Contacts of the helix formed by residues 295 - 308 (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 ASN 295 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31J MET* 6.4 0.2 - - - +
33J VAL* 3.0 37.3 - - - +
34J LYS 4.0 4.9 - - - +
35J LEU* 4.4 1.5 - - + +
85J ASP* 3.2 25.6 + - - +
293J ALA* 5.1 0.7 - - - -
294J GLU* 1.3 94.7 + - - +
296J ARG* 1.3 53.6 + - - +
297J GLU* 3.2 3.4 - - - -
298J LEU* 3.0 23.5 + - + +
299J ALA* 2.8 33.0 + - - +
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Residues in contact with ARG 296 (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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106J TRP* 5.5 4.2 - - - +
289J ILE* 3.3 29.1 + - - +
290J PRO 2.9 27.8 + - - -
291J LYS* 4.1 14.3 + - - +
293J ALA* 3.9 16.6 + - - +
294J GLU 3.9 2.0 + - - +
295J ASN* 1.3 71.6 - - - +
297J GLU* 1.3 58.3 + - + +
299J ALA* 2.9 7.6 - - - +
300J VAL* 2.8 42.4 + - + +
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Residues in contact with GLU 297 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295J ASN 3.1 1.0 + - - -
296J ARG* 1.3 76.2 - - + +
298J LEU* 1.3 69.7 + - + +
300J VAL* 3.6 9.0 + - - +
301J GLU* 3.2 27.6 + - - +
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Residues in contact with LEU 298 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J MET* 4.8 18.8 - - + -
33J VAL* 4.3 18.6 - - + -
35J LEU* 4.1 11.4 - - + -
54J PHE* 3.4 16.5 - - + -
58J HIS* 4.0 28.7 - - + +
61J VAL* 4.4 21.8 - - + -
295J ASN* 3.0 32.9 + - + +
297J GLU* 1.3 78.2 - - + +
299J ALA* 1.3 70.1 + - - +
301J GLU* 3.2 8.4 + - + +
302J PHE* 3.0 15.9 + - - +
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Residues in contact with ALA 299 (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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35J LEU* 4.2 8.9 - - - +
85J ASP* 3.7 12.8 - - + +
86J VAL* 4.5 3.4 - - - -
289J ILE* 3.2 35.4 - - + -
295J ASN 2.8 13.4 + - - +
296J ARG* 2.9 13.9 - - - +
298J LEU* 1.3 75.0 - - - +
300J VAL* 1.3 67.4 + - - +
302J PHE* 2.6 20.3 + - - +
303J VAL* 2.9 11.7 + - - +
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Residues in contact with VAL 300 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289J ILE* 3.3 16.6 - - + +
296J ARG* 2.8 29.5 + - + +
297J GLU* 3.6 9.4 - - - +
299J ALA* 1.3 72.8 - - - +
301J GLU* 1.3 68.2 + - - +
303J VAL* 3.0 4.0 + - - +
304J LYS* 2.8 54.7 + - - +
334J SER* 3.6 28.7 - - - +
335J LEU* 3.8 12.3 - - + -
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Residues in contact with GLU 301 (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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54J PHE* 3.5 15.9 - - + -
57J LYS* 5.6 4.3 - - - +
58J HIS* 4.0 22.9 + - + +
297J GLU 3.2 17.6 + - - +
298J LEU* 3.2 10.5 + - + +
299J ALA 3.1 0.6 - - - -
300J VAL* 1.3 77.8 - - - +
302J PHE* 1.3 62.7 + - - +
304J LYS* 3.4 30.1 - - - +
305J LEU* 3.1 22.0 + - - +
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Residues in contact with PHE 302 (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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35J LEU* 4.0 17.3 - - + -
37J VAL* 4.3 6.5 - - + -
47J MET* 3.5 31.9 - - + -
50J PHE* 3.5 43.7 - + + -
51J LYS* 4.6 0.7 - - - -
54J PHE* 3.3 30.2 - + + -
63J VAL* 4.5 12.8 - - + -
86J VAL* 3.7 32.8 - - + -
298J LEU 3.0 10.1 + - - +
299J ALA 2.6 15.5 + - - +
301J GLU* 1.3 67.8 - - - +
303J VAL* 1.3 67.1 + - - +
305J LEU* 2.9 17.0 + - + +
306J VAL* 2.9 25.6 + - + +
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Residues in contact with VAL 303 (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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86J VAL* 4.8 7.2 - - + -
106J TRP* 4.4 4.7 - - + -
108J ILE* 4.3 13.2 - - + -
287J ILE* 4.4 24.9 - - + -
289J ILE* 3.4 39.7 - - + -
299J ALA 2.9 5.1 + - - +
300J VAL 3.4 4.7 - - - +
302J PHE* 1.3 75.2 - - - +
304J LYS* 1.3 64.3 + - - +
306J VAL* 2.9 22.6 + - + +
307J ILE* 3.1 15.8 + - + +
335J LEU* 3.5 26.5 - - + -
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Residues in contact with LYS 304 (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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300J VAL* 2.8 39.4 + - + +
301J GLU* 3.4 29.2 - - - +
303J VAL* 1.3 71.1 - - - +
305J LEU* 1.3 59.2 - - - +
307J ILE* 3.1 6.4 - - - +
308J SER* 2.8 26.7 + - - -
334J SER 3.3 24.9 + - - -
335J LEU* 3.4 13.6 - - + +
337J ALA* 4.3 12.5 - - - +
338J MET* 3.0 35.1 - - + +
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Residues in contact with LEU 305 (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* 3.6 24.7 - - + +
53J ALA* 3.8 7.4 - - + -
54J PHE* 3.5 39.9 - - + +
301J GLU 3.1 8.8 + - - +
302J PHE* 2.9 12.2 + - + +
304J LYS* 1.3 78.5 - - - +
306J VAL* 1.3 65.4 + - - +
308J SER* 3.1 22.8 + - - +
310J GLU* 3.0 39.5 - - + +
311J GLY* 3.3 11.6 - - - +
314J ILE* 5.1 1.6 - - + -
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Residues in contact with VAL 306 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47J MET* 4.9 2.0 - - + -
50J PHE* 3.6 30.5 - - + -
110J PHE* 3.8 38.4 - - + +
287J ILE* 3.8 22.0 - - + -
302J PHE* 2.9 43.5 + - + +
303J VAL* 2.9 9.5 + - - +
305J LEU* 1.3 77.0 - - - +
307J ILE* 1.3 61.3 + - + +
311J GLY* 3.5 17.3 - - - -
312J GLN* 4.0 1.9 + - - +
315J LEU* 4.8 3.6 - - - +
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Residues in contact with ILE 307 (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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108J ILE* 4.2 22.0 - - + -
110J PHE* 4.2 15.7 - - + -
287J ILE* 5.6 0.9 - - + -
303J VAL* 3.1 20.1 + - + +
304J LYS* 3.1 22.0 - - - +
306J VAL* 1.3 79.5 - - + +
308J SER* 1.3 67.0 + - - +
312J GLN* 3.3 21.5 + - - +
326J PRO* 3.9 31.4 - - + +
335J LEU* 4.4 9.4 - - + -
338J MET* 3.6 36.3 - - + -
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Residues in contact with SER 308 (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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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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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