Contacts of the helix formed by residues 326 - 342 (chain B) in PDB entry 2XLR
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 SER 326 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83B CYS 5.5 3.4 + - - -
84B LEU* 4.1 8.8 - - - +
323B GLN* 4.5 9.0 - - - -
324B TRP 4.0 2.1 + - - -
325B TYR* 1.3 74.9 - - - +
327B PHE* 1.3 81.0 + - - +
328B ASN* 3.3 2.7 - - - +
329B MET* 2.9 14.7 + - - +
330B PHE* 3.1 36.1 + - - -
500B FAD 2.6 36.9 + - - -
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Residues in contact with PHE 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO* 4.0 23.3 - - + -
52B TRP* 3.9 25.8 - + - -
84B LEU* 3.4 55.7 - - + +
86B PHE* 3.8 29.4 - + + -
108B LEU* 5.3 4.5 - - + -
111B TYR* 5.6 0.4 - + - -
112B ILE* 4.1 22.9 - - + -
326B SER* 1.3 83.2 + - - +
328B ASN* 1.3 61.5 + - - +
330B PHE* 3.3 19.5 + + - +
331B ASP* 3.1 27.4 + - - +
500B FAD 3.6 19.7 - - - -
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Residues in contact with ASN 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83B CYS 3.5 23.4 + - - -
84B LEU* 4.3 4.0 + - - +
85B GLU 3.2 25.4 + - - +
86B PHE* 4.3 2.3 - - - -
87B ALA* 4.3 8.8 + - - +
325B TYR* 4.2 14.3 - - + +
326B SER 3.3 1.6 - - - +
327B PHE* 1.3 73.0 - - - +
329B MET* 1.3 66.7 + - - +
331B ASP* 3.5 11.3 + - - +
332B ALA* 3.2 21.1 + - - +
381B ILE* 4.6 4.0 - - + +
390B TYR* 4.8 7.8 + - - +
393B PHE* 3.8 41.0 - - + -
398B THR* 5.3 1.0 - - - +
425B MET* 4.9 2.2 - - - +
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Residues in contact with MET 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319B GLY* 5.6 0.7 - - - -
321B GLN* 4.3 13.7 - - + +
322B ASP 3.9 9.6 - - - +
323B GLN* 4.0 12.1 - - + -
325B TYR* 3.4 24.6 - - + +
326B SER 2.9 8.1 + - - +
328B ASN* 1.3 80.8 - - - +
330B PHE* 1.3 68.9 + - + +
332B ALA* 3.1 4.3 + - - +
333B GLN* 3.0 38.2 + - + +
377B GLN* 3.5 38.4 - - - +
380B TYR* 4.0 17.7 - - + -
381B ILE* 3.9 25.4 - - + +
384B LEU* 5.5 0.4 - - + -
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Residues in contact with PHE 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B PRO* 3.9 14.6 - - + -
18B SER* 3.6 20.0 - - - +
21B ALA* 4.2 15.5 - - + -
318B ILE* 4.2 3.6 - - + +
319B GLY* 3.8 19.1 - - - -
323B GLN* 3.6 39.7 - - + -
326B SER* 3.1 28.0 + - - -
327B PHE* 3.3 24.2 + + - +
329B MET* 1.3 79.8 - - + +
331B ASP* 1.3 58.3 + - - +
333B GLN* 3.2 9.0 + - - +
334B ALA* 2.8 32.9 + - - +
500B FAD 3.8 24.5 - - - -
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Residues in contact with ASP 331 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA* 3.4 14.9 - - - +
86B PHE* 3.8 11.7 - - - -
115B ARG* 3.0 40.3 + - - -
327B PHE 3.1 13.9 + - - +
328B ASN* 3.7 8.4 - - - +
329B MET 3.3 0.2 - - - -
330B PHE* 1.3 78.3 - - - +
332B ALA* 1.3 57.0 + - - +
334B ALA* 4.5 0.2 - - - -
335B TRP* 2.8 45.4 + - + +
390B TYR* 2.7 40.9 + - + +
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Residues in contact with ALA 332 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328B ASN 3.2 9.6 + - - +
329B MET* 3.1 9.4 + - - +
331B ASP* 1.3 77.6 - - - +
333B GLN* 1.3 58.9 + - - +
335B TRP* 3.9 4.8 - - - +
336B TYR* 3.0 30.0 + - - +
381B ILE* 4.0 8.5 - - + -
384B LEU* 3.9 24.1 - - + +
385B ILE* 3.7 30.5 - - + +
388B THR* 5.5 0.5 + - - -
390B TYR* 5.0 4.7 - - + -
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Residues in contact with GLN 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B GLY 3.8 7.5 + - - -
307B VAL* 3.8 10.0 - - + +
317B TYR 4.9 0.4 + - - -
318B ILE* 3.7 20.4 - - + +
319B GLY* 3.0 27.4 + - - +
321B GLN* 2.8 31.5 - - - +
329B MET* 3.0 26.4 + - + +
330B PHE* 3.7 6.4 - - - +
332B ALA* 1.3 78.2 - - - +
334B ALA* 1.3 52.0 + - - +
336B TYR* 3.0 5.3 + - - +
337B ALA* 2.6 36.7 + - - +
380B TYR* 3.0 27.6 + - - +
384B LEU* 3.9 10.5 - - + -
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Residues in contact with ALA 334 (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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18B SER 4.8 1.6 - - - +
21B ALA* 3.8 10.8 - - + +
22B GLN* 3.2 56.6 + - + +
25B ALA* 4.1 2.2 - - + -
318B ILE* 3.9 4.6 - - + +
330B PHE 2.8 21.5 + - - +
331B ASP* 3.9 2.7 - - - +
333B GLN* 1.3 73.1 - - - +
335B TRP* 1.3 58.5 + - - +
337B ALA 3.3 0.7 + - - -
338B ARG* 2.9 26.9 + - - +
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Residues in contact with TRP 335 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B ALA 4.2 4.3 - - - -
24B ARG* 4.1 19.7 - - + -
25B ALA* 3.6 32.1 - - + -
28B SER* 3.7 24.8 - - - -
88B ASP* 4.5 7.2 - - + -
115B ARG* 5.1 0.2 - - - -
331B ASP* 2.8 52.6 + - - +
332B ALA 3.9 2.9 - - - +
334B ALA* 1.3 68.3 - - - +
336B TYR* 1.3 66.7 + - - +
338B ARG* 3.3 31.5 + - - +
339B ASP* 3.2 25.5 + - - +
388B THR* 3.8 14.1 - - - +
389B ASP* 3.0 28.1 + - - -
390B TYR* 3.4 51.4 - + + +
391B PRO* 5.4 2.2 - - + +
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Residues in contact with TYR 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B TYR* 3.5 26.7 - - - -
305B LYS* 3.7 21.5 - - + +
307B VAL* 3.9 14.6 - - + -
308B VAL* 3.9 14.1 - - + -
332B ALA 3.0 19.2 + - - +
333B GLN 3.4 2.7 - - - +
335B TRP* 1.3 79.8 - - - +
337B ALA* 1.3 63.9 + - - +
339B ASP* 3.3 1.9 + - - +
340B VAL* 3.0 39.8 + - + +
345B LEU* 3.5 30.8 - - + +
347B LEU* 4.0 11.8 - - - +
384B LEU* 4.0 21.5 - - + +
387B MET* 3.8 31.0 - - + -
388B THR* 4.0 9.4 - - + +
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Residues in contact with ALA 337 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22B GLN* 3.7 16.2 - - - +
164B VAL* 5.1 0.7 - - + -
307B VAL* 4.2 6.7 - - + -
316B PHE* 4.2 24.5 - - + -
318B ILE* 4.3 6.1 - - + -
333B GLN 2.6 19.9 + - - +
334B ALA 3.7 4.5 - - - +
336B TYR* 1.3 75.7 - - - +
338B ARG* 1.3 62.9 + - - +
340B VAL* 3.2 9.5 + - - +
341B ILE* 3.0 30.1 + - + +
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Residues in contact with ARG 338 (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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22B GLN* 4.0 1.9 - - - +
25B ALA* 2.9 37.2 + - + -
26B PHE* 3.5 36.1 - - + +
28B SER* 4.3 1.4 - - - -
29B ALA* 3.9 15.1 - - - +
334B ALA 2.9 20.2 + - - +
335B TRP* 3.3 36.0 - - - +
337B ALA* 1.3 71.9 - - - +
339B ASP* 1.4 83.3 + - - +
341B ILE* 2.9 2.5 + - - +
342B MET* 2.7 51.6 + - - +
344B ARG* 3.4 18.6 - - - +
388B THR* 4.7 0.4 - - - -
389B ASP* 3.0 26.7 + - - -
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Residues in contact with ASP 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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335B TRP 3.2 12.5 + - - +
336B TYR 3.9 0.2 - - - +
338B ARG* 1.4 119.1 + - - +
340B VAL* 1.3 60.7 + - - +
342B MET* 3.6 0.8 + - - +
343B GLY 3.2 2.6 + - - -
344B ARG* 2.8 59.6 + - + +
345B LEU* 3.3 23.3 + - + +
387B MET 4.1 2.8 - - - +
388B THR* 3.4 25.6 - - - +
389B ASP 4.7 0.9 + - - -
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Residues in contact with VAL 340 (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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162B TYR* 5.6 2.1 + - + -
308B VAL* 4.8 0.4 - - + -
313B PRO 5.2 0.2 - - - +
316B PHE* 3.7 27.1 - - + -
336B TYR* 3.0 49.2 + - + +
337B ALA* 3.8 7.4 - - - +
339B ASP* 1.3 77.8 - - - +
341B ILE* 1.3 63.9 + - - +
343B GLY* 3.1 12.6 + - - -
345B LEU* 3.7 21.5 - - + +
347B LEU* 4.0 25.1 - - + -
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Residues in contact with ILE 341 (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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6B MET* 4.9 1.7 - - - +
8B THR* 5.4 1.0 + - - +
10B ILE* 3.8 24.2 - - + -
22B GLN* 5.5 0.4 - - - +
26B PHE* 4.0 24.9 - - + -
37B PRO* 4.4 9.9 - - + -
162B TYR* 4.1 38.2 + - + -
164B VAL* 4.0 21.8 - - + -
316B PHE* 3.6 32.1 - - + -
337B ALA* 3.0 20.9 + - + +
338B ARG* 2.9 7.5 + - - +
340B VAL* 1.3 80.4 - - - +
342B MET* 1.3 58.3 + - - +
343B GLY* 3.2 4.3 + - - -
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Residues in contact with MET 342 (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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6B MET* 3.2 28.1 - - + +
26B PHE* 4.2 18.4 - - + -
29B ALA* 4.3 5.2 - - + -
34B ALA* 4.1 11.2 - - + -
35B GLU 3.8 21.5 - - - +
36B ILE* 4.4 6.1 - - + -
338B ARG* 2.7 44.2 + - - +
339B ASP 4.1 3.6 - - - +
341B ILE* 1.3 70.8 - - - +
343B GLY* 1.3 60.5 + - - +
344B ARG* 3.5 41.6 + - + +
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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
------------------------------------------------------------
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