Contacts of the helix formed by residues 347 - 362 (chain C) in PDB entry 2ONL
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 347 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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345C ASP* 3.1 23.2 - - - +
346C LYS* 1.3 85.7 - - + +
348C ARG* 1.3 90.0 + - - +
349C TRP 2.9 4.3 - - - -
350C GLU* 3.1 24.1 + - - +
351C ASP* 3.2 10.7 + - - +
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Residues in contact with ARG 348 (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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260C TYR* 5.4 10.7 + - - -
341C VAL* 3.7 24.7 + - - +
342C LEU* 5.6 2.8 - - - +
344C GLU* 5.0 4.2 + - - +
345C ASP* 2.6 60.9 + - - +
347C GLU* 1.3 91.1 + - - +
349C TRP* 1.3 57.2 + - - +
351C ASP* 2.3 36.3 - - - +
352C VAL* 2.6 28.8 + - - +
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Residues in contact with TRP 349 (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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147C PHE* 3.4 45.1 + + + +
151C GLN* 3.6 22.7 + - - +
189C PRO* 4.5 8.7 - - + -
255C ILE* 3.5 33.2 - - + -
259C GLY 5.2 2.5 - - - -
342C LEU* 5.0 19.3 - - + +
345C ASP 4.3 4.3 - - - +
346C LYS* 4.0 21.8 - - - -
347C GLU 2.9 1.2 - - - +
348C ARG* 1.3 80.9 - - + +
350C GLU* 1.3 64.7 + - - +
352C VAL* 3.1 37.5 - - + -
353C LYS* 2.9 69.5 + - + +
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Residues in contact with GLU 350 (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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34A ALA* 5.1 0.8 - - - -
346C LYS 3.8 19.2 - - - +
347C GLU* 3.1 10.5 + - - +
349C TRP* 1.3 80.0 - - - +
351C ASP* 1.3 60.8 + - - +
353C LYS* 3.0 39.7 + - - +
354C GLU* 2.9 21.0 + - - +
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Residues in contact with ASP 351 (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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347C GLU* 3.2 5.7 + - - +
348C ARG* 2.3 42.8 - - - +
349C TRP 3.3 0.2 - - - -
350C GLU* 1.3 80.2 - - - +
352C VAL* 1.3 60.9 + - - +
354C GLU* 2.8 41.5 + - - +
355C GLU* 2.3 46.7 - - - +
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Residues in contact with VAL 352 (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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255C ILE* 5.2 9.4 - - + -
261C PRO* 4.0 29.8 - - + -
263C PHE* 4.1 11.2 - - + -
348C ARG* 2.6 25.8 + - - +
349C TRP* 3.1 40.8 - - + +
351C ASP* 1.3 77.4 - - - +
353C LYS* 1.3 66.1 + - - +
355C GLU* 3.1 15.1 + - - +
356C MET* 3.2 23.2 + - + +
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Residues in contact with LYS 353 (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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145C GLU* 3.5 31.3 + - - -
148C SER* 5.4 0.6 + - - -
188C LYS* 5.7 0.9 - - - +
189C PRO* 3.8 14.9 - - + +
190C GLU* 3.1 30.1 + - + +
349C TRP* 2.9 53.6 + - + +
350C GLU* 3.0 37.4 + - - +
352C VAL* 1.3 78.9 - - + +
354C GLU* 1.3 58.8 + - - +
356C MET* 3.5 7.6 + - - +
357C THR* 3.1 23.4 + - - -
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Residues in contact with GLU 354 (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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33A GLY* 3.5 10.5 - - - -
34A ALA* 2.8 49.9 + - - +
35A TYR* 4.6 1.2 + - - +
350C GLU 2.9 12.8 + - - +
351C ASP* 2.8 37.9 - - - +
353C LYS* 1.3 70.4 - - - +
355C GLU* 1.3 64.8 + - - +
357C THR* 2.8 11.7 + - - -
358C SER* 2.6 37.9 + - - +
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Residues in contact with GLU 355 (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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263C PHE* 3.7 26.0 - - + -
351C ASP* 2.3 44.4 + - - +
352C VAL* 3.1 15.1 + - - +
354C GLU* 1.3 87.4 - - - +
356C MET* 1.3 53.8 + - - +
358C SER* 3.7 9.6 - - - +
359C ALA* 2.6 36.0 + - - +
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Residues in contact with MET 356 (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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187C VAL 4.1 9.2 - - - +
188C LYS* 4.6 19.1 - - + -
189C PRO* 5.0 7.4 - - + -
247C TRP* 3.1 44.9 - - + -
248C SER* 4.0 15.7 - - - +
251C VAL* 3.1 30.5 - - + -
252C ILE* 4.7 6.5 - - + -
255C ILE* 5.1 9.4 - - + -
263C PHE* 5.0 8.7 - - + -
352C VAL* 3.2 14.0 + - + +
353C LYS* 3.6 11.9 - - - +
354C GLU 3.1 0.8 - - - -
355C GLU* 1.3 76.1 - - - +
357C THR* 1.3 58.6 + - - +
359C ALA* 4.2 0.4 - - - -
360C LEU* 3.0 29.8 + - + +
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Residues in contact with THR 357 (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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32A SER 4.4 18.2 - - - +
188C LYS* 2.9 41.9 + - - +
190C GLU* 4.2 1.9 + - - -
353C LYS 3.1 12.9 + - - -
354C GLU* 2.8 10.7 + - - -
356C MET* 1.3 76.2 - - - +
358C SER* 1.3 58.9 - - - +
360C LEU* 4.0 4.6 - - - +
361C ALA* 3.1 28.9 + - + +
364C ARG* 5.0 2.5 + - - +
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Residues in contact with SER 358 (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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32A SER 5.3 1.2 + - - -
33A GLY* 4.6 8.3 - - - -
354C GLU* 2.6 28.0 + - - +
355C GLU* 3.7 9.4 - - - -
357C THR* 1.3 71.2 - - - +
359C ALA* 1.3 62.5 + - - +
361C ALA* 3.5 4.3 + - - +
362C THR* 2.8 34.6 + - - +
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Residues in contact with ALA 359 (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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185A THR* 6.2 5.8 - - - -
247C TRP* 3.4 29.2 - - + -
263C PHE* 5.9 4.5 - - + -
355C GLU 2.6 23.6 + - - +
356C MET* 3.6 2.5 - - - +
358C SER* 1.3 72.6 - - - +
360C LEU* 1.3 55.2 + - - +
362C THR* 2.3 28.3 + - - -
363C MET* 2.8 21.6 - - + +
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Residues in contact with LEU 360 (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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185C ARG 3.1 29.2 - - - +
186C ASP* 3.9 15.5 - - - +
187C VAL 4.0 11.0 - - - +
188C LYS* 6.2 1.6 - - + -
244C CYS* 4.3 5.8 - - + +
247C TRP* 3.0 38.4 - - + -
248C SER* 4.3 7.2 - - - +
356C MET* 3.0 19.9 + - + +
357C THR* 4.0 5.6 - - - +
359C ALA* 1.3 75.2 - - - +
361C ALA* 1.3 55.1 + - - +
363C MET* 2.7 45.5 + - + +
364C ARG* 3.2 26.4 + - + +
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Residues in contact with ALA 361 (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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115A ASN* 5.5 2.6 + - - -
357C THR* 3.1 19.0 + - + +
358C SER* 4.0 5.4 - - - +
360C LEU* 1.3 77.7 - - - +
362C THR* 1.3 60.3 + - + +
363C MET 3.6 0.2 + - - -
364C ARG* 3.4 38.7 + - - +
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Residues in contact with THR 362 (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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114A ASN* 4.3 10.3 + - - +
118A LYS* 4.0 15.0 + - - -
152A LYS* 4.8 15.7 - - - +
154A SER* 4.9 14.8 - - - -
185A THR* 6.0 2.3 - - - -
358C SER* 2.8 22.9 - - - +
359C ALA* 2.3 29.7 + - - -
360C LEU 2.8 1.4 + - - -
361C ALA* 1.3 80.7 - - + +
363C MET* 1.3 58.7 + - - +
364C ARG 3.5 1.1 - - - -
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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