Contacts of the helix formed by residues 260 - 272 (chain A) in PDB entry 5M7R
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 PRO 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A PRO* 3.9 10.3 - - + -
258A GLU* 3.6 17.7 - - + +
259A ILE* 1.4 88.4 - - - +
261A VAL* 1.3 65.6 + - - +
262A GLU* 3.5 21.3 - - + +
263A SER* 3.0 35.0 + - - +
264A ILE* 3.4 6.2 + - - +
300A SER* 6.4 0.7 - - - -
303A LEU* 4.1 0.7 - - - -
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Residues in contact with VAL 261 (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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259A ILE 3.8 0.6 + - - -
260A PRO* 1.3 72.3 - - - +
262A GLU* 1.3 62.6 + - - +
264A ILE* 3.1 7.3 + - - +
265A GLU* 3.0 29.7 + - - +
300A SER* 4.5 12.6 - - - +
302A GLU* 4.4 23.8 - - + +
303A LEU* 3.8 16.4 - - + -
306A ARG* 3.4 36.1 + - - +
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Residues in contact with GLU 262 (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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260A PRO* 3.5 20.8 - - + +
261A VAL* 1.3 79.0 + - - +
263A SER* 1.3 62.6 + - - +
265A GLU* 3.7 20.0 - - - +
266A GLU* 2.8 31.2 + - - +
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Residues in contact with SER 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228A VAL* 5.4 1.4 - - - +
249A TRP* 4.8 6.8 + - - -
252A PRO* 4.0 21.8 - - - +
259A ILE* 4.2 1.7 - - - +
260A PRO* 3.0 36.9 + - - +
262A GLU* 1.3 82.0 - - - +
264A ILE* 1.3 63.5 + - - +
266A GLU* 3.7 13.3 - - - +
267A VAL* 3.2 27.5 + - - +
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Residues in contact with ILE 264 (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 TRP* 3.8 28.7 - - + +
259A ILE* 3.8 24.0 - - + -
260A PRO 3.9 0.9 - - - +
261A VAL 3.1 8.2 + - - +
263A SER* 1.3 78.1 + - - +
265A GLU* 1.3 59.6 + - - +
266A GLU 3.3 0.2 - - - -
267A VAL* 3.6 3.7 - - + +
268A SER* 2.9 40.6 + - - +
275A PRO* 4.3 4.3 - - + -
277A ILE* 4.1 12.6 - - + -
303A LEU* 3.6 26.0 - - + -
306A ARG* 3.8 34.5 - - + +
307A LEU* 4.0 11.7 - - + -
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Residues in contact with GLU 265 (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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261A VAL* 3.0 21.2 + - - +
262A GLU* 3.7 22.7 - - - +
264A ILE* 1.3 71.0 - - - +
266A GLU* 1.3 68.8 + - - +
268A SER* 3.3 5.8 + - - -
269A LYS* 3.1 36.2 + - + +
306A ARG* 2.8 42.0 + - + +
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Residues in contact with GLU 266 (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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227A ASN* 5.2 1.0 - - - +
228A VAL* 3.8 32.0 + - + +
229A SER* 3.8 27.1 + - - -
262A GLU 2.8 20.8 + - - +
263A SER* 3.7 12.3 - - - +
265A GLU* 1.3 74.5 - - - +
267A VAL* 1.3 63.6 + - - +
269A LYS* 3.3 15.4 + - - +
270A ILE* 3.7 10.7 + - - +
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Residues in contact with VAL 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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228A VAL* 3.8 13.9 - - + -
234A LEU* 4.3 4.5 - - + -
249A TRP* 3.7 59.9 - - + +
263A SER 3.2 18.9 + - - +
264A ILE* 3.6 12.6 - - + +
266A GLU* 1.3 78.8 - - - +
268A SER* 1.3 67.0 + - - +
269A LYS 3.1 0.9 + - - -
270A ILE* 3.2 2.9 + - + +
271A ILE* 3.1 46.5 + - + +
275A PRO* 4.5 9.2 - - + -
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Residues in contact with SER 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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264A ILE* 2.9 27.7 + - - +
265A GLU* 3.3 7.2 + - - -
267A VAL* 1.3 77.6 - - - +
269A LYS* 1.3 59.9 + - - +
271A ILE* 4.0 1.1 - - - -
272A LYS* 2.8 28.1 + - - -
273A ARG 3.3 25.5 + - - -
274A ALA* 3.7 5.4 - - - +
275A PRO* 3.4 15.1 - - - +
306A ARG* 4.3 2.4 + - - +
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Residues in contact with LYS 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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265A GLU* 3.1 27.3 + - - +
266A GLU* 3.9 7.4 - - - +
267A VAL 3.1 1.2 + - - -
268A SER* 1.3 80.7 - - - +
270A ILE* 1.3 60.2 + - - +
272A LYS* 3.6 20.1 + - - +
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Residues in contact with ILE 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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228A VAL* 3.8 21.8 - - + +
229A SER* 3.4 28.0 - - - +
231A SER 3.8 21.3 - - - +
234A LEU* 3.4 22.0 - - + +
235A ARG* 3.7 35.3 - - + +
238A GLY* 3.4 16.1 - - - -
266A GLU 3.7 9.4 + - - +
267A VAL* 3.5 13.0 - - - +
269A LYS* 1.3 75.7 - - - +
271A ILE* 1.3 64.1 + - - +
272A LYS* 3.7 9.1 - - - +
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Residues in contact with ILE 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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234A LEU* 3.8 31.0 - - + +
237A VAL* 4.5 14.8 - - + -
238A GLY* 3.4 8.0 - - - +
247A VAL* 4.1 25.4 - - + -
267A VAL* 3.1 32.0 + - + +
268A SER* 4.6 0.2 - - - -
270A ILE* 1.3 76.6 - - + +
272A LYS* 1.3 59.4 + - - +
273A ARG* 2.6 66.8 + - - +
275A PRO* 4.1 25.1 - - + -
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Residues in contact with LYS 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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235A ARG* 5.4 6.2 - - - +
238A GLY 3.7 23.1 - - - +
239A GLU* 4.7 17.8 + - - +
268A SER 2.8 17.2 + - - -
269A LYS* 3.6 14.6 + - - +
270A ILE* 3.3 12.7 - - - +
271A ILE* 1.3 79.7 - - - +
273A ARG* 1.3 63.6 + - - +
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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