Contacts of the helix formed by residues 262 - 273 (chain B) in PDB entry 3ENM
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 THR 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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224A ARG 3.8 12.1 + - - -
225A ILE* 2.8 29.7 + - - +
227A PRO* 3.8 8.3 - - - +
261B GLY* 1.3 74.8 - - - +
263B PRO* 1.3 69.6 - - + +
264B PHE* 3.0 13.2 - - + +
265B GLN* 3.0 37.1 + - + +
266B GLN* 2.7 28.6 + - - +
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Residues in contact with PRO 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267A LEU* 5.5 2.0 - - + -
217B LYS* 4.2 21.2 + - - +
261B GLY 4.6 1.3 - - - +
262B THR* 1.3 87.3 - - + +
264B PHE* 1.3 64.6 + - - +
266B GLN* 3.3 10.8 + - - +
267B LEU* 2.9 34.2 + - + +
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Residues in contact with PHE 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ILE* 3.5 30.1 - - + +
226A ASN* 4.1 18.8 - - + -
264A PHE* 3.5 28.0 - + - -
267A LEU* 3.6 33.8 - - + +
268A LYS* 3.5 34.3 - - + -
271A VAL* 4.2 13.5 - - + -
272A GLU* 5.3 2.2 - - - -
262B THR* 3.0 10.2 - - + +
263B PRO* 1.3 78.5 - - - +
265B GLN* 1.3 57.8 + - + +
267B LEU* 3.0 8.6 + - - +
268B LYS* 2.8 60.2 + - + +
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Residues in contact with GLN 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225A ILE 4.1 1.8 - - - +
226A ASN* 2.8 30.3 - - - +
227A PRO* 2.8 38.1 + - - +
260B TRP 4.7 2.0 - - - +
261B GLY* 3.6 12.4 - - - -
262B THR* 3.0 38.8 + - + +
264B PHE* 1.3 76.5 - - + +
266B GLN* 1.3 63.2 + - - +
268B LYS* 3.3 11.8 + - + +
269B GLN* 3.2 21.0 + - - +
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Residues in contact with GLN 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217B LYS* 2.6 54.8 - - - +
218B PRO* 4.4 8.5 - - + +
258B ASP* 4.7 3.8 - - - +
259B SER* 3.9 27.8 + - - -
260B TRP 3.5 14.6 - - - +
261B GLY 2.8 23.2 + - - -
262B THR 2.7 19.8 + - - +
263B PRO* 3.7 5.4 - - - +
265B GLN* 1.3 70.9 - - - +
267B LEU* 1.3 68.4 + - - +
269B GLN* 3.4 17.5 + - - +
270B VAL* 3.5 16.1 + - - +
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Residues in contact with LEU 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263A PRO* 5.7 2.0 - - + -
264A PHE* 3.8 35.9 - - + +
267A LEU* 5.8 3.6 - - + -
217B LYS* 4.9 8.3 - - - +
218B PRO* 4.0 20.0 - - + -
220B MSE 4.4 10.3 - - + -
225B ILE* 3.7 30.3 - - + +
263B PRO* 2.9 26.3 + - + +
264B PHE* 3.5 4.9 - - - +
266B GLN* 1.3 78.0 - - - +
268B LYS* 1.3 64.4 + - - +
270B VAL* 3.2 12.2 + - - +
271B VAL* 3.2 17.1 + - - +
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Residues in contact with LYS 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ASN* 4.9 12.1 + - - +
264A PHE* 3.8 20.3 - - + -
272A GLU* 5.9 1.7 + - - -
264B PHE* 2.8 43.4 + - + +
265B GLN* 3.4 19.1 - - + +
267B LEU* 1.3 76.1 - - - +
269B GLN* 1.3 66.4 + - - +
271B VAL* 2.9 5.1 + - - -
272B GLU* 2.7 61.3 + - - +
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Residues in contact with GLN 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B TYR* 3.6 30.2 - - + +
258B ASP* 2.5 55.2 + - - +
265B GLN 3.2 13.1 + - - +
266B GLN* 3.6 14.4 - - - +
267B LEU 3.3 0.4 - - - -
268B LYS* 1.3 74.9 - - - +
270B VAL* 1.3 58.9 + - - +
272B GLU* 5.2 0.2 - - - -
273B GLU* 2.8 73.0 + - + +
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Residues in contact with VAL 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B PRO* 3.9 25.4 - - + +
220B MSE 3.9 12.1 - - - +
222B PRO* 4.1 9.2 - - + +
225B ILE* 3.8 19.3 - - + -
241B TRP* 4.2 10.1 - - + +
257B TYR* 3.7 46.7 + - + +
266B GLN 3.5 12.8 + - - +
267B LEU 3.2 7.1 + - - +
268B LYS 3.0 0.8 - - - -
269B GLN* 1.3 79.4 - - - +
271B VAL* 1.3 64.6 + - - +
273B GLU 3.8 2.1 - - - +
297B LYS* 3.6 15.2 + - - +
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Residues in contact with VAL 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A PHE* 3.9 19.3 - - + -
222B PRO* 4.5 14.1 - - + +
225B ILE* 3.5 30.3 - - + -
226B ASN* 4.2 24.5 - - + +
267B LEU 3.3 15.5 - - - +
268B LYS 2.9 1.7 + - - +
270B VAL* 1.3 77.2 - - - +
272B GLU* 1.3 76.4 + - + +
297B LYS* 2.8 20.1 + - - -
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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264A PHE* 5.5 2.6 - - - -
268A LYS* 5.8 2.8 - - - +
272A GLU* 5.1 5.9 - - - +
268B LYS* 2.7 55.1 + - + +
271B VAL* 1.3 89.2 - - + +
273B GLU* 1.3 68.0 + - + +
274B PRO* 4.6 0.5 - - - +
297B LYS* 3.6 3.7 + - - -
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257B TYR* 5.3 1.0 + - + -
269B GLN* 2.8 62.7 + - + +
270B VAL* 3.8 5.2 - - - +
272B GLU* 1.3 78.0 - - + +
274B PRO* 1.3 79.4 - - + +
297B LYS* 2.5 27.2 + - - +
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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