Contacts of the helix formed by residues 3 - 12 (chain F) in PDB entry 5L08
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 PHE 3 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2F ASP* 1.3 82.9 - - - +
4F SER* 1.3 54.2 + - - +
5F ARG* 2.9 1.6 - - - +
6F ASN* 2.6 56.0 + - + +
7F LEU* 3.1 25.6 + - + -
10F ILE* 5.1 1.6 - - + -
56F GLU* 3.1 16.9 + - + +
59F LEU* 3.5 31.4 - - + -
78F TYR 4.1 14.1 - - - -
79F LEU* 3.9 16.8 - - + -
80F ASN* 6.2 1.3 - - - -
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Residues in contact with SER 4 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126E GLU* 3.0 40.0 - - - +
2F ASP 3.0 0.6 + - - -
3F PHE* 1.3 76.6 - - - +
5F ARG* 1.3 52.9 + - - +
7F LEU* 2.8 37.9 + - - +
8F TYR 2.9 13.0 + - - -
42F LEU* 5.7 1.3 - - - -
49F GLN* 5.8 0.3 + - - -
56F GLU* 2.8 31.5 + - - +
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Residues in contact with ARG 5 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123E LEU* 4.1 9.6 - - + -
126E GLU* 3.3 17.4 + - + +
127E GLU* 3.7 25.2 + - - +
162E ARG* 4.6 22.4 - - - +
163E VAL* 6.4 0.2 - - - +
166E GLN* 3.6 39.0 - - + +
2F ASP* 2.8 63.1 + - - +
4F SER* 1.3 78.2 - - - +
6F ASN* 1.3 70.9 + - - +
8F TYR* 3.3 7.6 - - - +
9F ASP* 3.2 22.2 + - - -
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Residues in contact with ASN 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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166E GLN* 5.3 0.9 + - - -
3F PHE* 2.6 54.4 + - + +
5F ARG* 1.3 86.5 + - - +
7F LEU* 1.3 57.0 + - - +
9F ASP* 3.2 16.5 + - - +
10F ILE* 2.8 35.0 + - + +
78F TYR* 5.7 5.5 - - + +
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Residues in contact with LEU 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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126E GLU* 5.3 0.4 - - - +
3F PHE* 3.1 29.2 + - + +
4F SER* 2.8 29.5 + - - +
6F ASN* 1.3 74.2 - - - +
8F TYR* 1.3 52.2 + - - +
10F ILE* 3.2 13.2 + - + +
11F GLY* 2.8 28.4 + - - -
42F LEU* 5.3 1.3 - - + -
45F PHE* 3.4 26.0 - - + -
54F LEU* 4.4 15.7 - - + -
55F GLU 5.6 0.4 - - - -
56F GLU* 5.2 3.4 - - + +
59F LEU* 3.9 23.8 - - + -
62F LEU* 3.6 27.1 - - + -
79F LEU* 4.2 5.4 - - + -
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Residues in contact with TYR 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34C LYS* 5.0 2.9 + - - -
119E SER* 3.2 34.5 + - - -
123E LEU* 5.1 5.2 - - + -
126E GLU* 3.9 15.2 + - - +
166E GLN* 2.8 48.4 + - + -
167E ILE* 4.5 1.3 - - + +
4F SER 2.9 10.2 + - - +
5F ARG 3.3 8.3 - - - +
7F LEU* 1.3 76.4 - - - +
9F ASP* 1.3 77.2 + - - +
11F GLY* 3.0 18.2 + - - -
12F GLU* 3.2 46.6 + - + +
40F ASP* 6.2 1.3 - - - -
42F LEU* 3.6 34.7 - - + +
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Residues in contact with ASP 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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165E ALA 5.4 0.2 - - - +
166E GLN* 3.1 32.1 + - - +
5F ARG 3.2 10.3 + - - +
6F ASN* 3.2 20.7 + - - +
8F TYR* 1.3 92.3 - - - +
10F ILE* 1.3 54.8 + - + +
12F GLU* 3.8 7.7 + - - +
13F GLN* 2.6 36.2 + - - +
78F TYR* 5.1 10.0 - - + -
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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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3F PHE* 5.1 2.0 - - + -
6F ASN* 2.8 23.4 + - + +
7F LEU* 3.3 20.6 - - + +
8F TYR 3.2 0.2 - - - -
9F ASP* 1.3 71.4 - - - +
11F GLY* 1.3 65.1 + - - +
13F GLN* 2.9 28.9 + - - +
14F LEU 4.2 0.2 + - - -
45F PHE* 5.5 2.5 - - + -
62F LEU* 5.0 7.4 - - + -
66F LEU* 5.0 8.5 - - + -
74F LEU* 3.7 34.7 - - + +
78F TYR* 3.4 37.9 - - + +
79F LEU* 3.7 30.7 - - + -
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Residues in contact with GLY 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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7F LEU 2.8 14.3 + - - -
8F TYR* 3.0 6.8 + - - -
10F ILE* 1.3 77.6 - - - +
12F GLU* 1.3 56.3 + - - +
13F GLN 3.0 1.3 - - - -
14F LEU* 3.0 29.0 + - - +
41F ALA* 3.4 31.1 + - - +
42F LEU 5.3 0.2 - - - -
45F PHE* 4.8 1.8 - - - -
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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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31C PRO* 3.3 22.9 - - + +
33C ARG 3.7 15.9 - - - +
34C LYS* 2.9 40.9 + - - +
119E SER* 5.0 0.3 + - - -
8F TYR* 3.2 52.0 + - + +
9F ASP* 3.9 7.2 - - - +
10F ILE 3.1 1.2 + - - -
11F GLY* 1.3 75.5 - - - +
13F GLN* 1.3 73.1 + - - +
14F LEU 3.3 2.9 + - - +
40F ASP* 5.9 4.5 - - - +
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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