Contacts of the helix formed by residues 7 - 17 (chain F) in PDB entry 4OA5
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 7 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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6F LEU* 1.3 77.0 - - - +
8F LYS* 1.3 65.5 + - - +
9F GLN* 3.5 10.0 + - - +
10F ASP* 3.1 32.6 + - - +
11F GLU* 3.1 23.0 + - - +
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Residues in contact with LYS 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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171A PHE* 4.0 25.4 - - + +
172A ASP* 5.5 4.9 - - - +
7F SER* 1.3 71.5 - - - +
9F GLN* 1.3 62.6 + - - +
11F GLU* 3.3 11.9 + - - +
12F TYR* 3.0 24.1 + - - +
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Residues in contact with GLN 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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165A PHE* 3.4 31.1 - - + -
171A PHE* 3.6 33.9 - - + -
206A PRO* 3.7 29.5 + - - +
207A THR 5.1 0.7 - - - +
7F SER* 3.2 10.0 + - - +
8F LYS* 1.3 78.9 - - - +
10F ASP* 1.3 69.7 + - - +
12F TYR* 3.2 3.6 + - - +
13F LEU* 3.0 36.2 + - + +
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Residues in contact with ASP 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 LEU* 4.4 10.8 - - + -
7F SER* 3.1 29.4 + - - +
9F GLN* 1.3 90.5 + - - +
11F GLU* 1.3 57.4 + - - +
13F LEU* 3.5 9.0 + - - +
14F ASN* 2.8 45.7 + - - +
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Residues in contact with GLU 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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58B HIS* 3.9 17.9 + - + +
79B PRO* 3.2 34.7 - - - +
80B SER* 3.7 12.8 + - - -
81B LYS* 3.8 16.9 + - + +
6F LEU* 4.9 4.4 - - + +
7F SER 3.1 16.7 + - - +
8F LYS* 3.6 9.7 - - - +
9F GLN 3.2 0.2 - - - -
10F ASP* 1.3 78.2 - - - +
12F TYR* 1.3 63.2 + - - +
14F ASN* 3.4 7.0 + - - +
15F LYS* 3.1 22.8 + - + +
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Residues in contact with TYR 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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170A VAL* 3.6 29.9 - - + +
171A PHE* 3.5 36.8 - + + +
188A ARG* 3.6 18.4 + - - -
191A ASN* 3.0 42.2 + - - +
204A ILE* 4.4 11.9 - - + -
314A IOD 4.2 13.5 - - + -
8F LYS 3.0 13.9 + - - +
9F GLN 3.5 7.0 - - - +
11F GLU* 1.3 76.5 - - - +
13F LEU* 1.3 72.0 + - + +
15F LYS* 3.2 7.9 + - - +
16F LEU* 3.0 47.2 + - + +
17F PHE* 4.5 1.3 - + - -
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Residues in contact with LEU 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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165A PHE* 4.0 17.9 - - + -
204A ILE* 4.0 33.4 - - + +
206A PRO* 5.0 6.1 - - + -
9F GLN* 3.0 41.4 + - + +
10F ASP* 4.0 9.6 - - - +
12F TYR* 1.3 81.2 - - + +
14F ASN* 1.3 59.5 + - - +
16F LEU 4.5 0.4 - - - +
17F PHE* 2.9 52.4 + - + -
43F VAL* 3.6 31.2 - - + +
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Residues in contact with ASN 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 ASP* 2.8 42.9 + - - +
11F GLU* 3.8 6.5 - - - +
13F LEU* 1.3 72.9 - - - +
15F LYS* 1.3 59.6 + - - +
18F ALA* 3.4 15.5 - - - +
42F THR* 3.0 26.3 + - - -
43F VAL* 3.7 16.7 + - - +
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Residues in contact with LYS 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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197A LYS* 5.7 0.9 + - - -
11F GLU* 3.1 12.9 + - + +
12F TYR* 3.2 10.0 + - - +
14F ASN* 1.3 79.6 - - - +
16F LEU* 1.3 74.6 + - + +
18F ALA 5.2 0.2 + - - -
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Residues in contact with LEU 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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188A ARG 5.6 0.4 - - - +
191A ASN* 4.3 15.0 - - + +
192A ASP* 4.5 13.0 - - + +
195A ALA* 3.3 35.7 - - + +
197A LYS* 4.0 8.3 + - - -
314A IOD 4.3 18.2 - - + -
12F TYR* 3.0 48.6 + - + +
15F LYS* 1.3 96.7 - - + +
17F PHE* 1.3 82.1 + - + +
18F ALA 3.8 1.8 - - - -
46F GLN* 4.7 0.3 + - - -
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Residues in contact with PHE 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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191A ASN* 3.5 21.8 - - + -
194A LEU 3.9 0.9 - - - -
195A ALA* 3.7 24.2 - - - -
202A SER* 3.7 39.6 - - - +
203A THR* 4.4 9.7 + - + +
204A ILE* 3.5 24.0 - - + +
212A MET* 3.6 17.9 - - + -
12F TYR* 4.5 3.8 - + - -
13F LEU* 2.9 33.4 + - + +
16F LEU* 1.3 101.9 - - + +
18F ALA* 1.3 58.5 + - - +
43F VAL* 3.8 15.7 - - + +
46F GLN* 3.4 26.8 - - - +
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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