Contacts of the strand formed by residues 265 - 274 (chain A) in PDB entry 4N22
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 LEU 265 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A TRP* 3.8 25.1 - - + +
208A ASP* 4.2 4.7 - - - +
262A PHE* 3.5 8.7 - - - -
263A SER* 3.2 17.5 + - - +
264A GLY* 1.3 79.1 - - - +
266A VAL* 1.3 66.4 + - - +
291A ILE* 4.2 10.8 - - + -
292A PHE 3.2 6.5 - - - +
293A ARG* 3.6 53.4 - - + +
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Residues in contact with VAL 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151A LEU* 4.1 5.8 - - + -
208A ASP* 3.7 15.5 - - + +
211A LYS* 3.6 30.7 - - + -
212A VAL* 3.4 26.5 - - + -
262A PHE* 3.9 12.1 - - + -
264A GLY 4.7 0.2 - - - +
265A LEU* 1.3 79.7 - - - +
267A SER* 1.3 65.3 + - - +
268A ILE* 5.5 1.6 - - + -
291A ILE* 3.4 6.6 - - - +
292A PHE* 2.9 58.1 + - + +
294A ILE* 4.5 4.9 - - + -
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Residues in contact with SER 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ILE* 3.6 17.2 - - - +
205A SER 5.0 0.5 + - - -
208A ASP* 3.2 18.2 + - - +
212A VAL* 5.7 0.5 - - - +
266A VAL* 1.3 74.9 - - - +
268A ILE* 1.3 71.5 + - - +
269A HIS* 3.8 25.2 - - - -
289A THR* 4.5 0.2 - - - +
290A VAL 3.5 4.3 - - - -
291A ILE* 2.9 26.4 - - - +
292A PHE* 6.0 0.2 - - - -
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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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120A LEU* 3.8 2.6 - - + +
184A MET* 3.8 37.9 - - + -
202A LEU* 4.1 19.1 - - + -
203A TYR 3.8 9.6 - - - +
204A ILE* 4.0 11.9 - - + -
212A VAL* 5.5 5.6 - - + -
214A VAL* 4.0 18.8 - - + -
230A LEU* 4.5 3.6 - - + -
252A VAL* 4.1 9.6 - - + -
266A VAL* 5.5 3.4 - - + -
267A SER* 1.3 81.2 - - - +
269A HIS* 1.3 63.9 + - - +
289A THR* 3.5 3.6 - - - +
290A VAL* 3.0 40.6 + - + +
292A PHE* 3.9 21.5 - - + -
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Residues in contact with HIS 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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120A LEU* 4.1 4.0 - - - -
202A LEU* 3.3 7.3 - - - +
203A TYR* 2.8 80.9 + + + +
204A ILE* 4.7 5.8 - - - -
205A SER* 5.2 3.2 + - - -
267A SER* 3.8 20.1 + - - -
268A ILE* 1.3 76.8 - - - +
270A VAL* 1.3 60.3 - - - +
287A THR* 4.2 6.3 - - + +
288A ASP 3.4 5.2 - - - +
289A THR* 2.6 41.2 + - + +
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Residues in contact with VAL 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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118A ILE* 4.5 9.9 - - + -
120A LEU* 3.8 16.1 - - + +
186A LEU* 4.0 21.5 - - + -
200A ILE* 3.4 33.7 - - + -
201A VAL 3.3 10.3 - - - +
202A LEU* 4.0 14.4 - - + +
239A VAL* 5.2 0.4 - - + -
269A HIS* 1.3 74.6 - - - +
271A SER* 1.3 63.9 + - - +
286A PHE* 5.0 1.6 - - + -
287A THR* 3.3 3.8 - - - +
288A ASP* 2.9 55.2 + - + +
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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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118A ILE* 6.4 0.9 - - - -
200A ILE* 3.4 5.0 - - - +
201A VAL* 2.9 35.0 + - - +
203A TYR* 3.4 25.1 + - - -
270A VAL* 1.3 75.3 - - - +
272A LEU* 1.3 60.3 + - - +
273A LEU* 3.7 24.2 + - - -
284A PRO* 4.4 4.6 - - - +
286A PHE* 3.1 8.1 - - - -
287A THR* 2.7 24.9 + - - +
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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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18A VAL* 3.5 25.8 - - + -
20A VAL* 4.1 11.7 - - + -
116A ILE* 4.2 6.5 - - + -
118A ILE* 4.1 17.1 - - + +
194A LEU* 4.4 7.4 - - + -
198A TYR* 4.2 21.5 - - + -
199A GLU 3.6 13.0 - - - +
200A ILE* 3.9 18.8 - - + +
271A SER* 1.3 70.7 - - - +
273A LEU* 1.3 59.8 + - - +
284A PRO* 3.6 2.9 - - - +
285A ILE* 2.9 56.3 + - + +
286A PHE* 2.9 19.0 + - + +
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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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197A GLY 3.8 0.2 - - - +
198A TYR* 3.3 10.9 - - - -
199A GLU* 2.9 41.6 + - + +
201A VAL* 3.4 34.8 - - + -
271A SER* 4.1 14.1 - - - +
272A LEU* 1.3 73.9 - - - +
274A GLU* 1.3 60.9 + - - +
275A TYR 4.1 0.2 + - - -
282A LEU* 3.9 28.8 - - + +
283A THR 3.2 2.0 - - - -
284A PRO* 3.6 36.1 - - + -
285A ILE* 5.3 0.2 - - - -
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Residues in contact with GLU 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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5A ARG* 5.2 3.1 + - - -
197A GLY* 3.3 6.1 - - - +
198A TYR* 3.7 33.5 + - + -
273A LEU* 1.3 72.7 - - - +
275A TYR* 1.3 74.3 + - - +
276A MET* 3.4 21.9 + - - +
282A LEU* 3.3 7.0 - - - -
283A THR* 2.7 43.1 + - - +
285A ILE* 3.6 20.1 - - + +
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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