Contacts of the helix formed by residues 262 - 276 (chain E) in PDB entry 1R4N
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 262 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209E HIS* 3.4 33.9 - - - +
210E SER* 4.4 4.6 + - - -
251E ILE* 3.3 36.6 - - + +
252E LEU* 3.7 20.6 + - - +
260E GLU* 5.0 1.9 - - - +
261E ASP* 1.3 100.9 + - - +
263E GLU* 1.3 65.5 + - - +
264E ASN* 3.3 17.2 + - - +
265E PHE* 3.5 18.3 - - + -
266E GLU* 3.3 18.2 + - - +
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Residues in contact with GLU 263 (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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210E SER* 5.3 3.6 - - - -
261E ASP* 3.8 2.6 - - + +
262E GLU* 1.3 75.7 - - - +
264E ASN* 1.3 56.7 + - - +
266E GLU* 3.1 8.3 + - + +
267E GLU* 2.7 34.5 + - + +
333E ILE* 3.5 28.4 - - + +
214F PRO* 6.1 1.0 - - - +
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Residues in contact with ASN 264 (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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209E HIS 3.2 12.1 - - - +
210E SER* 3.0 40.2 - - - +
212E THR* 3.1 18.7 - - - +
214E TRP* 4.1 6.8 - - + +
217E ILE* 4.4 2.1 - - - +
262E GLU* 3.6 11.1 + - - +
263E GLU* 1.3 80.0 - - - +
265E PHE* 1.3 70.7 + - - +
267E GLU* 3.0 15.0 + - - +
268E ALA* 2.6 35.9 + - - +
333E ILE* 4.0 22.9 - - + +
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Residues in contact with PHE 265 (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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209E HIS* 3.1 40.8 - + - -
217E ILE* 3.5 35.4 - - + -
221E TYR* 4.3 11.9 - + - -
247E ILE* 3.5 31.9 - - + +
250E GLY* 3.6 21.3 - - - -
251E ILE* 4.0 15.5 - - + -
262E GLU* 3.5 24.0 - - + -
263E GLU 3.2 0.4 - - - -
264E ASN* 1.3 95.9 - - - +
266E GLU* 1.3 58.0 + - - +
268E ALA* 3.0 9.6 + - - +
269E ILE* 2.9 34.7 + - + +
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Residues in contact with GLU 266 (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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248E ARG* 3.9 17.9 + - - +
262E GLU 3.3 11.0 + - - +
263E GLU* 3.1 11.9 + - + +
265E PHE* 1.3 79.4 - - - +
267E GLU* 1.3 61.3 + - - +
269E ILE* 3.2 34.3 - - - +
270E LYS* 3.0 50.2 + - - +
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Residues in contact with GLU 267 (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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214E TRP* 3.7 27.3 - - + +
263E GLU* 2.7 13.6 + - + +
264E ASN* 3.0 12.1 + - - +
266E GLU* 1.3 74.0 - - - +
268E ALA* 1.3 64.0 + - - +
270E LYS* 3.1 16.3 + - + +
271E ASN* 2.6 42.0 + - - +
331E ASP 4.6 1.0 - - - +
332E MET* 4.3 6.4 - - - +
333E ILE* 3.2 38.5 + - + +
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Residues in contact with ALA 268 (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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214E TRP* 3.9 13.4 - - + +
217E ILE* 3.9 22.0 - - + -
218E ILE* 3.1 31.3 - - + +
247E ILE* 4.7 3.4 - - + -
264E ASN 2.6 16.0 + - - +
265E PHE 3.1 9.6 - - - +
267E GLU* 1.3 71.3 - - - +
269E ILE* 1.3 65.9 + - - +
271E ASN* 2.9 17.6 + - - +
272E VAL* 3.0 9.7 + - - -
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Residues in contact with ILE 269 (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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244E ARG* 3.2 41.9 + - + +
247E ILE* 4.1 22.4 - - + +
248E ARG* 3.9 36.6 - - + +
251E ILE* 5.9 2.2 - - + -
265E PHE* 2.9 22.6 + - + +
266E GLU* 3.2 39.5 - - - +
268E ALA* 1.3 75.2 - - - +
270E LYS* 1.3 66.5 + - + +
272E VAL* 2.7 29.7 + - - +
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Residues in contact with LYS 270 (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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244E ARG* 4.3 4.4 + - - +
266E GLU* 3.0 40.0 + - - +
267E GLU* 3.1 13.6 + - + +
269E ILE* 1.3 80.5 - - + +
271E ASN* 1.3 60.7 + - - +
272E VAL 3.4 0.3 + - - -
273E ASN* 3.4 18.7 + - - +
274E THR* 5.7 0.2 + - - -
128K GLU* 5.0 5.8 - - - +
131K GLU* 5.0 4.3 - - - +
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Residues in contact with ASN 271 (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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214E TRP* 2.9 67.5 - - + +
218E ILE* 4.0 2.0 - - + -
267E GLU* 2.6 36.5 + - - +
268E ALA 2.9 8.0 + - - +
270E LYS* 1.3 73.0 - - - +
272E VAL* 1.3 55.1 + - - +
273E ASN 2.9 6.1 - - - -
274E THR* 2.8 25.6 + - - -
275E ALA* 3.0 16.4 + - + +
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Residues in contact with VAL 272 (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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218E ILE* 3.6 16.8 - - + -
240E LYS* 4.2 19.9 - - + +
243E PHE* 3.6 24.9 - - + -
244E ARG* 4.0 12.1 - - + +
247E ILE* 3.7 23.1 - - + -
268E ALA 3.0 11.3 + - - +
269E ILE* 2.7 25.0 + - - +
271E ASN* 1.3 71.4 - - - +
273E ASN* 1.3 60.6 + - - +
274E THR 3.1 0.7 + - - -
275E ALA* 4.4 3.6 - - - -
276E LEU* 3.7 32.0 - - + +
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Residues in contact with ASN 273 (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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240E LYS* 4.4 9.4 + - - +
244E ARG* 3.3 24.6 + - - +
270E LYS 3.4 11.4 + - - +
271E ASN 2.9 1.2 + - - -
272E VAL* 1.3 77.5 - - - +
274E THR* 1.3 58.2 + - - +
128K GLU* 3.0 53.1 + - - +
129K ARG* 5.0 8.0 + - - -
131K GLU* 3.8 15.0 + - - +
132K GLU* 3.6 36.4 - - - +
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Residues in contact with THR 274 (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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180E LEU* 4.0 25.8 - - + -
181E GLU* 5.4 7.9 - - + +
183E LEU* 5.8 3.6 - - + -
240E LYS* 5.5 1.2 + - - -
271E ASN* 2.8 9.6 + - - -
273E ASN* 1.3 82.3 + - - +
275E ALA* 1.3 55.4 + - - +
276E LEU* 2.5 23.7 + - - +
277E ASN 3.5 16.1 + - - +
278E THR* 4.0 12.0 - - + +
131K GLU* 3.7 33.3 + - - +
132K GLU* 5.5 2.9 - - - +
135K GLY* 6.0 0.2 - - - -
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Residues in contact with ALA 275 (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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183E LEU* 4.5 15.4 - - + +
185E LEU* 3.8 30.7 + - + +
214E TRP* 4.7 2.9 - - + +
218E ILE* 4.0 25.4 - - + -
271E ASN* 3.0 20.5 + - + +
272E VAL* 4.4 2.0 - - - -
274E THR* 1.3 74.3 - - - +
276E LEU* 1.3 66.9 + - + +
278E THR* 3.5 16.2 - - - +
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Residues in contact with LEU 276 (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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185E LEU* 5.4 2.7 - - + -
186E ASP* 3.4 26.0 + - - +
218E ILE* 4.8 8.7 - - + -
222E LEU* 4.3 25.8 - - + -
232E ARG 5.0 4.5 - - - +
233E ILE* 3.6 37.9 - - + +
234E PRO* 6.3 0.9 - - + -
240E LYS* 3.7 34.3 - - + +
243E PHE* 4.7 5.4 - - + -
272E VAL* 3.7 25.4 - - + +
274E THR 2.5 8.8 + - - +
275E ALA* 1.3 79.0 - - + +
277E ASN* 1.3 60.5 + - + +
278E THR 3.4 2.4 + - - -
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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