Contacts of the strand formed by residues 258 - 264 (chain A) in PDB entry 3APO
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 GLY 258 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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252A ALA* 4.8 1.1 - - - -
257A VAL* 1.3 76.7 - - - +
259A TRP* 1.3 67.5 + - - -
286A LEU 4.4 5.3 + - - -
287A VAL* 4.0 5.6 - - - -
288A ASN* 2.9 24.6 + - - +
313A TYR* 4.1 8.2 + - - -
314A PHE 3.2 14.1 - - - -
316A PRO* 3.5 20.0 - - - +
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Residues in contact with TRP 259 (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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238A THR* 3.4 26.7 - - - -
240A LEU* 4.0 24.5 - - + -
248A ALA* 3.6 42.1 + - + +
249A ILE* 4.8 4.9 - - + -
252A ALA* 4.4 6.8 - - + +
257A VAL 4.2 6.3 + - - -
258A GLY* 1.3 79.3 - - - -
260A LEU* 1.3 59.3 + - - +
261A ILE* 3.6 31.9 - - + -
288A ASN* 3.4 51.6 - - + +
289A VAL 3.9 8.7 - - - -
290A GLY* 4.2 1.8 - - - -
312A ALA 3.5 2.3 - - - +
313A TYR* 3.3 6.3 - - - -
314A PHE* 2.7 46.6 + - + +
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Residues in contact with LEU 260 (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 TRP* 1.3 73.4 - - - +
261A ILE* 1.3 60.4 + - - +
271A LEU* 5.7 0.7 - - + -
279A LEU* 3.9 30.5 - - + -
283A LEU* 3.9 24.2 - - + -
287A VAL* 3.4 15.5 - - + +
288A ASN 2.8 8.6 + - - +
289A VAL* 3.4 12.8 - - + +
290A GLY 2.9 26.0 + - - +
311A THR* 3.7 26.2 - - + -
312A ALA 3.5 8.3 - - - +
313A TYR* 4.0 6.3 - - + +
331A LEU* 5.1 2.0 - - + -
339A ILE* 4.0 11.7 - - + -
343A ILE* 3.9 24.2 - - + -
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Residues in contact with ILE 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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240A LEU* 3.7 24.7 - - + -
245A PHE* 3.7 22.7 - - + -
248A ALA* 5.8 1.1 - - + -
249A ILE* 4.8 2.5 - - + -
259A TRP* 3.6 29.8 - - + -
260A LEU* 1.3 80.9 - - - +
262A THR* 1.3 73.7 + - - +
263A PHE* 3.6 23.4 - - + -
290A GLY 3.5 7.9 - - - +
291A TRP* 4.1 3.1 - - - +
292A VAL* 3.8 19.1 - - + -
311A THR* 3.4 4.5 - - - -
312A ALA 2.8 35.5 + - - +
314A PHE* 4.1 7.6 - - + -
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Residues in contact with THR 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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261A ILE* 1.3 75.7 - - - +
263A PHE* 1.3 61.9 + - - +
264A CYS* 4.0 13.0 + - - -
270A CYS* 4.1 4.3 - - - +
271A LEU* 3.3 33.4 + - + +
276A ARG* 4.0 17.5 - - - +
290A GLY 3.2 6.5 + - - +
291A TRP* 3.3 20.4 - - + -
292A VAL 2.9 26.3 + - - +
310A THR 3.7 4.8 + - - -
311A THR* 2.8 23.8 + - - +
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Residues in contact with PHE 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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245A PHE* 3.9 26.7 - + - -
261A ILE* 3.6 24.9 - - + -
262A THR* 1.3 74.6 + - - +
264A CYS* 1.3 61.5 + - - +
265A SER* 4.1 1.7 + - - -
269A ASP 5.5 0.2 - - - +
270A CYS* 4.2 4.5 - - - +
292A VAL* 3.6 35.2 - - + -
294A CYS* 3.7 10.8 - - - -
300A LEU* 4.8 4.9 - - + -
301A CYS* 3.8 12.6 - - - -
304A LEU* 4.2 26.0 - - + -
310A THR* 2.9 49.1 + - + +
312A ALA* 4.3 15.9 - - + -
314A PHE* 4.4 7.0 - + - -
320A LEU* 4.6 9.2 - - + -
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Residues in contact with CYS 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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262A THR* 4.0 18.6 - - - -
263A PHE* 1.3 73.1 - - - +
265A SER* 1.3 58.1 + - - +
268A GLU* 6.3 0.2 - - - -
270A CYS* 3.0 43.3 - - - -
271A LEU 5.1 0.4 - - - -
276A ARG* 5.7 1.8 - - - -
291A TRP* 4.2 18.4 - - + -
292A VAL 2.9 15.9 + - - +
293A ASP* 3.5 8.8 - - - +
294A CYS* 2.6 31.3 + - - -
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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