Contacts of the helix formed by residues 230 - 240 (chain E) in PDB entry 2NPP
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 LYS 230 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225E PHE* 6.3 0.4 - - - -
226E ALA* 3.9 31.6 - - + +
228E PRO 4.3 2.2 - - - +
229E LEU* 1.3 74.9 - - - +
231E GLU* 1.3 69.1 + - - +
232E GLU* 4.5 7.4 - - + +
233E HIS* 2.9 48.4 + - + +
234E LYS* 3.6 3.4 + - - +
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Residues in contact with GLU 231 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E LEU 3.7 2.8 + - - -
230E LYS* 1.3 70.3 - - - +
232E GLU* 1.3 68.8 + - - +
234E LYS* 3.0 27.8 + - + +
235E ILE* 3.3 29.0 + - + +
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Residues in contact with GLU 232 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E ALA* 5.9 0.7 - - - +
191E ARG* 2.7 41.0 + - - +
192E LYS 5.7 0.2 + - - -
195E ASN* 5.1 6.9 + - - -
230E LYS* 3.0 7.2 + - + +
231E GLU* 1.3 84.3 + - - +
233E HIS* 1.3 74.9 + - + +
235E ILE* 3.0 14.0 + - + +
236E PHE* 2.9 29.3 + - - +
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Residues in contact with HIS 233 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E ARG* 4.0 34.4 + - - -
225E PHE* 3.1 56.7 - + + -
229E LEU* 4.5 8.7 - - + -
230E LYS* 2.9 48.3 + - + +
232E GLU* 1.3 85.4 + - + +
234E LYS* 1.3 62.8 + - - +
236E PHE* 3.4 10.6 - - - +
237E LEU 3.2 10.0 + - - -
264E PHE* 3.1 31.7 - - + -
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Residues in contact with LYS 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229E LEU* 4.1 33.3 + - + -
230E LYS 3.6 2.9 + - - +
231E GLU* 3.0 17.1 + - + +
233E HIS* 1.3 76.3 - - - +
235E ILE* 1.3 65.8 + - + +
237E LEU* 3.1 9.7 + - - +
238E LEU* 3.0 30.1 + - + +
268E ASP* 4.7 9.0 - - - -
270E THR* 6.4 0.7 - - - -
271E LEU* 3.9 39.7 - - + -
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Residues in contact with ILE 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140D TRP* 3.9 31.6 - - + +
199E TYR* 5.0 3.1 - - - +
231E GLU* 3.7 34.3 - - + +
232E GLU* 3.0 12.5 + - - +
234E LYS* 1.3 78.1 - - + +
236E PHE* 1.3 60.2 + - - +
238E LEU* 2.9 4.8 + - - +
239E LYS* 2.6 44.6 + - + +
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Residues in contact with PHE 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191E ARG* 6.6 0.4 - - - -
195E ASN* 3.2 32.1 - - - +
198E PHE* 4.7 2.5 - + - -
218E LEU* 3.4 46.9 - - + -
222E ILE* 4.2 8.5 - - + -
225E PHE* 5.5 2.9 - + - -
232E GLU* 2.9 15.2 + - - +
233E HIS* 3.4 16.8 - - - +
235E ILE* 1.3 76.4 - - - +
237E LEU* 1.3 50.3 + - - +
240E VAL* 3.0 33.2 + - + +
241E LEU* 2.8 56.9 + - + +
264E PHE* 3.7 23.3 - + - -
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Residues in contact with LEU 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233E HIS 3.2 8.1 + - - +
234E LYS 3.1 8.4 + - - +
236E PHE* 1.3 78.9 - - - +
238E LEU* 1.3 69.3 + - + +
241E LEU* 3.0 27.4 + - + +
242E LEU* 2.8 35.6 + - + +
261E VAL* 4.7 10.8 - - + -
264E PHE* 3.7 30.3 - - + -
265E LEU* 5.8 0.2 - - + -
271E LEU* 3.4 42.6 - - + -
275E VAL* 4.0 22.2 - - + -
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Residues in contact with LEU 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLU* 5.2 2.1 - - - +
234E LYS* 3.0 20.0 + - + +
235E ILE* 2.9 5.0 + - - +
237E LEU* 1.3 93.7 - - + +
239E LYS* 1.3 64.7 + - + +
240E VAL 3.3 0.4 - - - -
242E LEU* 3.4 29.9 - - + +
243E PRO* 3.0 21.5 - - - +
271E LEU* 5.5 5.4 - - + -
274E PRO* 4.2 32.3 - - + -
275E VAL* 4.5 1.8 - - + -
278E ALA* 5.9 0.2 - - + -
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Residues in contact with LYS 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D GLU* 3.7 44.2 + - - +
140D TRP* 3.4 59.2 - - + +
199E TYR* 3.4 16.0 - - - +
202E ILE* 5.3 0.2 - - - +
203E TYR* 4.5 1.6 + - - -
235E ILE* 2.6 27.4 + - + +
238E LEU* 1.3 78.8 - - + +
240E VAL* 1.3 55.6 + - - +
243E PRO* 3.2 12.3 - - - +
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Residues in contact with VAL 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195E ASN* 4.2 13.9 - - - +
198E PHE* 3.9 40.2 - - + -
199E TYR* 3.0 42.0 - - + +
202E ILE* 3.6 5.6 - - + +
235E ILE 5.3 0.2 - - - -
236E PHE* 3.0 34.1 + - + +
238E LEU 3.3 0.2 - - - -
239E LYS* 1.3 77.4 - - + +
241E LEU* 1.3 64.2 + - - +
243E PRO* 3.2 12.7 - - - +
244E LEU* 3.4 15.0 - - + +
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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