Contacts of the helix formed by residues 281 - 292 (chain I) in PDB entry 6O81
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 CYS 281 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30I VAL 5.9 3.4 - - - +
275I LEU 6.1 0.2 - - - -
277I PRO 4.3 4.8 + - - +
278I TYR* 3.7 24.4 + - + +
279I ASP 3.5 2.0 - - - -
280I ALA* 1.3 77.6 - - - +
282I TRP* 1.3 63.7 + - - +
283I ASN 3.4 0.2 - - - -
284I ALA* 3.6 17.5 + - - +
285I CYS* 4.3 4.5 + - - +
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Residues in contact with TRP 282 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278I TYR 4.7 2.6 + - - -
279I ASP 4.8 4.9 + - - +
280I ALA 3.3 0.8 - - - -
281I CYS* 1.3 80.8 - - - +
283I ASN* 1.3 57.7 + - - +
284I ALA 3.3 1.8 + - - -
285I CYS* 4.1 4.0 + - - +
286I ARG* 4.0 15.9 + - - +
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Residues in contact with ASN 283 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279I ASP 5.5 0.4 + - - +
280I ALA* 3.7 14.8 + - + +
281I CYS 3.4 0.4 - - - -
282I TRP* 1.3 75.0 - - - +
284I ALA* 1.3 58.6 + - - +
285I CYS 3.6 0.4 - - - -
286I ARG* 4.6 6.5 - - - -
287I GLY* 3.1 24.0 + - - -
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Residues in contact with ALA 284 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30I VAL 5.7 4.7 - - - +
109I ILE* 5.4 16.4 - - + +
274I ASN* 5.4 7.2 - - + -
280I ALA 3.6 10.5 + - - +
281I CYS* 3.6 15.0 + - - +
282I TRP 3.3 1.0 - - - -
283I ASN* 1.3 76.7 - - - +
285I CYS* 1.3 61.1 + - - +
287I GLY* 3.4 0.7 + - - -
288I ASP* 2.9 31.6 + - - +
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Residues in contact with CYS 285 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31I GLY* 6.0 1.3 - - - -
32I ASN* 4.6 24.1 - - + +
281I CYS 4.3 3.6 + - - +
282I TRP* 4.1 6.1 + - - +
284I ALA* 1.3 76.2 - - - +
286I ARG* 1.3 61.1 + - - +
288I ASP* 3.7 4.8 - - - -
289I ARG* 2.9 32.4 + - - +
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Residues in contact with ARG 286 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282I TRP 4.0 15.0 + - - +
283I ASN* 4.5 6.1 - - - +
284I ALA 3.4 0.4 - - - -
285I CYS* 1.3 79.6 - - - +
287I GLY* 1.3 60.0 + - - +
289I ARG* 4.0 8.7 + - - +
290I TRP* 4.2 12.5 + - - +
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Residues in contact with GLY 287 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I ILE* 5.3 10.3 - - - +
283I ASN 3.1 19.4 + - - -
284I ALA* 3.7 1.8 - - - -
285I CYS 3.2 0.2 - - - -
286I ARG* 1.3 78.0 - - - +
288I ASP* 1.3 57.2 + - - +
290I TRP* 4.3 1.5 - - - +
291I GLU* 3.3 29.3 + - - +
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Residues in contact with ASP 288 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32I ASN* 5.5 7.6 - - + -
38I TYR* 3.7 30.4 + - + +
109I ILE* 5.7 8.1 - - + -
284I ALA 2.9 18.9 + - - +
285I CYS* 3.3 5.6 + - - +
287I GLY* 1.3 73.8 - - - +
289I ARG* 1.3 63.1 + - - +
290I TRP 3.3 2.0 - - - -
291I GLU* 4.2 0.7 - - - -
292I ASP* 3.3 27.7 + - - +
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Residues in contact with ARG 289 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285I CYS 2.9 17.7 + - - +
286I ARG* 4.0 6.9 + - - +
287I GLY 3.4 0.4 - - - -
288I ASP* 1.3 77.7 - - - +
290I TRP* 1.3 58.9 + - + +
292I ASP 5.0 0.2 - - - -
293I LEU* 5.2 7.7 - - - +
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Residues in contact with TRP 290 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286I ARG 4.2 11.5 + - - +
287I GLY* 4.0 3.1 + - - +
288I ASP 3.3 0.2 - - - -
289I ARG* 1.3 80.5 - - + +
291I GLU* 1.3 58.4 + - + +
292I ASP 3.8 0.2 - - - -
293I LEU* 4.7 9.5 + - - +
294I SER 5.6 0.3 + - - -
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Residues in contact with GLU 291 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109I ILE* 6.3 1.8 - - + -
111I ASP* 4.6 20.8 - - + +
287I GLY 3.3 19.8 + - - +
288I ASP* 5.1 0.2 - - - -
290I TRP* 1.3 79.1 - - + +
292I ASP* 1.3 60.7 + - - +
293I LEU 3.2 3.6 + - - -
294I SER* 3.8 12.3 + - - -
295I ARG* 4.0 9.0 + - - +
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Residues in contact with ASP 292 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I TRP* 5.5 5.9 - - + -
38I TYR* 3.7 33.0 - - + +
288I ASP* 3.3 21.9 + - - +
291I GLU* 1.3 76.3 - - - +
293I LEU* 1.3 62.9 + - - +
294I SER 3.4 0.9 - - - -
295I ARG* 3.4 25.7 - - + +
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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