Contacts of the helix formed by residues 300 - 309 (chain K) in PDB entry 1OEY
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 ASP 300 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264K THR* 5.1 1.9 - - - +
265K PRO 4.4 1.6 - - - +
266K LEU* 3.6 22.3 - - - +
267K LEU* 2.8 34.6 + - - +
268K LYS 5.6 0.3 + - - -
299K SER* 1.3 75.1 - - - +
301K GLU* 1.3 61.5 + - - +
303K VAL* 3.3 8.9 + - - +
304K ALA* 3.0 21.0 + - - +
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Residues in contact with GLU 301 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B LYS* 4.1 26.7 - - - +
382B LYS* 5.4 3.6 + - - +
299K SER* 3.2 12.2 + - - +
300K ASP* 1.3 78.0 - - - +
302K ASP* 1.3 65.5 + - - +
304K ALA* 3.2 9.2 + - - +
305K LEU* 3.0 23.3 + - - +
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Residues in contact with ASP 302 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B VAL* 5.7 0.2 - - - +
363B VAL 3.9 13.3 + - - +
364B MSE 5.5 0.7 - - - -
382B LYS* 2.7 38.2 + - - -
287K TYR* 4.3 6.0 - - + -
295K VAL* 6.3 1.1 - - + -
296K ARG 3.9 7.5 - - - +
297K LEU* 3.5 24.1 - - + +
298K LEU* 2.9 27.3 + - - +
299K SER* 3.2 12.6 + - - +
301K GLU* 1.3 78.0 - - - +
303K VAL* 1.3 64.0 + - - +
305K LEU* 3.3 9.9 + - - +
306K MSE 3.1 18.2 + - - +
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Residues in contact with VAL 303 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264K THR* 4.0 6.7 - - + -
265K PRO* 3.3 37.2 - - + +
267K LEU* 4.1 31.0 - - + -
270K LEU* 4.3 9.4 - - + -
297K LEU* 3.8 15.5 - - + -
299K SER 3.6 12.6 - - - +
300K ASP* 3.3 8.7 + - - +
302K ASP* 1.3 77.5 - - - +
304K ALA* 1.3 60.5 + - - +
306K MSE 3.2 20.7 + - + +
307K VAL* 3.1 22.0 + - - +
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Residues in contact with ALA 304 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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251J THR* 5.9 5.2 - - + -
264K THR* 3.8 20.4 - - + +
300K ASP 3.0 13.2 + - - +
301K GLU* 3.2 12.5 + - - +
303K VAL* 1.3 74.3 - - - +
305K LEU* 1.3 57.3 + - - +
307K VAL* 3.3 3.4 + - - +
308K ARG* 2.9 42.4 + - + +
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Residues in contact with LEU 305 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353B THR* 4.5 15.3 - - + -
363B VAL* 3.9 31.2 - - + +
364B MSE 5.1 3.1 - - - +
365B LYS* 5.3 16.4 - - + +
287K TYR* 3.8 17.5 - - - +
301K GLU 3.0 12.4 + - - +
302K ASP* 3.3 12.1 + - - +
304K ALA* 1.3 76.8 - - - +
306K MSE 1.3 57.3 + - - +
308K ARG* 3.9 10.2 - - + +
309K GLN* 3.0 37.5 + - + +
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Residues in contact with MSE 306 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270K LEU* 4.6 1.6 - - + -
287K TYR* 3.6 51.3 - - + -
297K LEU* 4.1 8.7 - - + -
302K ASP 3.1 12.1 + - - +
303K VAL* 3.2 41.3 + - + +
305K LEU* 1.3 74.7 - - - +
307K VAL* 1.3 66.8 + - + +
309K GLN* 3.3 4.9 + - - +
310K ALA* 3.2 21.1 + - - +
322K TRP* 3.5 50.7 - - + -
323K LYS 4.3 4.9 - - - +
324K LEU* 4.0 19.7 - - + -
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Residues in contact with VAL 307 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249J ILE* 4.0 24.1 - - + +
262K SER 5.4 0.9 - - - +
263K SER 4.5 5.8 - - - +
264K THR* 3.9 20.9 - - + +
265K PRO* 4.2 15.3 - - + -
303K VAL 3.1 13.4 + - - +
304K ALA 3.3 6.9 + - - +
306K MSE 1.3 81.7 - - + +
308K ARG* 1.3 65.6 + - - +
310K ALA* 3.1 15.9 + - - +
311K ARG* 3.5 7.4 + - - +
321K PRO* 6.0 0.3 - - - +
322K TRP* 3.7 39.7 - - + +
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Residues in contact with ARG 308 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246J GLU* 3.9 22.8 + - - +
249J ILE* 4.5 13.2 - - + +
304K ALA* 2.9 27.0 + - + +
305K LEU* 3.9 10.5 - - + +
307K VAL* 1.3 76.6 - - + +
309K GLN* 1.3 61.4 + - - +
311K ARG* 3.1 53.9 + - - +
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Residues in contact with GLN 309 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287K TYR* 3.3 35.5 + - + -
289K ASP* 3.8 8.3 - - - +
290K ALA* 3.0 38.8 + - + +
305K LEU* 3.0 24.6 + - + +
306K MSE 3.7 5.2 - - - +
307K VAL 3.2 0.4 - - - -
308K ARG* 1.3 75.4 - - - +
310K ALA* 1.3 59.0 + - - +
311K ARG 3.3 1.1 + - - -
312K GLY 4.8 2.3 + - - -
313K LEU* 5.0 4.0 - - - +
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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