Contacts of the helix formed by residues 312 - 329 (chain I) in PDB entry 2ONM
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 GLU 312 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310I VAL 3.5 1.0 + - - -
311I GLN* 1.3 73.7 - - + +
313I ASP* 1.3 74.9 + - - +
314I ILE 3.2 1.0 + - - -
315I TYR* 3.3 20.2 + - - +
316I ASP* 4.7 3.8 + - - +
409I LYS* 3.9 23.0 - - + +
410I PHE 2.9 18.2 + - - +
411I LYS* 3.6 44.0 + - + +
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Residues in contact with ASP 313 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279I SER* 4.2 23.8 + - - -
311I GLN* 3.1 5.2 + - - +
312I GLU* 1.3 89.3 - - - +
314I ILE* 1.3 61.8 + - + +
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Residues in contact with ILE 314 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I ILE* 4.0 13.2 - - + +
278I MET 3.2 28.7 - - - +
279I SER* 3.6 29.8 - - - +
281I ALA* 5.3 2.2 - - + +
283I MET* 3.6 28.3 - - + -
310I VAL* 3.6 18.2 - - + -
311I GLN 3.0 14.5 + - - +
313I ASP* 1.3 81.3 - - + +
315I TYR* 1.3 59.7 + - - +
316I ASP 3.5 2.2 - - - -
317I GLU* 3.5 10.2 + - - +
318I PHE* 2.9 30.7 + - + +
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Residues in contact with TYR 315 (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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310I VAL* 4.0 17.7 - - + -
311I GLN 3.0 11.8 + - - +
312I GLU* 3.3 19.8 + - - +
314I ILE* 1.3 75.8 - - - +
316I ASP* 1.3 73.8 + - - +
318I PHE* 3.2 1.7 + - - +
319I VAL* 2.8 61.4 + - + +
368I LEU* 5.6 0.2 - - - +
387I GLY* 3.7 7.6 - - - -
388I ASP* 2.8 45.0 + - - -
407I ILE* 3.8 15.0 + - + +
408I LEU 4.1 5.4 - - - -
409I LYS* 3.5 46.7 - - + -
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Residues in contact with ASP 316 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
312I GLU 4.7 3.7 + - - +
313I ASP 5.6 0.2 + - - -
314I ILE 3.5 0.4 - - - -
315I TYR* 1.3 94.8 - - - +
317I GLU* 1.3 63.8 + - - +
319I VAL* 3.5 4.1 + - - +
320I GLU* 3.0 27.0 + - - +
409I LYS* 5.1 3.8 + - - -
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Residues in contact with GLU 317 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283I MET* 3.5 24.9 - - + +
314I ILE* 3.5 12.4 + - - +
315I TYR 3.3 0.4 - - - -
316I ASP* 1.3 77.8 - - - +
318I PHE* 1.3 62.8 + - - +
320I GLU* 3.3 10.3 + - + +
321I ARG* 3.1 58.5 + - + +
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Residues in contact with PHE 318 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277I ILE* 4.0 21.1 - - + -
283I MET* 4.1 17.7 - - + -
286I ALA* 4.0 5.4 - - + -
287I VAL* 3.7 35.2 - - + -
290I ALA* 3.6 25.4 - - + -
308I THR* 3.9 14.8 - - + -
310I VAL* 3.5 36.1 - - + -
314I ILE* 2.9 19.5 + - + +
315I TYR 3.5 2.9 - - - +
317I GLU* 1.3 77.7 - - - +
319I VAL* 1.3 61.9 + - + +
321I ARG* 3.2 3.8 + - - +
322I SER* 2.8 48.2 + - - -
405I MET* 5.6 1.1 - - + -
407I ILE* 4.3 11.0 - - + -
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Residues in contact with VAL 319 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315I TYR* 2.8 64.8 + - + +
316I ASP* 3.8 4.3 - - - +
318I PHE* 1.3 75.4 - - + +
320I GLU* 1.3 64.1 + - - +
322I SER* 3.3 4.5 + - - -
323I VAL* 2.9 31.2 + - + +
368I LEU* 3.3 33.9 - - + -
407I ILE* 3.9 19.5 - - + -
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Residues in contact with GLU 320 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316I ASP* 3.0 16.9 + - - +
317I GLU* 3.4 13.5 - - - +
319I VAL* 1.3 78.3 - - - +
321I ARG* 1.3 65.5 + - + +
323I VAL* 3.3 5.8 + - - +
324I ALA* 3.1 22.5 + - - +
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Residues in contact with ARG 321 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283I MET* 3.7 26.3 - - - +
284I ASP* 3.0 35.0 + - - +
287I VAL* 3.7 22.5 - - + +
317I GLU* 3.1 40.4 + - + +
318I PHE 3.7 5.8 - - - +
320I GLU* 1.3 77.4 - - + +
322I SER* 1.3 57.7 + - - +
324I ALA* 3.3 8.5 + - - +
325I ARG* 3.0 28.6 + - - +
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Residues in contact with SER 322 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287I VAL* 4.2 12.7 + - - +
290I ALA* 5.6 0.2 - - - +
291I HIS* 5.0 3.8 + - - -
318I PHE* 2.8 45.5 + - - -
319I VAL 3.6 4.5 - - - -
321I ARG* 1.3 75.9 - - - +
323I VAL* 1.3 60.1 + - - +
325I ARG* 3.3 5.6 + - - +
326I ALA* 2.9 29.5 + - - +
385I VAL* 4.7 2.9 - - - +
405I MET* 4.5 14.7 - - - +
407I ILE* 4.1 18.8 - - - -
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Residues in contact with VAL 323 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319I VAL* 2.9 24.4 + - + +
320I GLU* 3.7 5.6 - - - +
322I SER* 1.3 75.5 - - - +
324I ALA* 1.3 58.1 + - - +
326I ALA* 3.3 7.1 + - - +
327I LYS* 3.0 42.5 + - + +
368I LEU* 3.7 54.3 - - + +
369I CYS* 3.9 12.3 - - + -
385I VAL* 4.4 9.4 - - + -
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Residues in contact with ALA 324 (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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320I GLU 3.1 13.7 + - - +
321I ARG* 3.5 12.1 - - - +
323I VAL* 1.3 77.1 - - - +
325I ARG* 1.3 60.5 + - - +
327I LYS* 3.4 9.7 + - - +
328I SER* 3.1 24.0 + - - -
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Residues in contact with ARG 325 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287I VAL* 4.9 7.9 - - + +
288I GLU* 3.4 35.8 + - - +
291I HIS* 3.4 40.5 + - + +
321I ARG 3.0 15.8 + - - +
322I SER* 3.6 7.9 - - - +
323I VAL 3.3 0.2 - - - -
324I ALA* 1.3 75.7 - - - +
326I ALA* 1.3 63.1 + - - +
328I SER* 2.8 29.7 + - - -
329I ARG* 3.2 11.8 + - - +
340I GLU* 2.9 35.4 + - - -
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Residues in contact with ALA 326 (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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291I HIS* 4.1 10.5 - - - -
295I PHE* 4.3 8.1 - - + -
322I SER 2.9 16.6 + - - +
323I VAL 3.3 4.5 + - - +
325I ARG* 1.3 78.1 - - - +
327I LYS* 1.3 61.7 + - - +
329I ARG* 3.3 17.0 + - - +
369I CYS* 3.8 7.0 - - - -
383I PRO* 3.5 27.3 - - + +
385I VAL* 3.6 26.9 - - + -
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Residues in contact with LYS 327 (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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323I VAL* 3.0 30.8 + - + +
324I ALA* 3.7 8.3 - - - +
326I ALA* 1.3 76.9 - - - +
328I SER* 1.3 59.6 + - - +
329I ARG 3.6 4.2 + - - +
368I LEU 4.6 4.0 + - - -
369I CYS* 4.1 27.8 - - + -
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Residues in contact with SER 328 (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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324I ALA 3.1 13.4 + - - -
325I ARG* 2.8 34.0 + - - -
327I LYS* 1.3 75.3 - - - +
329I ARG* 1.3 62.5 + - - +
330I VAL* 3.1 12.5 + - - +
340I GLU* 3.4 6.9 - - - +
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Residues in contact with ARG 329 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291I HIS* 2.9 38.7 + - + -
292I PHE* 5.8 1.2 - - - +
295I PHE* 3.4 35.9 + - - +
296I PHE* 4.5 4.6 - - - +
297I ASN 5.0 2.0 - - - +
298I GLN* 5.1 1.4 + - - +
325I ARG* 3.2 12.6 + - - +
326I ALA 3.3 18.2 + - - +
327I LYS 4.4 3.6 - - - +
328I SER* 1.3 73.8 - - - +
330I VAL* 1.3 64.0 + - - +
331I VAL* 3.4 11.6 + - - +
340I GLU* 3.2 53.2 + - + +
341I GLN* 3.1 36.2 + - + +
383I PRO* 3.9 10.0 - - + +
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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