Contacts of the strand formed by residues 270 - 277 (chain B) in PDB entry 3A8X
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 ILE 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B LEU* 4.4 10.3 - - + -
261B LEU* 4.1 6.1 - - + -
262B VAL 3.2 12.6 - - - +
263B ARG* 3.6 31.6 - - + +
268B ASP 4.5 0.7 - - - +
269B ARG* 1.3 73.7 - - - +
271B TYR* 1.3 74.1 + - - +
325B TYR* 3.7 37.8 + - + +
537B GLU 5.6 0.7 - - - +
538B PHE* 4.4 19.7 - - + +
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Residues in contact with TYR 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
578A PRO 4.2 4.5 + - - -
579A LEU* 4.4 5.1 + - - -
245B PHE* 4.3 9.9 - + - -
261B LEU* 3.5 5.0 - - - +
262B VAL* 2.8 37.0 + - + +
264B LEU* 4.0 17.3 - - + -
267B THR* 4.8 1.0 + - - -
269B ARG* 3.6 50.5 + - + +
270B ILE* 1.3 78.3 - - - +
272B ALA* 1.3 60.0 + - - +
310B HIS* 3.6 36.8 + + + -
322B VAL* 3.4 29.2 - - + -
323B ILE 3.4 17.5 - - - +
324B GLU* 4.9 5.4 - - + -
325B TYR* 3.8 11.2 - - - -
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B ILE* 4.1 12.1 - - + -
259B VAL* 4.1 16.4 - - + -
260B LEU 3.3 6.3 - - - +
271B TYR* 1.3 75.4 - - - +
273B MET* 1.3 61.1 + - - +
322B VAL* 3.5 3.8 - - - +
323B ILE* 2.9 51.6 + - + +
324B GLU 3.7 10.1 - - - +
325B TYR* 3.7 11.0 - - - +
326B VAL 5.3 0.7 - - - +
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Residues in contact with MET 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B LEU* 4.2 6.5 - - + -
245B PHE* 5.0 3.8 - - - -
247B LEU* 3.8 19.7 - - + -
258B LYS 3.5 1.4 - - - +
259B VAL* 3.3 5.7 - - - -
260B LEU* 2.6 40.3 + - + +
262B VAL* 3.6 36.3 - - + -
272B ALA* 1.3 76.5 - - - +
274B LYS* 1.3 61.3 + - - +
275B VAL* 3.7 12.3 - - + +
313B PHE* 4.1 19.1 - - - -
320B PHE* 3.7 40.8 - - + -
321B PHE 3.4 8.3 - - - +
322B VAL* 4.2 10.5 - - + -
554B LEU* 5.0 2.2 - - + -
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Residues in contact with LYS 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TYR* 6.2 1.6 - - - -
257B ALA* 3.5 30.1 - - + -
258B LYS 3.6 3.4 - - - +
259B VAL* 4.5 13.1 - - + +
272B ALA 4.2 0.6 - - - -
273B MET* 1.3 71.7 - - - +
275B VAL* 1.3 59.3 + - - +
276B VAL* 4.6 11.4 - - + -
289B TRP* 6.0 2.0 - - - -
293B GLU* 3.1 37.3 + - - +
297B PHE* 5.0 7.4 - - + -
319B LEU 3.7 0.7 - - - +
320B PHE* 3.4 5.2 - - - +
321B PHE* 2.8 56.8 + - + +
323B ILE* 4.6 17.6 - - + +
387B ASP* 5.0 15.4 + - - +
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TYR 4.3 0.2 - - - +
257B ALA* 3.4 6.2 - - - -
258B LYS* 2.8 41.9 + - + +
260B LEU* 3.6 29.4 - - + -
273B MET* 3.7 8.3 - - + +
274B LYS* 1.3 77.7 - - - +
276B VAL* 1.3 63.0 + - - +
277B LYS* 4.1 3.2 + - + +
318B ARG* 3.6 38.4 - - + +
319B LEU 3.4 3.6 - - - +
320B PHE* 3.7 27.1 - - + -
554B LEU* 4.5 5.4 - - + -
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Residues in contact with VAL 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TYR 4.3 12.8 - - - +
257B ALA* 4.0 17.5 - - + -
274B LYS* 4.6 10.5 - - + -
275B VAL* 1.3 78.0 - - - +
277B LYS* 1.3 74.6 + - - +
278B LYS 3.5 0.2 + - - -
280B LEU* 4.3 10.5 - - + -
281B VAL* 4.4 16.4 - - + -
289B TRP* 5.1 13.5 - - + -
290B VAL* 5.6 2.2 - - + -
318B ARG* 4.5 1.8 - - - -
319B LEU* 2.8 51.9 + - + +
321B PHE* 4.3 18.8 - - + -
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Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
256B TYR 5.0 2.0 + - - -
275B VAL* 4.1 2.4 + - + +
276B VAL* 1.3 79.2 - - - +
278B LYS* 1.3 65.0 + - - +
279B GLU* 3.2 27.1 - - + +
280B LEU* 3.1 24.4 + - + +
281B VAL* 4.2 1.2 + - - +
317B SER* 3.6 8.3 - - - +
318B ARG* 3.7 33.7 - - + +
555B TPO 2.5 39.5 + - - +
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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
------------------------------------------------------------
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