Contacts of the helix formed by residues 263 - 273 (chain A) in PDB entry 4EF5
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 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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163A TYR* 4.2 6.6 - - - -
208A VAL* 5.6 5.4 - - - -
261A TYR* 3.0 9.8 + - - -
262A ALA* 1.3 71.6 - - - +
264A PRO* 1.4 63.0 - - - +
265A LEU 3.0 0.2 - - - -
266A GLN* 2.8 35.5 + - + +
267A THR* 3.9 1.6 + - - -
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Residues in contact with PRO 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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159A LEU* 3.9 24.8 - - + +
163A TYR* 3.6 36.6 - - + -
262A ALA* 3.3 7.9 - - + -
263A THR* 1.4 91.2 - - - +
265A LEU* 1.3 57.0 + - - +
266A GLN 3.1 0.4 - - - -
267A THR* 3.0 33.3 + - - +
268A LEU* 3.3 4.5 + - - +
291A PHE* 3.6 28.9 - - + -
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Residues in contact with LEU 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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201A LEU 4.4 2.5 - - - +
202A LEU* 3.7 29.4 - - + -
203A PRO* 3.6 28.9 - - + +
204A LEU* 6.2 0.4 - - + -
206A CYS* 3.4 30.4 - - - +
208A VAL* 4.4 7.2 - - + -
262A ALA* 3.5 19.5 - - + +
263A THR 2.9 1.0 + - - -
264A PRO* 1.3 76.6 - - - +
266A GLN* 1.3 58.0 + - - +
268A LEU* 3.3 22.3 + - + +
269A PHE* 3.0 22.3 + - - +
288A ALA* 4.5 11.0 - - + +
291A PHE* 4.0 24.7 - - + -
292A CYS* 5.8 0.7 - - - -
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Residues in contact with GLN 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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206A CYS 4.6 4.2 - - - +
208A VAL* 4.3 30.6 + - + +
263A THR* 2.8 21.0 + - + +
265A LEU* 1.3 79.0 - - - +
267A THR* 1.3 56.4 + - - +
269A PHE* 3.3 25.5 + - - +
270A ALA* 2.8 36.2 + - + +
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Residues in contact with THR 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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155A VAL* 5.7 0.9 - - + -
159A LEU* 4.3 26.0 - - + +
263A THR* 3.9 0.9 + - - +
264A PRO* 3.0 17.9 + - - +
266A GLN* 1.3 77.4 - - - +
268A LEU* 1.3 60.7 + - - +
270A ALA* 3.4 6.1 + - - +
271A MET* 3.0 43.0 + - + +
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Residues in contact with LEU 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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155A VAL* 3.5 32.1 - - + -
156A ALA* 5.1 0.9 - - + +
159A LEU* 3.5 22.9 - - + -
206A CYS* 3.9 10.1 - - - -
264A PRO 3.3 4.0 + - - +
265A LEU* 3.3 23.3 + - + +
267A THR* 1.3 77.9 - - - +
269A PHE* 1.3 63.2 + - - +
271A MET* 3.5 7.9 + - - +
272A SER* 3.1 21.1 + - - -
279A PHE* 3.7 9.2 - - + -
284A ARG* 3.7 13.0 - - + +
287A GLN* 3.8 13.2 - - + +
288A ALA* 3.6 33.4 - - - +
291A PHE* 4.8 3.6 - - + -
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Residues in contact with PHE 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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205A ASP 4.4 4.7 - - - -
206A CYS* 3.7 27.1 - - + +
207A GLY* 5.8 3.1 - - - -
265A LEU 3.0 8.4 + - - +
266A GLN* 3.6 24.9 - - - +
267A THR 3.2 0.2 - - - -
268A LEU* 1.3 75.2 - - - +
270A ALA* 1.3 67.1 + - - +
272A SER* 3.0 19.9 - - - -
273A GLN* 3.3 43.8 + - + +
284A ARG* 3.6 34.3 - - - +
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Residues in contact with ALA 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 GLN* 2.8 29.4 + - + +
267A THR* 4.0 6.3 - - - +
269A PHE* 1.3 76.4 - - - +
271A MET* 1.3 60.7 + - + +
273A GLN* 3.2 8.4 + - - +
274A TYR* 3.2 23.1 + - - +
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Residues in contact with MET 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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153A PHE* 4.0 20.6 - - + -
155A VAL* 4.0 29.4 - - + -
267A THR* 3.0 31.6 + - + +
268A LEU* 3.7 9.2 - - - +
270A ALA* 1.3 73.0 - - - +
272A SER* 1.3 64.8 + - - +
274A TYR* 3.2 29.2 + - + +
277A ALA* 4.0 12.0 - - + +
279A PHE* 3.7 44.9 - - + +
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Residues in contact with SER 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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268A LEU 3.1 9.2 + - - -
269A PHE 3.0 14.3 + - - -
271A MET* 1.3 79.1 - - - +
273A GLN* 1.3 59.6 + - - +
274A TYR 3.3 2.1 + - - +
279A PHE* 3.6 20.0 - - - +
280A SER* 3.9 17.8 + - - -
281A ARG* 4.2 5.5 - - - -
284A ARG* 3.0 42.0 + - - +
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Residues in contact with GLN 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 PHE* 3.5 46.6 - - + +
270A ALA* 3.2 9.8 + - - +
271A MET 3.2 0.8 - - - -
272A SER* 1.3 79.0 - - - +
274A TYR* 1.3 59.9 + - - +
275A SER* 3.8 2.8 + - - -
284A ARG* 5.7 0.7 - - - +
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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