Contacts of the helix formed by residues 8 - 17 (chain B) 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 LYS 8 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B SER* 1.3 73.4 - - - +
9B GLN* 1.3 62.5 + - - +
11B GLU* 3.3 6.5 + - - +
12B TYR* 3.0 24.1 + - - +
311B IOD 4.0 14.2 - - + +
171C PHE* 4.0 21.5 - - + +
172C ASP* 5.4 7.0 - - - +
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Residues in contact with GLN 9 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B SER* 3.2 9.1 + - - +
8B LYS* 1.3 78.2 - - - +
10B ASP* 1.3 69.4 + - - +
12B TYR* 3.2 3.5 + - - +
13B LEU* 3.0 41.7 + - + +
311B IOD 3.7 8.3 - - + +
165C PHE* 3.6 25.8 - - + -
171C PHE* 3.6 35.6 - - + -
206C PRO* 3.9 22.0 - - - +
207C THR 5.1 1.2 + - - -
208C SER* 5.7 0.6 + - - +
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Residues in contact with ASP 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B SER* 3.2 27.2 + - - +
9B GLN* 1.3 88.4 - - - +
11B GLU* 1.3 58.1 + - - +
13B LEU* 3.4 9.4 + - - +
14B ASN* 2.8 47.0 + - - +
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Residues in contact with GLU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B SER 3.1 16.5 + - - +
8B LYS* 3.6 7.9 - - - +
10B ASP* 1.3 76.1 - - - +
12B TYR* 1.3 61.6 + - - +
14B ASN* 3.4 6.0 + - - +
15B LYS* 3.1 22.9 + - - +
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Residues in contact with TYR 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B LYS 3.0 13.5 + - - +
9B GLN 3.5 7.0 - - - +
11B GLU* 1.3 76.9 - - - +
13B LEU* 1.3 72.3 + - + +
15B LYS* 3.2 7.8 + - + +
16B LEU* 3.0 48.0 + - + +
17B PHE* 4.4 8.7 - + - -
170C VAL* 3.5 34.6 - - + +
171C PHE* 3.5 39.5 - + + +
188C ARG* 3.6 18.3 + - - -
191C ASN* 3.0 39.2 + - - +
204C ILE* 4.4 5.2 - - + -
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Residues in contact with LEU 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLN* 3.0 40.5 + - + +
10B ASP* 4.0 9.2 - - - +
12B TYR* 1.3 84.4 - - + +
14B ASN* 1.3 59.3 + - - +
16B LEU 4.5 0.4 - - - +
17B PHE* 2.9 51.9 + - + -
43B VAL* 3.5 32.3 - - + +
165C PHE* 4.1 25.8 - - + -
204C ILE* 4.1 21.1 - - + +
206C PRO* 5.0 6.5 - - + -
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Residues in contact with ASN 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B ASP* 2.8 40.0 + - - +
11B GLU* 3.8 6.1 - - - +
12B TYR 3.2 0.2 - - - -
13B LEU* 1.3 77.4 - - - +
15B LYS* 1.3 59.9 + - - +
18B ALA* 3.4 15.1 - - - +
41B GLY* 5.9 0.2 - - - -
42B THR* 2.9 26.5 + - - -
43B VAL* 3.7 15.9 + - - +
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Residues in contact with LYS 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B GLU 3.1 14.0 + - - +
12B TYR* 3.2 10.1 + - + +
14B ASN* 1.3 80.0 - - - +
16B LEU* 1.3 70.3 + - + +
18B ALA* 5.2 1.1 + - - +
197C LYS* 5.6 1.2 + - - -
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Residues in contact with LEU 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TYR* 3.0 50.7 + - + +
15B LYS* 1.3 90.4 - - + +
17B PHE* 1.3 86.7 + - + +
18B ALA 3.7 1.8 - - - -
46B GLN* 4.8 0.3 + - - -
188C ARG 5.6 0.4 - - - +
191C ASN 4.3 13.5 - - - +
192C ASP* 4.1 18.4 - - + +
195C ALA* 3.3 32.6 - - + +
197C LYS* 3.9 11.2 + - - -
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Residues in contact with PHE 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B TYR* 4.4 4.0 - + - -
13B LEU* 2.9 33.4 + - + +
16B LEU* 1.3 103.0 - - + +
18B ALA* 1.3 57.7 + - - +
43B VAL* 3.8 15.0 - - + +
46B GLN* 3.4 27.7 - - - +
191C ASN* 3.5 20.6 - - + -
194C LEU 4.0 0.7 - - - -
195C ALA* 3.7 24.9 - - - -
202C SER* 3.7 38.3 - - - +
203C THR* 4.4 11.7 + - - +
204C ILE* 3.5 23.3 - - + +
212C MET* 3.7 17.0 - - + -
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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