Contacts of the strand formed by residues 254 - 262 (chain A) in PDB entry 3O8E
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 TYR 254 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A GLU* 3.2 59.6 + - + +
251A LYS* 3.5 16.6 + - - +
252A GLU 3.3 6.2 - - - +
253A ASN* 1.3 83.3 - - + +
255A ILE* 1.3 67.3 + - - +
256A TYR* 3.5 38.9 - + + +
274A SER* 6.4 1.3 - - - -
275A VAL 3.4 6.7 - - - -
276A MET* 3.7 24.5 - - + -
279A ARG* 4.4 9.1 + - + +
113B VAL* 3.7 40.0 - - + +
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Residues in contact with ILE 255 (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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242A TYR* 5.0 5.2 - - + +
252A GLU 5.9 0.2 - - - +
254A TYR* 1.3 77.8 - - - +
256A TYR* 1.3 74.0 + - - +
273A ILE 4.0 0.2 - - - +
274A SER* 3.8 0.2 - - - -
275A VAL* 2.7 54.8 + - + +
277A LEU* 3.6 26.9 - - + -
316A PHE* 4.6 2.9 - - + -
318A PHE* 3.9 29.8 - - + -
319A TYR 3.3 28.3 - - - +
320A TYR* 4.6 0.4 - - + -
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Residues in contact with TYR 256 (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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254A TYR* 3.5 44.7 - + + +
255A ILE* 1.3 83.9 - - - +
257A GLY* 1.3 56.8 + - - +
273A ILE* 3.3 7.4 - - - +
274A SER* 4.0 25.8 - - - -
275A VAL 5.5 0.2 - - - -
316A PHE* 4.6 5.5 - - - -
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Residues in contact with GLY 257 (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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256A TYR* 1.3 74.8 - - - +
258A THR* 1.3 67.0 + - - -
272A ASP* 3.8 3.5 - - - +
273A ILE* 2.9 34.7 + - - +
316A PHE* 3.6 20.8 - - - -
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Residues in contact with THR 258 (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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257A GLY* 1.3 75.6 + - - -
259A CYS* 1.3 69.5 + - - +
260A TYR* 4.3 21.7 - - + +
270A PRO* 4.1 19.5 - - + -
271A ILE 3.5 13.6 + - - +
272A ASP* 4.7 8.4 + - - +
273A ILE* 3.7 5.7 - - - +
316A PHE* 4.0 12.0 - - - +
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Residues in contact with CYS 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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258A THR* 1.3 73.4 - - - +
260A TYR* 1.3 69.3 + - - +
270A PRO* 3.6 1.2 - - - +
271A ILE* 2.8 46.3 + - - -
273A ILE* 3.4 13.6 - - + +
294A TRP* 3.6 31.4 - - - -
313A THR* 3.8 17.7 - - - -
314A SER* 3.4 24.5 - - - +
315A PRO 5.7 0.7 - - - -
316A PHE* 4.4 5.6 - - + -
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Residues in contact with TYR 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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258A THR* 4.3 21.5 - - + +
259A CYS* 1.3 79.9 - - - +
261A TYR* 1.3 60.9 + - - +
262A THR* 4.1 3.1 + - - +
268A ALA* 3.9 29.4 - - + -
269A PHE 3.3 3.4 - - - -
270A PRO* 3.7 33.4 - - + +
271A ILE* 4.7 3.8 - - - -
312A VAL 4.1 0.7 - - - +
313A THR* 3.7 1.4 - - - -
314A SER* 2.7 46.7 + - - +
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Residues in contact with TYR 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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186A THR* 3.6 22.2 + - + +
260A TYR* 1.3 73.4 - - - +
262A THR* 1.3 69.1 + - - +
263A ALA* 3.2 25.8 + - + -
267A THR 3.4 1.0 - - - +
268A ALA* 3.5 2.4 - - - -
269A PHE* 2.8 43.7 + - + +
271A ILE* 3.7 20.4 - - + -
302A PRO* 4.0 19.7 - - + -
303A GLU* 3.1 34.7 + - + +
309A THR* 4.9 6.1 + - - -
310A THR 3.6 25.8 + - - -
311A LEU* 4.0 10.1 - - + -
312A VAL* 3.3 30.3 - - + +
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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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260A TYR* 4.1 3.5 + - - +
261A TYR* 1.3 85.5 + - - +
263A ALA* 1.3 68.7 + - - +
266A ARG* 4.6 20.6 - - + +
267A THR 3.9 4.7 - - - +
268A ALA* 4.9 3.5 - - - +
312A VAL 4.5 2.8 + - - -
314A SER* 6.2 0.3 - - - -
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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