Contacts of the helix formed by residues 300 - 309 (chain M) 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 M).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264M THR* 5.4 1.0 - - - +
265M PRO 5.0 1.8 - - - +
266M LEU* 3.6 30.2 - - + +
267M LEU* 3.0 28.4 + - - +
268M LYS* 4.5 1.7 + - - +
299M SER* 1.3 73.2 - - - +
301M GLU* 1.3 62.5 + - - +
303M VAL* 3.3 10.6 + - - +
304M ALA* 3.1 21.1 + - - +
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Residues in contact with GLU 301 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364D MSE 5.8 0.7 - - - +
365D LYS* 3.1 45.3 + - + +
382D LYS* 5.7 1.6 - - - +
299M SER* 3.1 10.4 + - - +
300M ASP* 1.3 76.3 - - - +
302M ASP* 1.3 68.0 + - - +
304M ALA* 3.3 8.1 + - + +
305M LEU* 3.2 21.0 + - - +
308M ARG* 5.0 5.0 + - - +
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Residues in contact with ASP 302 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362D VAL* 5.6 0.2 - - - +
363D VAL 3.8 14.3 + - - +
364D MSE 5.5 0.3 - - - -
382D LYS* 2.8 38.9 + - - -
287M TYR* 4.5 4.9 - - + +
295M VAL* 6.3 0.9 - - + -
296M ARG 3.8 7.8 - - - +
297M LEU* 3.6 23.1 - - + +
298M LEU* 3.0 23.9 + - - +
299M SER* 3.0 15.0 + - - +
301M GLU* 1.3 76.6 - - - +
303M VAL* 1.3 66.6 + - - +
305M LEU* 3.2 11.3 + - - +
306M MSE 3.1 18.0 + - - +
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Residues in contact with VAL 303 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264M THR* 4.4 2.0 - - + -
265M PRO* 3.2 40.8 - - + +
267M LEU* 4.1 33.7 - - + +
270M LEU* 4.1 9.6 - - + -
297M LEU* 4.0 14.6 - - + -
299M SER 3.2 11.5 + - - +
300M ASP* 3.4 8.7 - - - +
301M GLU 3.3 0.2 - - - -
302M ASP* 1.3 78.4 - - - +
304M ALA* 1.3 62.3 + - - +
306M MSE 3.3 19.7 + - + +
307M VAL* 3.1 20.1 + - - +
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Residues in contact with ALA 304 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264M THR* 3.9 21.7 - - + +
300M ASP 3.1 13.1 + - - +
301M GLU* 3.6 10.1 - - - +
302M ASP 3.2 0.4 - - - -
303M VAL* 1.3 76.4 - - - +
305M LEU* 1.3 57.6 + - - +
307M VAL* 3.2 2.9 + - - +
308M ARG* 2.9 57.5 + - - +
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Residues in contact with LEU 305 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D THR* 4.9 10.8 - - + -
363D VAL* 3.7 29.4 - - + +
364D MSE 6.0 0.9 - - - -
365D LYS* 6.1 6.5 - - + -
287M TYR* 3.6 20.6 - - - +
301M GLU 3.2 11.9 + - - +
302M ASP* 3.2 14.4 + - - +
304M ALA* 1.3 76.2 - - - +
306M MSE 1.3 61.5 + - - +
308M ARG* 3.2 24.2 + - + +
309M GLN* 2.9 45.5 + - + +
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Residues in contact with MSE 306 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270M LEU* 4.2 9.6 - - + -
287M TYR* 3.6 51.2 - - + -
297M LEU* 4.1 13.9 - - + -
302M ASP 3.1 11.0 + - - +
303M VAL* 3.3 36.1 + - + +
305M LEU* 1.3 76.4 - - - +
307M VAL* 1.3 65.9 + - + +
309M GLN* 3.3 3.2 + - - +
310M ALA* 3.3 20.8 + - - +
322M TRP* 3.5 48.7 - - + -
323M LYS 4.3 5.8 - - - +
324M LEU* 4.1 8.5 - - - -
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Residues in contact with VAL 307 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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261M LEU 6.2 0.2 - - - +
262M SER 5.0 7.0 - - - +
263M SER 4.4 5.4 - - - +
264M THR* 4.0 21.3 - - + +
265M PRO* 4.3 14.8 - - + -
303M VAL 3.1 14.3 + - - +
304M ALA* 3.2 6.7 + - - +
306M MSE 1.3 83.5 - - + +
308M ARG* 1.3 64.4 + - + +
309M GLN 3.3 0.3 + - - -
310M ALA* 3.3 11.4 + - - +
311M ARG* 3.6 10.2 + - - +
321M PRO* 5.8 1.6 - - + +
322M TRP* 3.6 42.7 - - + +
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Residues in contact with ARG 308 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365D LYS* 4.8 18.2 - - - +
301M GLU* 5.0 5.3 + - - +
304M ALA* 2.9 36.2 + - - +
305M LEU* 3.6 42.4 - - + +
307M VAL* 1.3 77.9 - - + +
309M GLN* 1.3 62.2 + - + +
311M ARG* 3.3 59.2 + - - +
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Residues in contact with GLN 309 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287M TYR* 4.6 9.0 - - + -
289M ASP* 4.1 12.4 - - - +
290M ALA* 4.1 25.7 + - - +
305M LEU* 2.9 37.3 + - + +
306M MSE 3.9 6.5 - - - +
307M VAL 3.2 0.4 - - - -
308M ARG* 1.3 77.8 - - + +
310M ALA* 1.3 60.0 + - - +
311M ARG 4.7 2.6 - - - -
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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