Contacts of the helix formed by residues 265 - 274 (chain A) in PDB entry 2I91
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 SER 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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241A GLU* 2.3 35.9 + - - -
261A ILE 5.0 0.2 + - - -
262A HIS* 3.1 6.8 + - - -
264A LYS* 1.3 78.0 - - - +
266A LYS* 1.3 64.6 + - - +
267A GLU* 3.3 3.8 + - - +
268A ILE* 3.0 28.8 + - - +
269A TRP* 3.3 16.5 - - - -
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Residues in contact with LYS 266 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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264A LYS 3.7 4.8 + - - -
265A SER* 1.3 72.2 + - - +
267A GLU* 1.3 76.5 + - + +
269A TRP* 3.4 8.4 + - - +
270A LYS* 3.1 41.4 + - - +
291A ASP* 3.7 19.7 + - + +
292A SER* 3.6 33.3 + - - -
293A VAL* 4.5 12.6 - - - +
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Residues in contact with GLU 267 (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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241A GLU* 4.3 5.2 - - - +
245A ILE* 3.9 23.8 - - + +
265A SER* 3.2 6.5 + - - +
266A LYS* 1.3 87.5 - - + +
268A ILE* 1.3 65.9 + - - +
270A LYS* 3.4 34.5 + - - +
271A SER* 3.1 22.0 + - - -
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Residues in contact with ILE 268 (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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241A GLU* 3.4 23.6 - - + +
244A ILE* 3.7 30.1 - - + -
245A ILE* 4.4 8.3 - - + -
248A ILE* 4.5 2.2 - - + -
258A LEU* 3.3 30.5 - - + -
262A HIS* 3.4 20.6 - - + +
263A LEU* 4.6 3.4 - - + -
265A SER* 3.0 31.2 + - - +
267A GLU* 1.3 75.8 - - - +
269A TRP* 1.3 53.0 + - + +
271A SER* 3.0 12.1 + - - -
272A LEU* 2.6 38.7 + - + +
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Residues in contact with TRP 269 (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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255A ARG* 3.7 26.0 - - + -
263A LEU* 3.1 51.1 + - + +
264A LYS 5.1 0.7 - - - -
265A SER 3.3 24.0 - - - -
266A LYS* 3.4 7.3 + - - +
267A GLU 3.3 0.2 - - - -
268A ILE* 1.3 78.9 - - + +
270A LYS* 1.3 53.0 + - - +
271A SER 2.8 5.2 - - - -
272A LEU* 3.4 10.9 - - + +
273A LEU* 2.5 37.4 + - - +
276A MET* 4.2 9.4 - - + +
284A ASN* 3.9 22.9 - - + -
287A LYS* 3.5 30.4 - - + +
288A MET* 3.3 39.3 - - + -
291A ASP* 5.7 4.3 - - - -
293A VAL* 4.4 22.4 - - + -
6D G 5.4 0.7 - - - -
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Residues in contact with LYS 270 (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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266A LYS* 3.1 42.4 + - + +
267A GLU* 3.6 35.8 + - - +
269A TRP* 1.3 75.8 - - - +
271A SER* 1.3 58.6 + - - +
273A LEU* 4.0 8.1 - - - +
274A GLN* 3.8 19.4 + - - +
292A SER 5.0 1.3 - - - -
293A VAL* 4.5 20.4 - - + +
300A GLU* 3.1 32.6 + - + +
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Residues in contact with SER 271 (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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245A ILE* 4.0 27.0 + - - +
248A ILE* 3.5 36.0 - - - +
249A ASP* 4.1 4.8 + - - +
267A GLU 3.1 12.7 + - - -
268A ILE* 3.0 11.6 + - - -
270A LYS* 1.3 79.3 - - - +
272A LEU* 1.3 60.9 + - - +
273A LEU 3.4 0.4 - - - -
274A GLN* 3.6 23.5 + - - +
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Residues in contact with LEU 272 (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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248A ILE* 3.7 28.0 - - + -
253A LEU 4.0 17.5 - - - +
254A VAL* 4.3 1.1 - - - -
255A ARG* 4.1 31.4 - - + +
258A LEU* 3.8 22.7 - - + -
263A LEU* 4.2 11.2 - - + -
268A ILE* 2.6 19.2 + - + +
269A TRP* 2.8 18.6 + - + +
271A SER* 1.3 78.1 - - - +
273A LEU* 1.3 62.0 + - - +
274A GLN 3.6 0.2 + - - -
275A ASP 4.1 1.2 + - - -
276A MET* 3.0 35.3 + - + +
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Residues in contact with LEU 273 (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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269A TRP 2.5 19.9 + - - +
270A LYS* 4.3 6.5 - - - +
272A LEU* 1.3 74.1 - - - +
274A GLN* 1.3 68.1 + - - +
275A ASP 2.9 1.7 + - - -
276A MET* 3.0 20.1 + - + +
281A LEU* 3.8 30.5 - - + -
288A MET* 3.8 18.8 - - + -
293A VAL* 4.7 7.9 - - + -
294A LEU* 4.4 7.2 - - + -
300A GLU* 3.8 42.4 - - + +
303A SER* 5.7 3.6 - - - +
304A VAL* 3.9 9.4 - - + -
307A ARG* 3.9 6.1 + - - +
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Residues in contact with GLN 274 (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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249A ASP* 4.1 16.2 + - - -
270A LYS 3.8 14.0 + - - +
271A SER* 3.6 20.0 + - - +
272A LEU 3.4 0.2 - - - -
273A LEU* 1.3 79.0 - - - +
275A ASP* 1.3 71.8 + - + +
303A SER* 5.6 2.3 + - - -
307A ARG* 4.5 7.3 + - - -
219B SER* 3.9 8.6 - - - +
220B PRO* 3.3 42.7 - - + +
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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