Contacts of the helix formed by residues 246 - 254 (chain A) in PDB entry 3NKO
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 ARG 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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81A SER 5.8 2.9 - - - +
245A GLY* 1.3 70.7 - - - -
247A GLU* 1.3 67.1 + - - +
248A LYS 3.1 3.1 - - - -
249A PHE* 2.9 33.8 + - + +
250A ASN 4.1 1.4 + - - -
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Residues in contact with GLU 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ALA* 4.6 4.6 - - - +
240A THR 3.3 27.6 - - - +
241A PHE* 4.3 3.4 - - - -
242A HIS* 5.2 2.0 - - + +
245A GLY 3.6 0.6 - - - -
246A ARG* 1.3 77.6 - - - +
248A LYS* 1.3 62.2 + - - +
250A ASN* 3.0 29.2 + - - +
252A ARG* 2.9 30.6 + - - -
253A TRP* 2.8 36.3 + - + +
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Residues in contact with LYS 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PHE* 3.8 20.9 - - + -
241A PHE* 3.5 34.7 - - + -
242A HIS 3.7 11.6 + - - +
243A LEU 2.8 29.3 + - - +
244A ARG* 3.8 1.2 - - - +
245A GLY 2.8 36.6 + - - +
247A GLU* 1.3 77.0 - - - +
249A PHE* 1.3 89.3 + - + +
250A ASN 3.2 1.1 - - - -
253A TRP* 4.7 0.2 - - - -
254A TRP* 2.8 34.4 + - + -
1007A NKO 4.2 1.8 - - + +
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Residues in contact with PHE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A LEU* 5.9 1.3 - - + -
81A SER* 3.5 39.3 - - - -
82A TYR* 3.5 40.6 + + + +
245A GLY 3.8 7.4 - - - -
246A ARG* 2.9 32.6 + - + +
248A LYS* 1.3 105.0 - - + +
250A ASN* 1.3 62.5 + - - +
251A HIS* 3.3 19.4 + - - -
254A TRP* 4.9 0.4 - - - -
1007A NKO 4.4 14.3 - - + +
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Residues in contact with ASN 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ARG 4.1 1.2 + - - -
247A GLU* 3.0 26.8 + - - +
249A PHE* 1.3 76.0 - - - +
251A HIS* 1.3 78.2 + - - +
252A ARG* 3.0 46.0 + - - +
253A TRP* 3.4 12.0 - - + -
254A TRP* 3.4 15.1 + - - -
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Residues in contact with HIS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82A TYR* 4.9 6.9 + - - -
249A PHE 3.3 16.3 + - - -
250A ASN* 1.3 70.1 + - - +
252A ARG* 1.3 65.4 + - - +
253A TRP 3.0 4.7 + - - -
254A TRP* 3.0 25.7 + - - +
1007A NKO 3.8 49.3 - - + +
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Residues in contact with ARG 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A PHE* 3.5 59.1 + - + +
239A ALA* 3.5 19.4 - - - +
247A GLU* 2.9 28.5 + - - -
250A ASN* 3.0 34.6 + - - +
251A HIS* 1.3 76.5 - - - +
253A TRP* 1.3 66.8 + - + +
254A TRP 3.5 0.5 + - - -
439A ARG* 3.5 11.4 + - - -
5C MAN 4.8 7.8 + - - -
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Residues in contact with TRP 253 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A HIS 3.9 2.8 - - - +
226A GLY* 4.2 0.2 - - - -
227A ILE* 3.5 9.7 - - + +
232A MET* 3.6 18.2 - - + -
234A ASP* 3.7 29.2 - - + -
237A PHE* 3.9 13.7 - + - -
239A ALA* 3.5 26.9 - - + -
240A THR 4.1 0.4 - - - -
241A PHE* 3.5 46.4 - + + -
247A GLU* 2.8 46.1 + - + +
250A ASN* 3.4 14.1 - - + -
251A HIS 3.0 1.4 + - - -
252A ARG* 1.3 85.7 - - + +
254A TRP* 1.3 70.3 + - + +
255A GLY 3.7 3.1 + - - -
439A ARG* 2.9 50.6 + - - +
1024A EDO 5.2 0.3 - - - -
5C MAN 5.4 1.2 + - - -
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Residues in contact with TRP 254 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A PHE* 4.0 31.0 - + - -
214A TYR* 3.7 44.0 - + + +
225A HIS 4.2 1.6 - - - -
227A ILE* 3.6 25.8 - - + -
241A PHE* 3.7 19.7 - + - -
248A LYS* 2.8 31.8 + - + -
250A ASN 3.4 17.8 + - - -
251A HIS* 3.0 11.5 + - - +
252A ARG 3.3 0.6 - - - +
253A TRP* 1.3 82.0 - - + +
255A GLY* 1.3 61.2 + - - +
260A TRP* 6.4 0.2 - + - -
1007A NKO 3.2 65.9 - - + +
5C MAN 4.9 2.3 + - - -
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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