Contacts of the helix formed by residues 379 - 391 (chain A) in PDB entry 1XLB
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 PHE 379 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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338A SER* 3.7 38.1 - - - -
340A VAL* 5.5 4.0 - - + -
377A PHE* 3.6 30.3 - + + -
378A ALA* 1.3 73.6 - - - +
380A ILE* 1.3 60.5 + - + +
382A LEU* 3.4 11.1 + - + +
383A ASN* 2.9 30.0 + - - +
296B SER* 6.3 0.4 - - - -
298B THR* 3.5 36.3 - - + +
299B ASP* 2.8 10.1 + - - +
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Residues in contact with ILE 380 (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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379A PHE* 1.3 75.3 - - - +
381A ARG* 1.3 53.7 - - - +
383A ASN* 3.2 6.7 + - - +
384A GLN* 2.7 32.8 + - - +
258B VAL* 4.3 7.9 - - + -
261B HIS* 3.7 19.3 - - + +
295B PRO* 4.1 4.3 - - + -
296B SER* 3.4 44.9 - - - +
299B ASP* 3.3 25.5 + - + +
303B GLY* 4.3 8.1 - - - +
306B ASP* 5.1 1.6 - - + -
307B SER* 4.0 39.0 - - - +
310B ALA* 4.8 4.0 - - + -
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Residues in contact with ARG 381 (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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330A GLU* 3.6 28.1 + - - +
333A GLU* 5.4 6.9 + - - +
334A ALA* 4.0 25.0 - - + +
337A THR* 6.3 0.6 - - - +
378A ALA* 4.0 15.3 + - + +
379A PHE 3.4 0.2 - - - -
380A ILE* 1.3 74.9 - - - +
382A LEU* 1.3 64.7 + - - +
384A GLN* 3.2 8.7 + - + +
385A LEU* 3.0 44.7 + - + +
299B ASP* 4.8 0.6 + - - -
303B GLY* 6.2 0.4 - - - -
306B ASP* 3.5 38.4 + - + +
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Residues in contact with LEU 382 (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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325A PHE* 4.8 8.0 - - + -
326A ARG* 5.4 1.1 - - - +
331A VAL* 4.2 11.2 - - + +
334A ALA* 4.0 22.1 - - + +
335A MET* 3.7 26.2 - - + -
338A SER* 3.6 25.8 - - - +
340A VAL* 4.0 18.8 - - + -
378A ALA 3.4 15.9 + - - +
379A PHE* 3.9 12.1 - - + +
380A ILE 3.4 0.2 - - - -
381A ARG* 1.3 76.1 - - - +
383A ASN* 1.3 60.4 + - - +
385A LEU* 3.4 7.1 + - + +
386A ALA* 3.2 22.2 + - - +
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Residues in contact with ASN 383 (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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265A THR* 5.3 2.8 - - - +
269A PHE* 4.3 22.2 - - - -
379A PHE 2.9 18.5 + - - +
380A ILE* 3.2 6.5 + - - +
382A LEU* 1.3 73.7 - - - +
384A GLN* 1.3 61.0 + - - +
386A ALA* 3.2 4.8 + - - +
387A ILE* 3.1 33.6 + - - +
261B HIS* 3.3 39.6 + - + +
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Residues in contact with GLN 384 (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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380A ILE* 2.7 19.5 + - + +
381A ARG* 3.2 10.5 + - + +
383A ASN* 1.3 69.8 - - - +
385A LEU* 1.3 64.9 + - + +
387A ILE* 3.4 1.9 + - - +
388A GLU* 3.0 50.7 + - - +
261B HIS* 2.7 35.7 + - + +
310B ALA* 3.8 24.7 - - + +
313B SER* 3.9 13.7 - - - -
314B MET* 3.5 31.5 - - - +
317B LEU* 4.8 0.3 - - - +
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Residues in contact with LEU 385 (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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325A PHE* 4.6 2.0 - - + -
330A GLU* 3.9 18.6 - - + +
331A VAL* 4.0 17.3 - - + -
334A ALA* 3.8 29.8 - - + -
381A ARG* 3.0 42.1 + - + +
382A LEU* 3.6 8.7 - - + +
383A ASN 3.3 0.2 - - - -
384A GLN* 1.3 74.9 - - + +
386A ALA* 1.3 57.3 + - - +
388A GLU* 3.2 8.6 + - - +
389A HIS* 2.9 33.4 + - - -
394A ARG* 3.4 40.6 - - - +
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Residues in contact with ALA 386 (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 PHE* 4.0 8.3 - - + -
269A PHE* 3.8 24.5 - - + -
325A PHE* 3.5 34.7 - - + -
382A LEU 3.2 8.6 + - - +
383A ASN* 3.2 10.7 + - - +
385A LEU* 1.3 77.3 - - - +
387A ILE* 1.3 56.1 + - + +
389A HIS* 3.1 6.1 + - - +
390A LEU* 2.9 26.3 + - - +
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Residues in contact with ILE 387 (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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265A THR* 3.7 37.5 - - + +
268A PHE* 6.1 0.4 - - + -
269A PHE* 5.2 1.3 - - + -
383A ASN* 3.1 33.2 + - - +
384A GLN* 4.1 4.0 - - - +
386A ALA* 1.3 73.3 - - + +
388A GLU* 1.3 59.8 + - - +
390A LEU* 3.1 9.9 + - + +
391A LEU* 2.8 44.2 + - + +
260B GLY 4.4 6.5 - - - +
261B HIS* 4.3 12.3 - - + -
264B LEU* 4.2 14.4 - - + -
314B MET* 3.5 37.2 - - + -
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Residues in contact with GLU 388 (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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384A GLN* 3.0 45.9 + - - +
385A LEU* 3.4 8.3 - - - +
387A ILE* 1.3 78.1 - - + +
389A HIS* 1.3 59.3 + - - +
391A LEU* 4.6 2.0 - - - -
392A GLY 3.4 2.4 + - - -
393A SER* 3.2 33.6 + - - -
394A ARG* 2.9 45.5 + - + -
313B SER* 4.5 7.1 - - - -
314B MET* 5.7 0.2 - - - -
317B LEU* 3.7 25.4 - - + +
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Residues in contact with HIS 389 (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 PHE* 4.9 0.7 - - + -
321A ARG* 3.3 21.7 - - - +
324A ALA* 3.7 27.3 - - + +
325A PHE* 3.8 30.8 + + + -
328A ASP* 2.6 34.6 + - + +
331A VAL* 3.9 15.5 - - + -
385A LEU 2.9 16.5 + - - +
386A ALA 3.6 7.2 - - - +
388A GLU* 1.3 73.0 - - - +
390A LEU* 1.3 62.1 + - - +
392A GLY* 3.2 12.4 + - - +
394A ARG* 3.5 45.5 + - + +
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Residues in contact with LEU 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264A LEU* 4.5 4.5 - - + -
265A THR* 4.0 26.9 - - - +
268A PHE* 3.8 23.0 - - + -
318A LEU* 3.5 32.3 - - + -
321A ARG* 3.4 19.4 + - - -
386A ALA 2.9 13.7 + - - +
387A ILE* 3.1 15.0 + - + +
389A HIS* 1.3 74.8 - - - +
391A LEU* 1.3 56.8 + - + +
264B LEU* 3.5 30.7 - - + -
391B LEU* 3.3 26.7 - - + +
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Residues in contact with LEU 391 (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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387A ILE* 2.8 23.5 + - + +
388A GLU 4.0 3.6 - - - +
389A HIS 3.4 0.2 - - - -
390A LEU* 1.3 72.1 - - + +
392A GLY* 1.3 53.8 + - - +
393A SER* 4.6 3.1 - - - -
264B LEU* 4.3 18.8 - - + -
314B MET* 3.8 22.2 - - + -
317B LEU* 3.8 34.5 - - + -
318B LEU* 4.6 4.9 - - + -
321B ARG* 2.7 42.9 + - - +
390B LEU* 3.3 42.6 - - + +
391B LEU* 3.4 11.9 - - + +
392B GLY 3.5 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