Contacts of the helix formed by residues 2 - 17 (chain F) in PDB entry 1F9N
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 ASN 2 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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143A ASN* 4.1 12.5 + - - -
146A LEU* 3.8 18.2 - - - +
1F MET* 1.3 80.3 + - + +
3F LYS* 1.3 62.3 + - - +
4F GLY* 3.2 6.4 + - - -
5F GLN* 2.7 64.0 + - + +
6F ARG* 3.8 14.4 + - - +
34F TYR* 5.5 1.9 - - - -
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Residues in contact with LYS 3 (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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147A GLU* 5.3 15.7 + - + +
149A LEU 5.2 2.7 - - - +
1F MET 4.0 2.4 + - - -
2F ASN* 1.3 70.7 + - - +
4F GLY* 1.3 68.0 + - - +
6F ARG* 3.0 21.7 + - + +
7F HIS* 3.2 34.0 + - + +
43F ARG* 5.6 1.1 - - - +
44F ASP* 4.8 4.3 - - - +
47F GLU* 2.7 40.7 + - - -
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Residues in contact with GLY 4 (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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146A LEU* 3.0 33.0 + - - -
147A GLU* 5.0 2.6 - - - +
149A LEU* 4.3 6.2 - - - +
2F ASN* 3.2 5.0 + - - -
3F LYS* 1.3 81.6 - - - +
5F GLN* 1.3 61.2 + - - +
7F HIS* 3.1 19.1 + - - +
8F ILE* 3.2 19.4 + - - +
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Residues in contact with GLN 5 (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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142A LYS* 5.3 8.3 - - - +
146A LEU* 3.9 19.1 - - + +
2F ASN* 2.7 47.5 + - + +
4F GLY* 1.3 71.2 - - - +
6F ARG* 1.3 61.5 + - - +
8F ILE* 3.4 15.8 + - + +
9F LYS* 3.3 16.5 + - - +
34F TYR* 3.9 19.1 + - + +
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Residues in contact with ARG 6 (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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2F ASN 3.8 11.4 + - - +
3F LYS* 3.0 14.6 + - - +
5F GLN* 1.3 78.2 - - - +
7F HIS* 1.3 67.1 + - + +
9F LYS* 3.2 5.7 + - - +
10F ILE* 3.1 28.5 + - + +
29F LEU* 4.7 2.8 - - + +
34F TYR* 3.6 25.7 - - + -
44F ASP* 5.1 7.2 - - - +
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Residues in contact with HIS 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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149A LEU* 3.1 32.7 + - + -
3F LYS* 3.4 44.2 + - + +
4F GLY* 3.1 9.0 + - - +
6F ARG* 1.3 76.9 - - + +
8F ILE* 1.3 64.6 - - - +
10F ILE* 3.1 10.2 + - + +
11F ARG* 3.0 30.3 + - - +
44F ASP* 3.1 38.8 + - + +
47F GLU* 4.0 21.3 - - + -
48F LEU* 4.0 19.1 - - + +
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Residues in contact with ILE 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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84A PHE* 4.0 25.6 - - + -
87A ILE* 4.8 4.3 - - + -
146A LEU* 3.8 16.2 - - + -
149A LEU* 3.5 31.4 - - + -
4F GLY 3.2 11.6 + - - +
5F GLN* 3.6 14.8 - - + +
6F ARG 3.3 0.2 - - - -
7F HIS* 1.3 77.2 - - - +
9F LYS* 1.3 58.1 + - + +
11F ARG* 3.7 10.5 + - - +
12F GLU* 3.1 31.1 + - + +
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Residues in contact with LYS 9 (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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5F GLN 3.3 6.9 + - - +
6F ARG* 3.2 9.3 + - - +
7F HIS 3.1 0.8 - - - -
8F ILE* 1.3 79.8 - - + +
10F ILE* 1.3 58.0 - - - +
12F GLU* 3.1 33.1 + - - +
13F ILE* 2.7 51.9 + - + +
29F LEU* 4.3 10.8 - - + -
32F ASP* 3.6 37.7 + - + +
34F TYR* 3.9 28.0 + - + +
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Residues in contact with ILE 10 (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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6F ARG* 3.1 17.3 + - + +
7F HIS* 3.1 14.3 + - + +
9F LYS* 1.3 74.7 - - - +
11F ARG* 1.3 58.2 + - - +
13F ILE* 4.0 3.5 - - - +
14F ILE* 3.0 32.0 + - + +
25F LEU* 4.1 20.1 - - + +
29F LEU* 4.1 30.1 - - + -
41F VAL* 5.8 0.9 - - + -
44F ASP* 3.5 39.9 - - + +
45F ILE* 4.7 4.3 - - + -
48F LEU* 3.5 22.2 - - + -
50F LEU* 3.7 14.8 - - + -
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Residues in contact with ARG 11 (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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81A MET* 3.1 64.0 + - - +
84A PHE* 3.9 30.1 + - - +
149A LEU* 4.7 13.4 - - - +
7F HIS* 3.0 23.1 + - - +
8F ILE* 3.8 8.7 - - - +
10F ILE* 1.3 74.3 - - - +
12F GLU* 1.3 64.3 + - - +
14F ILE* 2.7 30.7 - - - +
15F THR* 2.9 10.3 + - - -
48F LEU* 3.8 28.8 - - + +
50F LEU* 5.5 1.6 - - + -
64F LEU* 3.7 25.7 - - + +
65F PRO* 5.1 9.9 - - + +
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Residues in contact with GLU 12 (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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8F ILE* 3.1 20.8 + - + +
9F LYS* 3.1 35.4 + - - +
11F ARG* 1.3 78.0 - - - +
13F ILE* 1.3 65.8 + - - +
15F THR* 3.0 8.0 + - - -
16F SER* 2.9 34.9 + - - +
32F ASP* 5.1 0.7 - - - +
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Residues in contact with ILE 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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9F LYS* 2.7 30.5 + - + +
10F ILE* 4.1 3.4 - - - +
12F GLU* 1.3 77.6 - - - +
14F ILE* 1.3 51.2 + - - +
16F SER* 4.6 4.0 - - - +
17F ASN* 2.6 43.5 + - + +
19F ILE* 3.6 20.4 - - + -
25F LEU* 4.5 1.6 - - + -
28F MET* 3.1 36.6 - - + -
29F LEU* 3.7 29.8 - - + +
32F ASP* 3.2 29.4 - - - +
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Residues in contact with ILE 14 (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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10F ILE* 3.0 17.7 + - + +
11F ARG* 2.7 28.3 - - - +
13F ILE* 1.3 77.9 - - - +
15F THR* 1.3 63.1 + - - +
17F ASN 3.1 7.8 - - - +
18F GLU* 3.0 20.4 - - - +
19F ILE* 4.5 11.7 - - + +
25F LEU* 6.3 1.3 - - + -
50F LEU* 3.6 22.9 - - + -
62F TYR* 2.8 63.4 - - + +
63F SER* 3.2 12.6 - - - +
64F LEU* 4.3 15.3 - - + +
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Residues in contact with THR 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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56B ASN* 3.2 37.9 + - - +
11F ARG 2.9 13.1 + - - -
12F GLU* 3.0 9.6 + - - -
14F ILE* 1.3 83.0 - - - +
16F SER* 1.3 67.9 + - - +
18F GLU* 3.1 14.0 - - - +
64F LEU* 4.6 17.1 - - + +
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Residues in contact with SER 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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56B ASN* 3.5 30.3 + - - +
57B ASN* 4.7 15.4 - - - +
12F GLU* 2.9 25.6 + - - +
13F ILE* 4.2 3.1 - - - -
15F THR* 1.3 80.7 - - - +
17F ASN* 1.3 60.7 + - - +
18F GLU* 4.0 4.9 + - - +
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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
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13F ILE* 2.6 37.3 + - + +
14F ILE* 3.1 9.0 - - - +
16F SER* 1.3 75.2 - - - +
18F GLU* 1.3 66.7 - - - +
19F ILE* 3.2 9.0 + - + +
28F MET* 5.1 10.5 - - - -
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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