Contacts of the helix formed by residues 265 - 279 (chain I) in PDB entry 6RAR
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 265 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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263I ASN 5.0 0.2 - - - +
264I THR* 1.3 77.9 - - - +
266I GLN* 1.3 67.1 + - - +
267I THR* 3.3 2.9 - - - +
268I ALA* 3.1 9.7 + - + +
269I ARG* 2.9 22.7 + - - +
326I PRO 3.9 9.0 - - - +
327I ASP* 3.7 43.5 - - - +
328I GLY 3.7 5.2 - - - -
329I MET* 3.7 23.0 - - + +
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Residues in contact with GLN 266 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163I GLN* 3.9 20.3 - - - +
165I GLU* 4.8 0.2 + - - -
249I PHE 4.3 5.3 + - - -
250I ASP* 3.6 12.3 + - - -
265I LYS* 1.3 73.3 - - - +
267I THR* 1.3 65.5 + - - +
269I ARG* 3.1 26.9 + - - +
270I SER* 2.8 45.4 + - - +
324I LYS* 3.6 19.6 - - + +
325I ASP 3.3 26.2 - - - +
326I PRO* 3.3 3.8 + - + +
328I GLY 2.9 13.8 + - - +
337I SER* 5.5 1.4 - - - -
338I TRP* 2.9 30.7 + - - +
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Residues in contact with THR 267 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163I GLN* 3.9 14.7 + - - +
265I LYS* 3.3 2.0 - - - -
266I GLN* 1.3 77.2 - - - +
268I ALA* 1.3 57.3 + - - +
270I SER* 3.3 3.3 + - - -
271I LEU* 2.9 46.1 + - + +
292I TRP* 4.8 11.2 - - + +
294I ASN* 5.1 4.8 + - - +
326I PRO* 3.0 33.4 + - - +
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Residues in contact with ALA 268 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264I THR* 3.9 16.8 - - + -
265I LYS* 3.1 15.0 + - + +
267I THR* 1.3 78.8 - - - +
269I ARG* 1.3 58.1 + - - +
271I LEU* 3.3 13.4 + - + +
272I LEU* 2.9 36.5 + - + +
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Residues in contact with ARG 269 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250I ASP* 2.6 49.1 + - - +
251I LEU* 3.5 16.0 - - + +
262I TRP* 3.5 35.2 - - + -
264I THR* 2.9 29.6 + - + +
265I LYS 2.9 16.5 + - - +
266I GLN* 3.2 34.9 + - - +
268I ALA* 1.3 73.8 - - - +
270I SER* 1.3 66.4 + - - +
272I LEU* 3.1 3.4 + - - -
273I VAL* 3.0 24.6 + - - +
328I GLY 2.9 21.4 + - - -
329I MET 4.3 2.0 + - - -
330I TYR* 3.2 28.5 - - - +
338I TRP* 4.5 4.0 - - - +
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Residues in contact with SER 270 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163I GLN* 2.9 30.3 + - - -
165I GLU* 4.2 2.9 + - - -
249I PHE 4.3 6.4 + - - -
266I GLN* 2.8 30.5 + - - +
267I THR* 3.6 4.7 - - - -
269I ARG* 1.3 71.7 - - - +
271I LEU* 1.3 63.6 + - - +
273I VAL* 3.2 12.7 - - - +
274I LYS* 3.1 22.9 + - - +
292I TRP* 3.6 25.8 - - - -
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Residues in contact with LEU 271 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267I THR* 2.9 30.8 + - + +
268I ALA* 3.5 14.6 - - + +
270I SER* 1.3 75.0 - - - +
272I LEU* 1.3 62.9 + - + +
274I LYS* 3.2 12.5 + - + +
275I LYS* 3.1 22.2 + - - +
292I TRP* 3.6 25.4 - - + -
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Residues in contact with LEU 272 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251I LEU* 3.9 15.9 - - + +
262I TRP* 4.2 26.0 - - + -
264I THR* 4.8 6.3 - - + -
268I ALA* 2.9 25.9 + - + +
269I ARG* 3.1 6.2 + - - +
271I LEU* 1.3 76.0 - - + +
273I VAL* 1.3 58.1 + - - +
275I LYS* 3.3 9.0 + - + +
276I TRP* 3.0 26.0 + - - +
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Residues in contact with VAL 273 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217I LEU* 4.7 8.7 - - + -
248I LEU* 3.9 37.9 - - + +
249I PHE* 4.3 6.1 - - - -
250I ASP 4.1 31.6 - - - +
251I LEU* 4.2 6.7 - - + +
269I ARG 3.0 15.6 + - - +
270I SER* 3.2 19.3 - - - +
272I LEU* 1.3 74.9 - - - +
274I LYS* 1.3 68.1 - - - +
276I TRP* 3.3 13.6 + - + +
277I VAL* 3.3 15.3 + - + +
289I THR* 3.8 7.1 - - + +
292I TRP* 5.9 0.4 - - + -
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Residues in contact with LYS 274 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270I SER 3.1 10.0 + - - +
271I LEU* 3.2 15.5 + - + +
273I VAL* 1.3 84.0 - - - +
275I LYS* 1.3 58.8 + - - +
277I VAL* 4.0 1.6 - - - +
278I ALA* 2.9 34.2 + - + +
289I THR* 4.1 21.4 + - - +
291I GLU* 4.0 25.3 + - - -
292I TRP* 4.4 20.8 - - + -
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Residues in contact with LYS 275 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271I LEU 3.1 12.9 + - - +
272I LEU* 3.7 12.1 - - + +
273I VAL 3.2 0.4 - - - -
274I LYS* 1.3 75.3 - - - +
276I TRP* 1.3 65.9 + - - +
278I ALA* 4.2 6.5 - - - -
279I LYS* 3.1 25.5 + - - +
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Residues in contact with TRP 276 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177I ILE* 4.0 18.8 - - + -
202I ILE* 4.3 21.8 - - + -
205I VAL* 4.9 12.8 - - + -
206I LEU* 4.9 10.5 - - + -
215I LEU* 3.9 24.7 - - + +
217I LEU* 4.1 27.4 - - + -
248I LEU* 4.9 2.2 - - + -
251I LEU* 5.4 5.4 - - + -
272I LEU 3.0 14.1 + - - +
273I VAL* 3.3 15.2 + - + +
275I LYS* 1.3 79.1 - - - +
277I VAL* 1.3 72.9 + - + +
279I LYS* 4.0 10.0 + - - +
280I HIS* 4.2 8.6 + + - -
284I LEU* 3.6 28.6 - - + +
287I ILE* 5.2 2.0 - - + -
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Residues in contact with VAL 277 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248I LEU* 3.9 24.7 - - + -
273I VAL 3.3 6.9 + - - +
274I LYS 4.2 0.2 - - - +
276I TRP* 1.3 85.0 - - + +
278I ALA* 1.3 62.8 + - - +
279I LYS 3.2 0.2 - - - -
280I HIS 3.1 4.9 + - - -
281I SER* 2.8 31.2 + - - -
284I LEU* 4.1 13.9 - - + +
287I ILE* 4.0 26.7 - - + +
288I GLN* 4.7 1.8 - - - -
289I THR* 3.5 34.3 - - + +
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Residues in contact with ALA 278 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274I LYS* 2.9 25.5 + - + +
275I LYS* 3.5 7.8 + - - +
277I VAL* 1.3 78.0 - - - +
279I LYS* 1.3 61.3 + - - +
280I HIS 3.0 1.4 + - - -
281I SER* 3.1 22.4 + - - -
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Residues in contact with LYS 279 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209I ASP* 3.6 28.0 - - - +
275I LYS 3.1 18.8 + - - +
276I TRP* 4.2 5.8 - - - +
277I VAL 3.2 0.4 - - - -
278I ALA* 1.3 76.6 - - - +
280I HIS* 1.3 76.6 + - + +
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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