3.7 18.6 - - + -
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Residues in contact with GLN 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 ASN 3.1 12.5 + - - +
16A ALA* 3.7 9.4 - - - +
18A LEU* 1.3 73.1 - - - +
20A LEU* 1.3 59.3 + - - +
22A GLU* 3.2 16.9 + - - +
23A GLN* 2.9 36.3 + - + +
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Residues in contact with LEU 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 ALA 2.9 12.3 + - - +
17A PHE* 3.1 16.6 + - + +
19A GLN* 1.3 74.1 - - - +
21A LEU* 1.3 59.5 + - - +
23A GLN* 3.4 27.0 - - - +
24A LYS* 2.9 51.4 + - + +
128A ILE* 3.7 24.9 - - + -
130A GLN* 3.8 40.6 - - + +
132A TYR* 4.1 5.8 - - - +
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Residues in contact with LEU 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 PHE* 3.0 38.3 + - + +
18A LEU* 3.2 15.0 + - + +
20A LEU* 1.3 75.3 - - + +
22A GLU* 1.3 60.6 + - - +
24A LYS* 3.8 1.1 - - - -
25A ASN 3.2 1.7 + - - -
26A LEU* 2.8 38.7 + - + -
27A PHE* 3.2 20.4 + - + +
30A THR* 4.0 13.7 - - + +
33A VAL* 5.2 0.7 - - + -
86A LEU* 4.1 27.6 - - + -
119A ALA* 3.8 15.3 - - + -
128A ILE* 3.7 30.5 - - + -
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Residues in contact with GLU 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 LEU 3.4 15.2 - - - +
19A GLN* 3.2 20.6 + - - +
20A LEU 3.2 0.6 - - - -
21A LEU* 1.3 73.4 - - - +
23A GLN* 1.3 66.2 + - - +
24A LYS 3.1 1.8 - - - -
25A ASN* 3.0 17.1 + - - +
27A PHE* 3.9 25.1 - - - +
87A ALA* 4.7 3.8 - - - +
89A LYS* 2.3 36.5 + - - +
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Residues in contact with GLN 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 GLN* 2.9 26.0 + - + +
20A LEU* 3.4 28.7 - - - +
22A GLU* 1.3 77.0 - - - +
24A LYS* 1.3 82.1 + - - +
25A ASN 3.7 0.3 + - - -
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Residues in contact with LYS 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 LEU* 2.9 36.7 + - + +
21A LEU 4.2 0.7 - - - +
23A GLN* 1.3 98.3 + - - +
25A ASN* 1.3 66.3 + - - +
26A LEU* 3.3 27.5 + - + +
128A ILE* 4.0 21.1 - - + -
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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