Contacts of the strand formed by residues 340 - 356 (chain A) in PDB entry 1XI1
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 340 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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292A PHE* 3.5 28.3 - + + -
293A GLU 3.5 5.8 - - - +
294A LEU* 3.6 32.1 - - + -
295A LYS* 3.0 21.3 - - - -
300A PRO 3.8 0.3 - - - -
301A THR* 2.8 29.5 + - + -
302A ILE* 2.6 51.1 + - + +
316A LEU 3.1 23.6 + - - -
317A LYS 4.4 0.9 - - - -
336A MET* 2.9 25.1 + - + +
337A LYS* 3.2 12.8 - - - +
339A HIS* 1.3 84.4 - - + +
341A ASP* 1.3 67.3 + - - +
342A LEU* 3.9 6.8 + - + +
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Residues in contact with ASP 341 (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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292A PHE* 3.1 6.4 - - - -
293A GLU* 2.8 37.9 + - + +
294A LEU 5.2 0.3 - - - +
295A LYS* 3.3 33.7 - - - +
340A TYR* 1.3 71.1 - - - +
342A LEU* 1.3 63.4 + - - +
343A TYR* 3.9 29.4 + - + +
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Residues in contact with LEU 342 (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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288A ILE* 5.5 1.8 - - + -
290A CYS* 4.1 9.0 - - - -
291A GLU 3.5 0.9 - - - +
292A PHE* 3.8 22.2 - - + -
333A LEU* 5.4 0.7 - - + -
336A MET* 3.2 39.3 - - + -
337A LYS* 3.5 39.7 - - + +
340A TYR* 4.0 7.4 + - + +
341A ASP* 1.3 75.0 - - - +
343A TYR* 1.3 70.6 + - - +
344A ASN 4.3 0.3 + - - -
345A VAL* 3.6 24.6 - - + +
347A TYR* 6.1 1.1 - - - +
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Residues in contact with TYR 343 (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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290A CYS* 3.6 1.9 - - - +
291A GLU* 2.7 50.7 + - + +
293A GLU* 4.2 21.2 - - + +
341A ASP* 3.9 37.0 + - + +
342A LEU* 1.3 79.4 - - - +
344A ASN* 1.3 82.7 + - - +
345A VAL 3.3 2.0 + - - -
407B LYS* 5.2 11.2 - - - -
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Residues in contact with ASN 344 (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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289A ARG 3.6 6.2 - - - +
290A CYS* 4.0 2.9 - - - -
291A GLU* 3.6 22.5 + - + +
323A ILE* 5.9 2.3 - - + +
342A LEU 4.3 0.2 + - - -
343A TYR* 1.3 78.7 - - - +
345A VAL* 1.3 63.1 + - - +
346A GLU* 3.5 5.5 + - - +
405B TYR* 3.5 17.2 + - - +
407B LYS* 3.7 19.5 + - - +
412B LEU 4.4 1.5 + - - +
413B GLY* 3.4 17.5 - - - -
414B PHE* 3.4 46.2 + - - +
415B ARG* 5.8 1.7 - - - +
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Residues in contact with VAL 345 (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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288A ILE* 3.2 30.7 - - + -
289A ARG 3.6 4.3 - - - -
290A CYS* 4.1 8.5 - - + -
342A LEU* 3.6 41.1 - - + +
343A TYR 4.4 0.2 - - - -
344A ASN* 1.3 75.8 - - - +
346A GLU* 1.3 60.1 + - - +
347A TYR* 3.4 36.3 + - + +
405B TYR* 5.6 0.3 + - - -
415B ARG* 5.7 1.0 + - - -
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Residues in contact with GLU 346 (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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288A ILE* 3.5 2.6 - - - -
289A ARG* 2.8 76.9 + - + +
344A ASN 3.5 3.3 + - - +
345A VAL* 1.3 74.3 - - - +
347A TYR* 1.3 68.7 + - - +
348A ILE* 3.4 9.2 + - + +
415B ARG* 3.2 52.5 + - + +
416B LEU 5.0 3.6 + - - +
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Residues in contact with TYR 347 (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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273A GLY* 3.6 9.8 - - - -
274A LYS* 3.6 54.7 + - + +
286A GLN* 3.3 36.3 - - + +
287A HIS 4.0 1.8 - - - -
288A ILE* 4.2 12.8 - - + +
333A LEU* 4.8 12.4 - - + +
337A LYS* 4.8 14.9 + - - +
342A LEU* 6.1 1.2 - - - +
345A VAL* 3.4 33.4 - - + +
346A GLU* 1.3 75.7 - - - +
348A ILE* 1.3 63.2 + - - +
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Residues in contact with ILE 348 (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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272A GLU* 4.1 2.1 - - - +
273A GLY* 2.8 23.2 + - - -
287A HIS* 2.9 52.1 + - + +
288A ILE 4.6 0.2 - - - -
289A ARG* 3.2 52.3 - - + +
346A GLU* 3.8 17.9 - - + +
347A TYR* 1.3 73.4 - - - +
349A SER* 1.3 62.5 + - - +
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Residues in contact with SER 349 (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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270A VAL* 5.5 4.5 - - - +
271A PHE 3.1 17.5 - - - -
272A GLU* 4.0 8.3 - - - -
273A GLY 3.6 12.8 + - - +
286A GLN* 4.1 1.8 - - - -
287A HIS* 2.7 43.6 + - - +
327A TRP* 4.8 7.3 - - - -
348A ILE* 1.3 89.3 - - - +
350A GLY* 1.3 55.2 + - - +
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Residues in contact with GLY 350 (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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270A VAL* 3.7 2.4 - - - +
271A PHE* 3.1 42.3 + - - +
285A ILE 3.0 14.8 - - - -
286A GLN* 4.2 0.4 - - - -
287A HIS 4.3 0.4 - - - -
327A TRP* 5.0 5.8 - - - -
349A SER* 1.3 78.7 + - - +
351A LEU* 1.3 75.2 + - - +
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Residues in contact with LEU 351 (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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218A LEU* 4.1 23.1 - - + +
221A GLU* 4.4 18.8 - - + +
222A VAL* 3.7 31.4 - - + +
268A PRO* 4.4 7.6 - - + -
269A ILE 3.7 3.8 - - - +
270A VAL* 3.5 30.1 - - + +
271A PHE* 3.4 4.2 - - - -
284A HIS* 3.0 7.3 - - - +
285A ILE* 2.8 38.3 + - + +
327A TRP* 5.1 6.3 - - + -
350A GLY* 1.3 84.7 - - - +
352A LYS* 1.3 60.3 + - - +
353A PHE* 3.3 20.8 - - + -
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Residues in contact with LYS 352 (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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268A PRO* 3.3 7.8 - - - +
269A ILE* 3.0 56.5 + - + +
271A PHE* 3.5 24.4 - - + +
275A TYR* 3.4 35.2 - - + -
276A VAL 4.7 2.2 + - - +
278A ASP* 2.5 32.6 + - + +
281A TYR* 3.6 23.3 - - + -
283A LEU 3.4 4.7 - - - +
351A LEU* 1.3 71.5 - - - +
353A PHE* 1.3 64.6 + - - +
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Residues in contact with PHE 353 (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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222A VAL* 4.6 1.1 - - + -
264A PRO* 3.9 13.7 - - + -
265A TYR 4.6 2.0 - - - +
266A GLY 4.8 0.9 - - - -
267A GLU 5.2 0.4 - - - -
268A PRO* 3.6 23.8 - - + -
281A TYR* 3.0 28.9 - - - -
282A PRO* 3.4 1.6 - - - +
283A LEU* 3.0 23.5 + - + +
284A HIS* 4.1 3.8 - - - -
285A ILE* 4.0 28.3 - - + -
351A LEU* 3.3 44.9 - - + -
352A LYS* 1.3 77.1 - - - +
354A LYS* 1.3 71.4 + - - +
426A TYR* 3.9 16.6 - - - -
428A PRO* 3.6 31.9 - - + -
432A PHE* 4.8 5.4 - + - -
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Residues in contact with LYS 354 (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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209A LYS 6.0 0.2 + - - -
264A PRO* 3.3 4.5 - - - +
265A TYR* 3.2 75.5 + - + +
266A GLY* 4.2 10.7 - - - -
267A GLU* 4.7 6.5 + - - +
280A ASP* 3.5 21.5 - - + +
281A TYR* 3.6 29.8 + - + +
353A PHE* 1.3 78.0 - - - +
355A ALA* 1.3 60.8 + - - +
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Residues in contact with ALA 355 (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 LEU* 3.6 29.4 - - + +
263A LEU 3.1 14.1 - - - +
265A TYR* 3.7 9.7 + - - -
280A ASP 4.5 0.4 + - - -
282A PRO* 3.9 18.3 - - + +
283A LEU* 3.8 18.2 - - + -
353A PHE 3.9 0.2 + - - -
354A LYS* 1.3 77.8 - - - +
356A THR* 1.3 64.0 - - - +
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Residues in contact with THR 356 (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 ARG 3.7 0.9 - - - +
262A LEU* 4.1 4.9 - - - +
263A LEU* 2.9 32.1 + - - +
265A TYR* 3.7 16.8 - - + -
355A ALA* 1.3 75.1 - - - +
357A THR* 1.3 69.8 + - - +
358A GLY* 3.2 11.8 + - - +
359A LEU* 3.3 40.4 + - + +
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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