Contacts of the helix formed by residues 11 - 21 (chain A) in PDB entry 1IEW
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 PRO 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A THR 4.4 1.6 - - - +
10A LYS* 1.3 95.7 - - + +
12A VAL* 1.3 66.7 + - - +
13A GLU* 4.5 4.5 - - + +
14A ASP* 3.1 34.0 + - - +
15A ARG* 3.1 18.4 + - - +
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Residues in contact with VAL 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 LYS 3.5 2.8 + - - +
11A PRO* 1.3 71.1 - - - +
13A GLU* 1.3 63.4 + - + +
15A ARG* 3.0 13.0 + - - +
16A VAL* 2.9 31.1 + - + +
192A MET* 6.5 0.2 - - + -
351A ARG* 3.8 18.2 - - + +
354A PHE* 3.7 20.9 - - + +
355A THR* 3.6 38.8 - - + +
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Residues in contact with GLU 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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11A PRO* 3.3 4.3 - - + +
12A VAL* 1.3 79.3 - - + +
14A ASP* 1.3 66.2 + - - +
16A VAL* 3.8 7.9 - - - +
17A ALA* 3.1 24.6 + - - +
192A MET* 4.2 12.9 - - + +
347A THR* 5.3 0.9 - - - +
351A ARG* 2.7 51.1 + - - +
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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
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4A LEU* 3.6 17.7 - - + +
10A LYS* 4.9 2.6 - - + +
11A PRO* 3.1 40.8 + - + +
13A GLU* 1.3 80.0 - - - +
15A ARG* 1.3 58.2 + - - +
17A ALA* 3.5 5.1 + - - +
18A ASP* 2.9 30.8 + - - +
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Residues in contact with ARG 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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4A LEU* 4.0 12.3 - - - +
5A TYR* 3.0 35.6 + - - +
6A LYS* 4.3 6.7 - - - +
7A ASP 3.4 18.6 + - - +
8A ALA* 3.6 14.1 + - - +
10A LYS* 3.5 26.6 + - + +
11A PRO 3.1 11.3 + - - +
12A VAL* 3.0 10.7 + - - +
14A ASP* 1.3 74.5 - - - +
16A VAL* 1.3 64.8 + - - +
19A LEU* 3.1 21.0 + - - +
354A PHE* 3.3 41.2 + - + +
359A PHE* 3.5 10.1 - - - +
360A GLU* 2.9 40.8 + - - -
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Residues in contact with VAL 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 VAL* 2.9 21.9 + - + +
13A GLU* 3.8 11.2 - - - +
14A ASP 3.3 0.2 - - - -
15A ARG* 1.3 78.0 - - - +
17A ALA* 1.3 60.0 + - - +
19A LEU* 3.8 1.0 - - - +
20A LEU* 2.8 34.6 + - + +
347A THR* 3.7 41.5 - - + +
350A LEU* 3.9 9.4 - - + +
351A ARG* 3.6 35.9 - - + +
354A PHE* 3.6 16.4 - - + -
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Residues in contact with ALA 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 GLU 3.1 15.3 + - - +
14A ASP* 3.8 5.8 - - - +
16A VAL* 1.3 80.5 - - - +
18A ASP* 1.3 63.9 + - - +
20A LEU* 3.7 8.6 - - - +
21A GLY* 3.0 22.3 + - - -
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Residues in contact with ASP 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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4A LEU* 3.2 27.8 - - + +
5A TYR* 2.9 23.1 + - - +
14A ASP 2.9 18.4 + - - +
15A ARG 3.9 1.8 - - - +
17A ALA* 1.3 77.0 - - - +
19A LEU* 1.3 61.4 + - - +
21A GLY* 3.6 4.3 + - - -
22A ARG* 2.9 58.5 + - - +
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Residues in contact with LEU 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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5A TYR* 3.7 40.8 - - + +
15A ARG 3.1 17.9 + - - +
16A VAL 3.8 2.0 - - - +
18A ASP* 1.3 74.0 - - - +
20A LEU* 1.3 68.9 + - - +
22A ARG* 2.9 14.9 + - - +
23A MET* 3.2 16.6 + - + +
86A LEU* 4.0 22.7 - - + -
88A ILE* 3.9 13.5 - - + -
350A LEU* 3.5 35.9 - - + -
354A PHE* 4.0 6.3 - - + -
359A PHE* 3.8 22.4 - - + -
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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 VAL* 2.8 23.6 + - + +
17A ALA* 3.7 7.6 - - - +
19A LEU* 1.3 72.8 - - - +
21A GLY* 1.3 59.4 + - - +
22A ARG 2.9 6.4 + - - -
23A MET* 3.1 24.6 + - - +
28A LYS* 3.7 18.4 + - - +
343A ASP* 3.7 34.3 - - + +
346A VAL* 3.8 28.7 - - + -
347A THR* 3.5 23.8 - - - +
350A LEU* 4.3 4.7 - - + +
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Residues in contact with GLY 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 ALA 3.0 16.7 + - - -
18A ASP 4.0 2.2 - - - -
19A LEU 3.1 1.0 - - - -
20A LEU* 1.3 76.0 - - - +
22A ARG* 1.3 60.0 + - - +
23A MET 5.3 0.7 - - - -
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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