Contacts of the helix formed by residues 8 - 17 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B PHE* 4.0 23.3 - - + -
172B ASP* 5.5 6.3 - - - +
318B EDO 3.4 11.5 + - - +
7C SER* 1.3 72.9 - - - +
9C GLN* 1.3 63.3 + - - +
11C GLU* 3.3 9.8 + - - +
12C TYR* 3.0 21.0 + - - +
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Residues in contact with GLN 9 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165B PHE* 3.5 34.7 - - + -
171B PHE* 3.5 38.8 - - + -
206B PRO* 3.9 20.2 + - - +
207B THR 5.2 0.5 + - - +
7C SER* 3.2 11.1 + - - +
8C LYS* 1.3 78.1 - - - +
10C ASP* 1.3 64.4 + - - +
12C TYR* 3.2 3.8 + - - +
13C LEU* 3.0 42.5 + - + +
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Residues in contact with ASP 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7C SER* 3.2 27.6 + - - +
9C GLN* 1.3 90.2 + - - +
11C GLU* 1.3 58.1 + - - +
13C LEU* 3.8 8.6 - - - +
14C ASN* 2.8 46.2 + - - +
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Residues in contact with GLU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B EDO 3.7 26.3 + - - +
7C SER 3.1 16.6 + - - +
8C LYS* 3.6 8.8 - - - +
10C ASP* 1.3 77.8 - - - +
12C TYR* 1.3 62.3 + - - +
14C ASN* 3.4 6.6 + - - +
15C LYS* 3.1 22.2 + - - +
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Residues in contact with TYR 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B VAL* 3.6 19.5 - - + +
171B PHE* 3.6 28.9 - + + -
188B ARG* 3.5 27.0 + - - -
191B ASN* 3.0 42.3 + - - +
204B ILE* 4.5 4.3 - - + -
318B EDO 3.5 32.5 + - - +
8C LYS 3.0 9.7 + - - +
9C GLN 3.5 6.3 - - - +
11C GLU* 1.3 76.5 - - - +
13C LEU* 1.3 71.0 + - + +
15C LYS* 3.1 5.2 + - - +
16C LEU* 3.0 47.9 + - + +
17C PHE* 4.4 8.7 - + - -
302C IOD 4.4 4.7 - - + -
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Residues in contact with LEU 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B PHE* 4.1 16.8 - - + -
204B ILE* 4.1 33.0 - - + +
206B PRO* 5.1 5.6 - - + -
9C GLN* 3.0 41.4 + - + +
10C ASP* 4.0 9.6 - - - +
12C TYR* 1.3 81.6 - - + +
14C ASN* 1.3 59.0 + - - +
16C LEU 4.5 0.2 - - - +
17C PHE* 2.9 51.2 + - + -
43C VAL* 3.6 32.6 - - + +
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Residues in contact with ASN 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ASP* 2.8 40.2 + - - +
11C GLU* 3.8 5.6 - - - +
13C LEU* 1.3 76.4 - - - +
15C LYS* 1.3 60.0 + - - +
18C ALA* 3.4 15.5 - - - +
41C GLY* 5.9 0.2 - - - -
42C THR* 3.0 26.2 + - - -
43C VAL* 3.7 16.8 + - - +
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Residues in contact with LYS 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192B ASP* 5.3 4.9 + - - -
197B LYS* 5.6 1.4 + - - -
318B EDO 3.8 14.6 - - - +
11C GLU 3.1 13.8 + - - +
12C TYR 3.1 7.6 + - - +
14C ASN* 1.3 80.2 - - - +
16C LEU* 1.3 69.1 + - + +
18C ALA* 5.3 0.9 + - - +
302C IOD 3.3 36.4 - - + +
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Residues in contact with LEU 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188B ARG 5.7 0.2 - - - +
191B ASN* 4.4 10.8 - - + +
192B ASP* 4.6 10.8 - - + +
195B ALA* 3.3 35.9 - - + +
197B LYS* 3.8 9.0 + - - -
12C TYR* 3.0 50.1 + - + +
15C LYS* 1.3 106.9 - - + +
17C PHE* 1.3 85.2 + - + +
18C ALA 3.8 1.8 - - - -
46C GLN* 4.7 0.3 + - - -
302C IOD 3.9 18.8 - - + -
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Residues in contact with PHE 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B ASN* 3.4 22.0 - - + -
194B LEU 3.9 0.9 - - - -
195B ALA* 3.6 24.5 - - - -
202B SER* 3.7 39.2 - - - +
203B THR* 4.5 9.6 + - + +
204B ILE* 3.6 22.4 - - + +
212B MET* 3.7 17.3 - - + -
12C TYR* 4.4 4.5 - + - -
13C LEU* 2.9 33.3 + - + +
16C LEU* 1.3 102.5 - - + +
18C ALA* 1.3 57.3 + - - +
43C VAL* 3.8 15.4 - - + +
46C GLN* 3.4 27.1 - - - +
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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