Contacts of the strand formed by residues 247 - 260 (chain I) in PDB entry 2B4X
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 CYS 247 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237I GLU 3.2 0.7 - - - +
238I LEU* 3.0 18.1 - - - +
239I PHE* 2.9 40.2 + - - -
241I LYS* 4.0 25.1 - - - +
246I SER* 1.3 76.4 - - - +
248I SER* 1.3 61.0 + - - +
249I ALA 3.5 0.2 + - - -
428I ASN* 4.1 3.8 - - - -
430I CYS* 2.0 45.3 - - + -
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Residues in contact with SER 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236I LYS* 3.8 30.6 + - - +
237I GLU 3.9 4.3 - - - -
238I LEU* 4.9 3.6 - - - -
247I CYS* 1.3 74.0 - - - +
249I ALA* 1.3 59.5 + - - +
430I CYS* 3.3 18.8 - - - +
431I VAL* 4.0 5.7 + - - +
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Residues in contact with ALA 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236I LYS* 3.2 5.9 - - - -
237I GLU* 2.6 45.2 + - - +
239I PHE* 4.2 7.2 - - + -
247I CYS 3.5 0.2 + - - -
248I SER* 1.3 74.8 - - - +
250I SER* 1.3 63.1 + - - +
251I MET* 3.4 5.1 + - + +
321I PRO* 4.6 9.9 - - + -
322I ARG 5.7 0.4 - - - +
429I PRO* 3.9 22.0 - - + -
430I CYS* 3.8 19.5 - - - +
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Residues in contact with SER 250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234I THR* 3.9 10.1 - - - -
235I ARG 4.8 0.2 - - - -
236I LYS* 3.3 33.5 + - - +
249I ALA* 1.3 69.9 - - - +
251I MET* 1.3 60.1 + - - +
321I PRO* 4.3 1.8 - - - -
322I ARG* 3.0 68.6 + - - +
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Residues in contact with MET 251 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233I ASN 4.1 1.2 - - - +
234I THR* 3.2 3.7 - - - +
235I ARG* 3.0 46.5 + - - +
237I GLU* 3.6 43.5 - - + +
238I LEU 4.8 2.2 - - - +
239I PHE* 4.9 4.0 - - + -
249I ALA* 3.4 5.1 + - + -
250I SER* 1.3 70.7 - - - +
252I MET* 1.3 70.2 - - - +
253I TYR* 4.1 0.5 + - - +
319I HIS* 4.1 14.6 - - + -
320I MET 3.6 5.6 - - - -
321I PRO* 3.3 42.2 - - + -
403I LYS* 5.1 1.1 - - - -
404I ALA 3.8 4.7 - - - +
405I ASN* 3.8 34.1 - - + -
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Residues in contact with MET 252 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229I PHE* 3.8 27.1 - - + -
234I THR* 4.1 8.1 - - - +
251I MET* 1.3 75.7 - - - +
253I TYR* 1.3 61.0 + - - +
319I HIS* 3.5 5.9 - - - -
320I MET* 3.0 61.4 + - + +
321I PRO 4.1 8.7 - - - +
322I ARG* 3.4 24.2 - - + -
375I VAL* 4.3 13.0 - - + -
376I ASN 3.4 38.1 - - - +
377I GLU* 3.4 23.1 - - - +
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Residues in contact with TYR 253 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229I PHE* 3.8 11.2 - - - +
230I SER 4.3 2.5 + - - -
233I ASN* 3.8 51.1 + - + +
234I THR* 5.1 0.2 + - - -
235I ARG* 6.0 3.4 - - + -
251I MET 5.0 0.9 - - - +
252I MET* 1.3 77.6 - - - +
254I GLN* 1.3 76.2 + - - +
255I GLU* 2.3 40.3 + - + -
317I VAL* 3.3 23.7 - - + +
318I VAL 3.5 5.8 - - - -
319I HIS* 3.3 29.6 - + + -
288L PRO* 6.5 0.7 - - + -
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Residues in contact with GLN 254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227I SER* 2.9 40.7 + - - +
228I LYS 4.2 4.6 - - - +
229I PHE* 3.2 52.5 - - + +
230I SER 5.2 0.7 - - - +
233I ASN* 5.7 1.6 - - - +
253I TYR* 1.3 88.0 - - - +
255I GLU* 1.3 75.7 + - - +
258I PHE* 3.6 21.9 - - + -
317I VAL* 3.8 1.0 - - - +
318I VAL* 2.9 34.3 + - + +
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Residues in contact with GLU 255 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227I SER* 5.2 0.9 + - - -
253I TYR* 2.3 35.2 + - + +
254I GLN* 1.3 95.2 - - - +
256I GLY* 1.3 58.9 + - - +
258I PHE* 4.5 2.2 - - - -
316I LEU 3.3 12.8 - - - +
317I VAL* 3.6 9.2 - - + +
390I ILE* 5.0 6.8 - - - +
393I ARG* 3.9 15.3 + - - +
395I LEU* 4.3 17.2 - - + +
399I ARG* 2.8 30.5 + - - -
288L PRO* 6.1 0.3 - - - +
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Residues in contact with GLY 256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255I GLU* 1.3 78.1 - - - +
257I LYS* 1.3 65.8 - - - -
258I PHE* 3.4 14.4 - - - -
314I MET 3.3 1.2 - - - +
315I MET* 4.0 6.3 - - - -
316I LEU 3.2 23.9 + - - +
393I ARG* 4.2 13.5 - - - -
395I LEU* 4.8 5.2 - - - +
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Residues in contact with LYS 257 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227I SER* 5.8 0.9 - - - -
256I GLY* 1.3 70.8 - - - -
258I PHE* 1.3 74.0 + - - +
313I GLU* 2.9 46.6 + - + +
314I MET* 3.1 13.9 - - - +
315I MET* 4.7 3.4 - - - +
235L ARG* 6.1 2.3 - - - +
236L LYS 4.1 18.2 + - - -
237L GLU* 5.5 9.9 - - + +
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Residues in contact with PHE 258 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227I SER* 3.8 19.3 - - - -
229I PHE* 5.9 0.2 - + - -
254I GLN* 3.6 37.7 - - + -
255I GLU 4.5 0.2 - - - -
256I GLY* 3.4 26.9 - - - +
257I LYS* 1.3 85.1 - - - +
259I ARG* 1.3 64.3 + - - +
260I TYR* 3.2 8.8 + - - +
270I LEU* 3.8 17.0 - - + -
271I GLU 3.5 8.3 - - - -
272I LEU* 3.4 30.5 - - + -
273I PRO* 4.1 17.9 - - + -
313I GLU* 4.4 1.8 - - - +
314I MET 2.8 25.0 + - - +
316I LEU* 3.8 6.4 - - + +
318I VAL* 4.3 19.3 - - + -
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Residues in contact with ARG 259 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258I PHE* 1.3 71.7 - - - +
260I TYR* 1.3 58.7 + - - +
270I LEU* 3.9 2.1 - - - +
271I GLU* 2.8 84.3 + - + +
273I PRO* 6.1 0.2 - - - +
308I LEU 3.2 15.4 + - - -
309I ASP 5.2 1.8 + - - -
311I LEU* 3.1 53.8 + - + +
312I GLU 3.3 6.3 - - - +
313I GLU* 4.0 22.2 - - + +
413I ARG* 5.0 2.4 - - - +
415I VAL* 6.1 2.0 - - - +
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Residues in contact with TYR 260 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258I PHE 3.7 1.1 - - - +
259I ARG* 1.3 75.1 - - - +
261I ARG* 1.3 107.9 + - - +
262I ARG* 3.7 17.4 + - + +
268I GLN* 2.5 48.1 + - + +
269I VAL 3.4 16.4 - - - -
270I LEU* 4.7 2.9 - - + -
311I LEU* 3.3 5.8 - - - +
312I GLU 2.9 28.8 + - - +
314I MET* 4.7 8.7 - - + -
316I LEU* 3.6 32.5 - - + -
400I VAL* 3.2 33.8 - - + +
402I PHE* 4.1 14.8 - + + -
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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