Contacts of the helix formed by residues 6 - 18 (chain F) in PDB entry 1IRJ
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 SER 6 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43E LYS 4.7 4.0 - - - -
44E ASP* 2.8 44.2 + - - -
46E GLN 6.0 0.4 - - - -
4F LYS* 4.1 2.9 + - - +
5F MET* 1.3 74.4 - - - +
7F GLN* 1.3 55.1 + - - +
8F LEU* 3.2 4.5 + - - +
9F GLU* 2.9 26.2 + - - +
10F ARG* 2.8 32.7 + - - +
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Residues in contact with GLN 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E THR* 4.1 13.0 - - + +
18E THR* 5.7 0.3 + - - -
44E ASP* 5.5 1.1 + - - +
6F SER* 1.3 75.0 - - - +
8F LEU* 1.3 59.2 + - - +
10F ARG* 3.7 5.1 + - - +
11F ASN* 2.6 46.4 + - - +
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Residues in contact with LEU 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14E THR* 4.8 3.3 - - + +
15E ILE* 4.1 38.6 - - + +
18E THR* 4.1 22.2 + - + +
40E LEU* 3.9 28.7 - - + -
44E ASP* 3.9 25.0 + - + +
45E LEU* 4.0 8.3 - - + -
79E PHE* 4.5 11.2 - - + -
6F SER* 3.1 7.4 + - - +
7F GLN* 1.3 78.7 - - - +
9F GLU* 1.3 60.3 + - - +
11F ASN* 3.4 2.7 + - - +
12F ILE* 2.9 47.9 + - + +
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Residues in contact with GLU 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44E ASP 3.3 19.7 - - - +
45E LEU* 3.2 18.3 - - + -
46E GLN* 4.2 1.8 + - - +
47E ASN* 2.7 40.6 + - - +
48E PHE* 2.8 37.9 + - + -
4F LYS 4.2 1.0 - - - +
5F MET* 3.2 16.2 - - + -
6F SER* 2.9 29.8 + - - +
8F LEU* 1.3 75.7 - - - +
10F ARG* 1.3 58.2 + - - +
12F ILE* 3.4 1.3 + - - -
13F GLU* 2.8 30.1 + - - +
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Residues in contact with ARG 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4F LYS* 5.9 0.4 - - - +
5F MET* 3.8 36.7 + - + +
6F SER 2.8 21.4 + - - +
7F GLN* 4.0 6.3 - - - +
9F GLU* 1.3 73.5 - - - +
11F ASN* 1.3 58.6 + - - +
13F GLU* 2.4 38.5 + - - +
14F THR* 3.0 37.5 + - - +
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Residues in contact with ASN 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10E ARG* 4.2 1.9 - - - +
11E ASN* 2.6 48.9 + - - +
14E THR* 3.1 35.1 + - + +
15E ILE* 4.8 4.0 - - + -
7F GLN* 2.6 36.5 + - - +
8F LEU* 3.9 3.6 - - - +
10F ARG* 1.3 74.3 - - - +
12F ILE* 1.3 67.3 + - - +
14F THR* 3.1 3.8 + - - -
15F ILE* 3.0 28.4 + - - +
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Residues in contact with ILE 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15E ILE* 4.4 6.1 - - + -
45E LEU* 4.4 8.1 - - + -
48E PHE* 3.7 21.3 - - + -
79E PHE* 6.0 2.9 - - + -
82E LEU* 6.4 0.2 - - + -
83E MET* 4.0 39.9 - - + -
86E LEU* 4.2 15.7 - - + -
8F LEU* 2.9 46.9 + - + +
9F GLU 3.7 3.8 - - - +
11F ASN* 1.3 76.3 - - - +
13F GLU* 1.3 64.7 + - - +
15F ILE* 3.1 9.1 + - - +
16F ILE* 3.0 38.7 + - + +
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Residues in contact with GLU 13 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E PHE* 4.5 5.8 - - + -
5F MET* 3.5 25.3 - - + +
9F GLU 2.8 18.5 + - - +
10F ARG* 2.4 42.5 + - - +
11F ASN 3.3 0.2 - - - -
12F ILE* 1.3 78.3 - - - +
14F THR* 1.3 62.5 + - - +
16F ILE* 3.6 7.1 + - - +
17F ASN* 3.1 46.4 + - - +
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Residues in contact with THR 14 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E GLN* 4.7 19.5 - - + +
8E LEU 5.5 0.2 - - - +
11E ASN* 2.7 36.1 + - - +
10F ARG* 3.0 23.5 + - - +
11F ASN 3.4 5.4 - - - -
12F ILE 3.1 0.2 - - - -
13F GLU* 1.3 76.3 + - - +
15F ILE* 1.3 53.6 + - - +
17F ASN* 3.0 6.8 + - - +
18F THR* 2.6 49.7 + - - +
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Residues in contact with ILE 15 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E LEU* 5.2 6.7 - - + +
11E ASN* 3.6 24.5 - - + +
12E ILE* 4.3 8.1 - - + -
15E ILE* 3.4 33.0 - - + -
83E MET* 4.9 3.1 - - - -
11F ASN 3.0 15.5 + - - +
12F ILE* 3.6 7.0 - - - +
14F THR* 1.3 75.0 - - - +
16F ILE* 1.3 64.3 + - - +
18F THR* 2.9 18.4 + - - -
19F PHE* 3.0 11.8 + - - +
76F PHE* 4.0 19.7 - - + -
79F PHE* 4.1 17.4 - - + -
80F ILE* 4.4 7.9 - - + -
83F MET* 3.9 18.4 - - + -
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Residues in contact with ILE 16 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48E PHE* 5.9 2.0 - - + -
83E MET 4.5 3.6 - - - +
86E LEU* 3.9 21.3 - - + +
12F ILE* 3.0 36.5 + - + +
13F GLU* 3.8 7.4 - - + +
15F ILE* 1.3 75.4 - - - +
17F ASN* 1.3 68.2 + - - +
19F PHE* 3.3 1.7 + - - +
20F HIS* 2.6 53.5 + - + +
76F PHE* 3.2 34.8 - - + -
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Residues in contact with ASN 17 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13F GLU* 3.1 36.3 + - - +
14F THR* 3.0 7.4 + - + +
16F ILE* 1.3 82.9 + - - +
18F THR* 1.3 58.5 + - - +
19F PHE 3.0 9.0 + - - -
20F HIS* 3.8 5.8 + - - +
21F GLN* 3.4 22.9 + - - +
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Residues in contact with THR 18 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7E GLN* 4.6 9.9 + - + +
8E LEU* 3.7 33.8 - - + +
11E ASN* 4.7 0.3 + - - -
14F THR* 2.6 40.6 + - - +
15F ILE* 2.9 9.8 + - - -
17F ASN* 1.3 72.9 - - - +
19F PHE* 1.3 57.6 + - - +
21F GLN* 4.0 19.8 + - - +
22F TYR* 3.7 18.9 - - + -
40F LEU* 4.1 9.7 - - + +
44F ASP* 4.2 10.8 - - - +
79F PHE* 5.8 1.6 - - + -
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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