Contacts of the helix formed by residues 261 - 268 (chain A) in PDB entry 4I7C
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 261 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ASN* 5.4 2.0 - - - +
195A LYS* 3.9 13.7 - - - +
203A GLN* 3.2 43.6 + - + +
205A PHE* 3.8 22.9 - - + -
260A ASP* 1.3 74.3 - - - +
262A SER* 1.3 61.9 + - - +
264A ALA* 3.2 14.6 - - - +
265A GLN* 3.2 23.2 + - - +
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Residues in contact with SER 262 (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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260A ASP* 2.8 8.8 + - - -
261A THR* 1.3 77.7 + - - +
263A ILE* 1.3 65.0 + - - +
265A GLN* 3.2 19.7 + - - +
266A LEU* 3.6 13.2 + - - +
252C MET 5.1 2.5 + - - -
253C ASN* 3.6 11.8 + - - +
254C SER* 2.8 29.8 + - - -
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Residues in contact with ILE 263 (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 LEU* 4.9 0.2 - - + -
234A LEU* 4.3 13.5 - - + -
258A VAL 4.8 2.5 - - - +
259A PHE* 3.6 25.6 - - + -
260A ASP* 2.7 46.5 + - - +
262A SER* 1.3 71.5 + - - +
264A ALA* 1.3 65.8 + - - +
266A LEU* 3.1 18.5 + - + +
267A PHE* 3.2 35.7 - - + -
236C TRP* 5.8 2.0 - - + -
254C SER* 3.7 24.7 - - - +
256C CYS 5.8 0.4 - - - +
258C VAL* 4.1 23.3 - - + +
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Residues in contact with ALA 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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170A ILE* 4.1 17.7 - - + -
205A PHE* 3.9 20.0 - - + -
259A PHE* 4.1 10.9 - - + -
260A ASP 3.0 13.3 + - - +
261A THR* 3.2 15.7 - - + +
263A ILE* 1.3 76.7 - - - +
265A GLN* 1.3 62.2 + - - +
267A PHE* 3.1 4.1 + - - +
268A ALA* 2.8 32.3 + - - +
273A LEU* 4.2 6.0 - - - +
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Residues in contact with GLN 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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170A ILE* 4.9 1.8 - - - +
171A ASN* 2.9 36.3 + - - +
261A THR* 3.2 27.4 + - - +
262A SER* 3.2 10.9 + - - +
263A ILE 3.2 1.2 - - - -
264A ALA* 1.3 84.3 - - - +
266A LEU* 1.3 62.9 + - + +
267A PHE 3.3 0.3 + - - -
268A ALA* 3.8 19.5 + - - +
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Residues in contact with LEU 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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229A GLY* 4.5 9.0 - - - -
230A HIS 5.5 0.3 + - - -
232A ARG* 4.3 24.0 + - - +
262A SER 3.6 10.5 + - - +
263A ILE* 3.1 12.8 + - + +
265A GLN* 1.3 78.8 - - + +
267A PHE* 1.3 72.8 + - + +
268A ALA 5.2 0.2 - - - -
236C TRP* 4.7 6.1 - - + -
253C ASN* 4.0 14.4 - - + +
254C SER 3.5 11.7 - - - +
255C ASP* 3.4 46.2 - - + +
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Residues in contact with PHE 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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227A LEU* 3.6 39.7 - - + -
228A ASN 3.4 34.8 - - - +
229A GLY* 3.6 10.5 - - - -
232A ARG* 3.8 20.6 - - + -
234A LEU* 4.2 10.1 - - + -
263A ILE* 3.2 38.4 - - + -
264A ALA* 3.1 2.5 + - - +
266A LEU* 1.3 89.0 - - + +
268A ALA* 1.3 62.7 + - - +
269A GLU* 3.7 9.8 + - - +
272A ASN 4.6 0.7 - - - +
273A LEU* 3.5 24.8 - - + +
274A GLY 5.1 2.1 + - - -
236C TRP* 3.9 27.8 - + - -
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Residues in contact with ALA 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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170A ILE* 4.5 16.8 - - + -
171A ASN* 5.9 0.2 - - - +
264A ALA 2.8 24.0 + - - +
265A GLN* 3.8 19.1 + - - +
266A LEU 5.2 0.2 - - - -
267A PHE* 1.3 74.2 - - - +
269A GLU* 1.3 65.6 + - - +
270A ASN 4.2 0.7 + - - -
271A GLY* 4.8 5.8 - - - +
272A ASN 3.3 20.6 - - - +
273A LEU* 3.9 5.6 - - + +
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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