Contacts of the helix formed by residues 334 - 350 (chain B) in PDB entry 1XR2
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 334 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285B PRO* 3.8 22.4 - - + -
314B LEU* 4.6 4.5 - - - -
315B PRO* 3.3 46.7 - - + +
316B VAL 4.0 4.7 - - - +
317B THR 3.3 26.9 - - - -
318B LEU* 3.6 28.0 - - + +
321B GLU* 4.3 8.1 - - + -
332B LEU* 4.5 7.4 - - + -
333B ALA* 1.3 79.8 - - - +
335B ALA* 1.3 57.6 + - - +
336B LYS 3.4 0.9 - - - -
337B GLU* 2.7 20.0 + - - +
338B LYS* 2.7 38.6 + - - +
482B THR* 4.3 17.5 - - + -
485B GLY* 4.5 6.5 - - - -
499B ILE* 4.5 8.1 - - + -
541B TYR* 5.3 1.3 - + - -
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Residues in contact with ALA 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PHE* 3.9 9.0 - - + -
9B PRO* 3.4 32.5 - - + -
311B LEU* 4.2 16.0 - - + +
314B LEU* 4.1 6.7 - - + +
315B PRO 3.1 19.3 + - - +
316B VAL 3.8 3.4 - - - +
334B PHE* 1.3 76.4 - - - +
336B LYS* 1.3 63.7 + - - +
338B LYS* 3.1 19.0 + - - +
339B LEU* 3.1 13.3 + - - +
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Residues in contact with LYS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B PHE* 3.8 13.2 - - + -
13B GLU* 3.0 31.4 + - - -
44B TYR* 4.4 3.3 - - - -
48B ASN* 3.8 22.9 - - - +
52B ASN* 5.9 2.5 - - - +
316B VAL* 3.0 18.9 + - - +
317B THR* 3.6 21.9 - - + +
335B ALA* 1.3 73.5 - - - +
337B GLU* 1.3 70.4 + - - +
339B LEU* 3.1 17.1 + - + +
340B GLU* 3.1 32.4 + - + +
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Residues in contact with GLU 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317B THR* 3.0 27.6 - - - +
318B LEU* 3.2 21.3 + - + +
319B GLU* 4.4 1.8 + - - +
332B LEU 5.0 1.1 - - - +
333B ALA* 3.6 16.8 - - + -
334B PHE* 2.7 49.1 + - - +
336B LYS* 1.3 80.1 - - - +
338B LYS* 1.3 59.1 + - - +
340B GLU* 3.4 18.3 + - - +
341B GLU* 2.9 31.9 + - - +
344B MET* 5.3 0.5 - - - +
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Residues in contact with LYS 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 3.8 16.4 - - + +
281B ASN* 3.0 30.2 + - - +
284B GLN 3.0 28.3 + - - -
285B PRO* 4.4 0.2 - - - -
286B TRP 3.6 16.9 + - - +
311B LEU* 3.9 17.3 - - + -
314B LEU* 3.8 14.4 - - + -
333B ALA* 3.5 24.9 - - + +
334B PHE 2.7 28.2 + - - +
335B ALA 3.1 7.4 + - - +
337B GLU* 1.3 70.6 - - - +
339B LEU* 1.3 65.9 + - - +
341B GLU* 3.1 15.9 + - - +
342B LEU* 3.1 27.5 + - + +
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Residues in contact with LEU 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B ALA* 3.5 26.7 - - + -
8B PHE* 3.6 28.5 - - + -
48B ASN* 3.7 32.3 - - + +
49B TYR* 4.1 12.8 - - + +
52B ASN* 3.4 27.5 - - + +
53B VAL* 5.0 0.9 - - + -
311B LEU* 3.5 28.3 - - + -
335B ALA 3.1 6.3 + - - +
336B LYS* 3.2 10.8 - - + +
338B LYS* 1.3 78.0 - - - +
340B GLU* 1.3 60.5 + - - +
342B LEU* 3.1 19.1 + - + +
343B LYS 3.1 9.0 + - - -
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Residues in contact with GLU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B ASN* 3.3 25.1 + - - +
336B LYS* 3.1 35.5 + - - +
337B GLU* 3.7 22.2 - - - +
338B LYS 3.3 0.2 - - - -
339B LEU* 1.3 74.0 - - - +
341B GLU* 1.3 61.0 + - - +
343B LYS* 3.2 3.3 + - + +
344B MET* 2.9 42.5 + - + +
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Residues in contact with GLU 341 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B ILE* 3.7 30.5 - - + +
286B TRP 4.3 0.6 - - - +
287B LYS* 3.6 34.6 - - + +
288B VAL* 3.8 14.6 + - - +
290B LEU* 3.8 16.9 - - + +
333B ALA* 3.7 16.0 - - + +
337B GLU 2.9 18.3 + - - +
338B LYS* 3.1 17.0 + - - +
340B GLU* 1.3 78.9 - - - +
342B LEU* 1.3 61.2 + - - +
344B MET* 3.5 21.0 + - + +
345B LEU* 3.1 23.0 + - - +
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Residues in contact with LEU 342 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B ALA* 4.8 1.9 - - + +
4B TYR 3.5 20.4 - - - +
5B ALA* 3.9 17.0 - - + -
52B ASN 4.7 1.3 - - - -
53B VAL* 4.2 12.6 - - + -
280B ILE* 3.7 20.6 - - + -
305B ILE* 3.9 16.9 - - + +
306B SER* 3.6 32.8 - - - +
307B ASN* 4.1 13.5 - - + +
311B LEU* 5.7 0.9 - - + -
338B LYS* 3.1 17.4 + - + +
339B LEU* 3.1 14.4 + - + +
341B GLU* 1.3 75.6 - - - +
343B LYS* 1.3 60.4 + - - +
345B LEU* 3.3 6.3 + - + +
346B LYS* 2.9 28.6 + - - +
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Residues in contact with LYS 343 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B LYS 3.5 16.8 - - - +
52B ASN* 3.4 47.5 + - - +
339B LEU 3.1 5.4 + - - +
340B GLU* 3.2 6.5 + - + +
342B LEU* 1.3 74.7 - - - +
344B MET* 1.3 66.6 + - + +
346B LYS* 3.1 8.2 + - + +
347B ASP* 3.0 48.2 + - - +
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Residues in contact with MET 344 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B LEU* 3.7 23.8 - - + -
337B GLU 5.3 0.2 - - - +
340B GLU* 2.9 31.7 + - + +
341B GLU* 3.8 21.8 - - + +
343B LYS* 1.3 76.2 - - + +
345B LEU* 1.3 62.9 + - - +
347B ASP* 3.2 7.6 + - - +
348B PHE* 3.0 25.8 + - - +
353B THR* 4.5 1.2 + - - -
356B LEU* 6.2 1.8 - - + -
357B PRO* 4.4 22.7 - - + -
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Residues in contact with LEU 345 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279B VAL* 4.0 13.5 - - + -
280B ILE* 4.8 11.2 - - + -
290B LEU* 3.7 35.2 - - + +
293B VAL* 3.8 22.9 - - + -
294B ALA* 4.0 20.9 - - + +
297B VAL* 4.6 1.8 - - + -
305B ILE* 3.6 23.8 - - + -
341B GLU 3.1 18.1 + - - +
342B LEU* 3.5 7.6 - - + +
344B MET* 1.3 76.7 - - - +
346B LYS* 1.3 60.6 + - - +
348B PHE* 3.8 5.3 - - + +
349B LEU* 3.1 36.1 + - + +
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Residues in contact with LYS 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0B PHE* 5.4 2.8 - - - +
1B THR* 2.9 17.0 + - - +
2B LYS* 4.7 0.4 - - - +
3B ALA* 4.1 15.3 - - + -
52B ASN 4.7 9.0 - - - +
53B VAL* 5.5 0.4 - - - -
54B ASP* 2.7 42.6 + - - +
305B ILE* 4.0 6.7 - - + +
342B LEU 2.9 14.2 + - - +
343B LYS* 3.1 10.5 + - + +
345B LEU* 1.3 77.7 - - - +
347B ASP* 1.3 70.4 + - - +
349B LEU* 3.5 4.2 + - - +
350B GLU* 2.7 63.0 + - - +
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Residues in contact with ASP 347 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343B LYS* 3.0 43.4 + - - +
344B MET* 3.7 8.6 - - - +
346B LYS* 1.3 83.2 - - - +
348B PHE* 1.3 67.2 + - - +
350B GLU* 3.2 8.3 + - - +
352B LYS* 3.0 38.2 + - + +
353B THR* 3.2 23.8 - - + +
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Residues in contact with PHE 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290B LEU 5.5 0.7 - - - -
291B ARG* 5.4 9.9 - - + -
294B ALA* 3.8 31.0 - - + -
298B GLU* 4.6 11.7 - - - -
344B MET 3.0 16.3 + - - +
345B LEU* 3.8 7.4 - - + +
347B ASP* 1.3 75.0 - - - +
349B LEU* 1.3 63.0 + - + +
351B GLY* 2.9 23.0 + - - -
353B THR* 3.1 32.5 + - - +
356B LEU* 4.9 26.0 - - + -
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Residues in contact with LEU 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B THR* 3.7 32.9 + - + +
294B ALA* 4.2 14.1 - - + +
297B VAL* 3.8 27.1 - - + -
298B GLU* 3.7 36.8 - - + +
305B ILE* 4.3 3.4 - - + -
345B LEU* 3.1 35.0 + - + +
346B LYS 3.8 2.5 - - - +
348B PHE* 1.3 84.2 - - + +
350B GLU* 1.3 58.6 + - - +
351B GLY 3.3 1.3 + - - -
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Residues in contact with GLU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0B PHE* 3.7 17.7 - - - +
1B THR* 2.9 28.2 + - - +
346B LYS* 2.7 61.3 + - - +
347B ASP* 3.8 8.3 - - - +
348B PHE 3.0 1.6 + - - -
349B LEU* 1.3 77.6 - - - +
351B GLY* 1.3 63.0 + - - +
352B LYS* 3.2 7.9 + - + +
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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