Contacts of the strand formed by residues 283 - 294 (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 LEU 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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262A LEU* 3.3 39.3 - - + +
263A LEU 3.8 2.9 - - - -
264A PRO* 3.6 33.0 - - + -
275A TYR* 4.9 0.2 - - - -
281A TYR 3.3 4.2 - - - +
282A PRO* 1.3 81.4 - - - +
284A HIS* 1.3 66.2 + - - +
330A ASN* 3.4 27.6 - - - +
352A LYS* 3.4 2.6 - - - -
353A PHE* 3.0 38.0 + - + +
355A ALA* 3.8 13.7 - - + -
432A PHE* 3.7 18.8 - - + -
436A TRP* 5.1 6.3 - - + -
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Residues in contact with HIS 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271A PHE* 4.1 2.5 - + + -
275A TYR* 3.4 62.8 - + + +
282A PRO 4.7 1.6 + - - -
283A LEU* 1.3 79.3 - - - +
285A ILE* 1.3 63.9 + - - +
286A GLN* 3.9 25.9 + - + +
329A SER* 3.4 3.1 - - - -
330A ASN* 2.9 61.2 + - + +
333A LEU* 4.6 10.2 - - + +
351A LEU 3.0 18.8 - - - +
353A PHE* 4.1 2.9 - - - -
432A PHE* 3.5 2.8 - - - -
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Residues in contact with ILE 285 (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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221A GLU 5.0 2.5 - - - +
222A VAL* 3.9 31.9 - - + -
225A ALA* 3.8 28.9 - - + -
271A PHE* 4.2 1.6 - - - -
284A HIS* 1.3 78.3 - - - +
286A GLN* 1.3 61.7 + - - +
327A TRP* 4.1 22.2 - - + -
328A LEU 3.3 9.2 - - - +
329A SER* 4.1 7.9 - - - -
350A GLY* 3.0 5.4 - - - -
351A LEU* 2.8 38.5 + - + +
353A PHE* 4.0 19.1 - - + -
428A PRO* 5.4 0.9 - - + -
431A VAL* 4.4 4.3 - - + -
432A PHE* 3.9 19.3 - - + -
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Residues in contact with GLN 286 (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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271A PHE* 3.5 10.7 - - - -
273A GLY 2.7 26.4 + - - -
274A LYS* 4.7 0.2 - - - +
275A TYR* 3.2 24.6 + - - +
284A HIS* 3.9 13.7 + - + +
285A ILE* 1.3 76.3 - - - +
287A HIS* 1.3 72.7 + - - +
288A ILE* 3.6 8.2 + - + +
326A LEU 3.5 1.4 - - - +
327A TRP* 3.3 3.7 - - - -
328A LEU* 2.8 37.7 + - + +
333A LEU* 4.6 11.4 - - + -
347A TYR* 3.3 41.4 - - + +
349A SER 4.0 5.3 + - - +
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Residues in contact with HIS 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A ILE 4.2 0.2 + - - -
286A GLN* 1.3 75.1 + - - +
288A ILE* 1.3 63.0 + - - +
289A ARG* 4.4 5.4 - - - -
325A ASP* 2.8 31.5 + - - -
326A LEU 3.3 11.2 - - - -
327A TRP* 3.3 51.3 + + + -
348A ILE* 2.9 59.7 + - + +
349A SER* 2.7 27.2 + - - +
350A GLY* 4.3 0.6 - - - -
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Residues in contact with ILE 288 (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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286A GLN* 4.5 13.5 - - + +
287A HIS* 1.3 79.8 - - - +
289A ARG* 1.3 73.3 + - - +
290A CYS* 4.4 17.9 - - - -
325A ASP* 3.8 1.7 - - - -
326A LEU* 2.8 53.2 + - + +
328A LEU* 4.8 12.6 - - + -
333A LEU* 4.6 8.7 - - + -
336A MET* 4.5 11.7 - - + -
342A LEU* 5.5 1.6 - - + -
345A VAL* 3.2 33.2 - - + -
346A GLU 3.5 13.7 - - - +
347A TYR* 4.2 13.2 - - + +
348A ILE* 4.6 0.9 - - - -
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Residues in contact with ARG 289 (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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287A HIS* 4.4 4.8 - - - -
288A ILE* 1.3 77.4 - - - +
290A CYS* 1.3 63.2 + - - +
323A ILE* 4.0 10.3 - - + -
324A ALA 3.2 16.4 - - - +
325A ASP* 3.3 26.5 + - + +
344A ASN 3.6 2.9 - - - +
345A VAL* 3.6 0.3 - - - -
346A GLU* 2.8 65.8 + - + +
348A ILE* 3.2 27.2 - - + +
416B LEU* 3.7 44.0 + - + +
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Residues in contact with CYS 290 (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* 4.4 17.0 - - + -
289A ARG* 1.3 76.9 - - - +
291A GLU* 1.3 66.8 + - - +
292A PHE* 4.1 11.9 - - - -
323A ILE* 3.4 6.3 - - - +
324A ALA* 2.5 44.1 + - - +
326A LEU* 4.9 7.9 - - - -
336A MET* 4.4 5.6 - - - -
342A LEU* 4.1 22.0 - - - -
343A TYR 3.6 13.7 - - - +
344A ASN 4.0 3.4 - - - -
345A VAL* 4.1 15.0 - - + -
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Residues in contact with GLU 291 (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* 1.3 81.9 - - - +
292A PHE* 1.3 64.7 - - - +
319A SER* 3.4 14.6 - - - +
321A GLY* 3.1 34.3 + - - +
322A GLU 4.0 0.5 - - - +
323A ILE* 3.9 25.5 - - + +
342A LEU* 3.5 2.6 - - - -
343A TYR* 2.7 44.0 + - + +
344A ASN* 3.6 22.0 + - + +
402B LYS* 3.7 9.2 + - - -
414B PHE* 5.6 4.4 - - - +
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Residues in contact with PHE 292 (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* 4.1 13.5 - - - -
291A GLU* 1.3 80.7 - - - +
293A GLU* 1.3 71.1 + - - +
302A ILE* 3.6 26.5 - - + -
316A LEU* 4.1 29.8 - - + -
318A SER* 3.1 41.2 - - - -
319A SER* 3.1 22.5 + - - -
324A ALA* 3.5 26.2 - - + -
326A LEU* 4.5 6.7 - - + -
340A TYR* 3.5 24.5 - + + -
341A ASP 3.1 10.3 - - - +
342A LEU* 3.8 14.1 - - + -
343A TYR* 4.7 1.8 - - - -
309B PHE* 4.3 2.7 - + - -
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Residues in contact with GLU 293 (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* 1.3 77.7 - - - +
294A LEU* 1.3 70.4 + - - +
295A LYS 3.2 0.2 + - - -
317A LYS 3.5 3.0 - - - +
318A SER* 3.0 32.8 + - - -
319A SER* 5.1 0.7 + - - -
320A GLY* 4.3 6.6 + - - -
340A TYR* 3.9 3.4 - - - -
341A ASP* 2.8 42.9 + - + +
343A TYR* 4.2 17.0 - - + -
557B LYS* 4.4 15.1 + - - -
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Residues in contact with LEU 294 (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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293A GLU* 1.3 76.4 + - - +
295A LYS* 1.3 67.3 + - - +
296A GLU 3.9 0.2 + - - -
298A TYR 3.4 22.9 - - - +
299A ILE 3.4 23.3 - - - +
300A PRO* 3.6 31.0 - - + -
317A LYS* 2.6 41.4 + - + +
339A HIS 3.3 17.0 - - - +
340A TYR* 3.6 20.6 - - + -
341A ASP* 5.2 0.5 - - - +
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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
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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