Contacts of the helix formed by residues 308 - 318 (chain J) in PDB entry 2ONK
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 SER 308 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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304J LYS 2.8 19.0 + - - -
305J LEU* 3.1 18.3 + - - +
307J ILE* 1.3 74.9 - - - +
309J GLU* 1.3 65.2 + - - +
310J GLU* 3.2 21.4 + - - +
311J GLY 3.0 2.4 + - - -
312J GLN* 2.9 21.1 + - - +
338J MET* 4.2 12.1 - - - -
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Residues in contact with GLU 309 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308J SER* 1.3 72.7 - - - +
310J GLU* 1.3 66.0 + - - +
312J GLN* 2.9 22.2 + - - +
313J GLU* 2.7 30.0 + - + +
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Residues in contact with GLU 310 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53J ALA* 4.6 13.0 - - - +
305J LEU* 3.0 25.2 - - + +
308J SER* 3.2 9.8 + - - +
309J GLU* 1.3 79.4 - - - +
311J GLY* 1.3 58.7 + - - +
313J GLU* 3.2 5.6 + - - +
314J ILE* 2.9 41.4 + - + +
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Residues in contact with GLY 311 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50J PHE* 3.9 13.6 - - - -
305J LEU* 3.3 22.5 + - - -
306J VAL 3.5 11.2 - - - -
308J SER 3.0 5.1 + - - -
310J GLU* 1.3 80.7 - - - +
312J GLN* 1.3 61.7 + - - +
314J ILE* 3.1 9.1 + - - +
315J LEU* 3.0 27.8 + - - +
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Residues in contact with GLN 312 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306J VAL 4.0 2.3 + - - +
307J ILE* 3.3 21.6 + - - +
308J SER 2.9 13.2 - - - +
309J GLU* 2.9 24.5 + - - +
311J GLY* 1.3 74.2 - - - +
313J GLU* 1.3 57.6 + - + +
315J LEU* 3.7 1.9 + - - +
316J ARG* 3.1 29.0 + - - +
322J PRO* 3.3 35.5 - - + +
323J LEU 4.6 2.4 + - - -
324J VAL* 3.4 39.9 - - + +
326J PRO* 4.3 13.3 - - - +
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Residues in contact with GLU 313 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309J GLU* 2.7 22.2 + - + +
310J GLU* 3.6 5.4 - - - +
312J GLN* 1.3 72.2 - - + +
314J ILE* 1.3 58.5 + - - +
316J ARG* 2.6 39.3 + - - +
317J GLU* 2.6 63.4 + - + +
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Residues in contact with ILE 314 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46J PRO* 4.2 13.9 - - + +
49J ALA* 3.5 46.7 - - + +
50J PHE* 4.0 24.5 - - + +
53J ALA* 4.8 6.5 - - + -
305J LEU* 5.1 1.1 - - + -
310J GLU* 2.9 30.4 + - + +
311J GLY* 3.1 12.6 - - - +
313J GLU* 1.3 79.3 - - - +
315J LEU* 1.3 65.0 + - - +
317J GLU* 3.0 19.9 + - - +
318J LEU* 3.1 12.7 + - + +
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Residues in contact with LEU 315 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43J LEU* 4.5 6.7 - - + -
46J PRO* 3.9 19.5 - - + -
50J PHE* 4.1 15.3 - - + -
110J PHE* 3.9 35.4 - - + +
111J ALA* 4.2 2.7 - - + -
306J VAL 4.8 3.4 - - - +
311J GLY 3.0 16.6 + - - +
312J GLN* 3.8 4.5 - - - +
314J ILE* 1.3 82.5 - - + +
316J ARG* 1.3 61.0 + - - +
318J LEU* 2.9 16.1 + - - +
320J GLN* 2.9 65.5 + - + +
322J PRO* 4.0 11.0 - - + -
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Residues in contact with ARG 316 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263E GLU* 5.1 7.1 + - - -
312J GLN* 3.1 28.5 + - - +
313J GLU* 2.6 43.1 + - - +
315J LEU* 1.3 76.8 - - - +
317J GLU* 1.3 66.3 + - - +
319J GLY* 3.0 12.9 + - - -
320J GLN 3.2 10.7 + - - +
321J GLU* 4.2 21.6 + - - +
322J PRO* 3.1 33.1 + - + +
324J VAL* 4.1 13.3 - - - +
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Residues in contact with GLU 317 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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313J GLU* 2.6 46.0 + - + +
314J ILE* 3.0 12.8 + - - +
316J ARG* 1.3 72.3 - - - +
318J LEU* 1.3 66.0 + - + +
319J GLY* 3.1 4.9 + - - -
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Residues in contact with LEU 318 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45J GLU* 3.5 17.9 - - + +
46J PRO* 3.3 43.5 - - + -
49J ALA* 5.2 3.4 - - + -
238J SER 3.7 2.9 - - - +
241J LYS* 5.2 1.5 - - - +
242J GLN* 3.3 38.2 + - + +
314J ILE* 3.1 15.5 + - + +
315J LEU* 2.9 8.8 + - - +
317J GLU* 1.3 80.3 - - + +
319J GLY* 1.3 61.0 + - - +
320J GLN* 3.2 2.8 + - + -
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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