Contacts of the helix formed by residues 326 - 342 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83A CYS 5.5 1.2 + - - -
84A LEU* 4.0 10.4 - - - +
323A GLN* 4.6 7.9 - - - -
324A TRP 4.0 2.0 + - - -
325A TYR* 1.3 77.7 - - - +
327A PHE* 1.3 83.8 + - - +
328A ASN* 3.4 2.7 - - - +
329A MET* 2.9 16.6 + - - +
330A PHE* 3.1 34.9 + - - -
500A FAD 2.7 38.3 + - - -
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Residues in contact with PHE 327 (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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17A PRO* 3.9 26.0 - - + -
52A TRP* 3.9 27.8 - + - -
84A LEU* 3.5 54.6 - - + +
86A PHE* 4.1 28.4 - + + -
108A LEU* 5.5 2.7 - - + -
111A TYR* 5.6 0.2 - + - -
112A ILE* 4.2 23.1 - - + -
326A SER* 1.3 81.9 + - - +
328A ASN* 1.3 62.7 + - - +
330A PHE* 3.2 19.0 + + - +
331A ASP* 3.1 26.5 + - - +
500A FAD 3.7 18.4 - - - -
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Residues in contact with ASN 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A CYS 3.5 23.2 + - - -
84A LEU* 4.1 4.4 + - - +
85A GLU 3.2 25.3 + - - +
86A PHE* 4.2 6.8 - - - -
87A ALA* 4.3 5.5 + - - +
325A TYR* 4.2 13.3 - - + +
326A SER 3.4 1.8 - - - +
327A PHE* 1.3 76.4 - - - +
329A MET* 1.3 63.5 + - - +
331A ASP* 3.3 9.6 + - - +
332A ALA* 3.0 22.9 + - - +
381A ILE* 4.8 2.2 - - + +
390A TYR* 4.7 7.0 + - - +
393A PHE* 3.7 42.9 - - + -
398A THR* 5.4 0.8 - - - +
425A MET* 4.9 2.2 - - - +
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Residues in contact with MET 329 (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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319A GLY* 5.4 0.9 - - - -
321A GLN* 4.5 13.5 - - + +
322A ASP 4.1 2.0 - - - +
323A GLN* 3.9 20.0 - - + -
325A TYR* 3.3 25.9 - - + +
326A SER 2.9 7.7 + - - +
328A ASN* 1.3 77.9 - - - +
330A PHE* 1.3 75.3 + - + +
332A ALA* 3.1 3.4 + - - +
333A GLN* 2.9 42.4 + - + +
377A GLN* 3.6 37.2 - - - +
380A TYR* 4.2 15.5 - - + -
381A ILE* 3.8 27.0 - - + +
384A LEU* 5.6 0.2 - - + -
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Residues in contact with PHE 330 (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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17A PRO* 4.0 13.9 - - + -
18A SER* 3.6 22.4 - - - +
21A ALA* 4.2 15.5 - - + -
318A ILE* 4.3 3.1 - - + +
319A GLY* 3.8 19.7 - - - -
323A GLN* 3.5 43.7 - - + -
326A SER* 3.1 25.9 + - - -
327A PHE* 3.2 22.0 + + - +
329A MET* 1.3 81.3 - - + +
331A ASP* 1.3 59.5 + - - +
333A GLN* 3.2 8.7 + - - +
334A ALA* 2.8 32.7 + - - +
500A FAD 3.9 24.5 - - - -
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Residues in contact with ASP 331 (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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21A ALA* 3.4 13.1 - - - +
86A PHE* 3.7 13.0 - - - -
115A ARG* 3.0 40.1 + - - -
327A PHE 3.1 14.8 + - - +
328A ASN* 3.4 9.4 - - - +
329A MET 3.1 0.2 - - - -
330A PHE* 1.3 77.7 - - - +
332A ALA* 1.3 64.2 + - - +
335A TRP* 2.8 38.0 + - - +
390A TYR* 2.7 38.4 + - + +
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Residues in contact with ALA 332 (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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328A ASN 3.0 13.1 + - - +
329A MET* 3.7 6.7 - - - +
331A ASP* 1.3 76.5 - - - +
333A GLN* 1.3 61.8 + - - +
335A TRP* 3.5 5.8 + - - +
336A TYR* 3.1 23.7 + - - +
381A ILE* 4.0 10.5 - - + -
384A LEU* 3.9 27.2 - - + +
385A ILE* 3.8 29.6 - - + +
388A THR* 5.4 0.3 + - - +
390A TYR* 4.9 4.8 - - - -
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Residues in contact with GLN 333 (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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306A GLY 3.8 7.7 + - - -
307A VAL* 3.8 15.0 - - + +
318A ILE* 3.8 15.5 - - + +
319A GLY* 2.8 31.4 + - - +
321A GLN* 2.8 30.1 + - - +
329A MET* 2.9 27.8 + - + +
330A PHE* 3.7 7.3 - - - +
332A ALA* 1.3 71.7 - - - +
334A ALA* 1.3 61.1 + - - +
336A TYR* 3.2 3.3 + - - +
337A ALA* 2.8 30.1 + - - +
380A TYR* 2.9 30.2 + - - +
384A LEU* 3.8 11.0 - - + -
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Residues in contact with ALA 334 (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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18A SER 4.8 1.3 - - - +
21A ALA* 3.6 30.3 - - + +
22A GLN* 3.2 37.6 + - + +
25A ALA* 4.1 2.5 - - + -
318A ILE* 4.0 5.3 - - + +
330A PHE 2.8 21.8 + - - +
331A ASP* 3.8 2.5 - - - +
333A GLN* 1.3 74.4 - - - +
335A TRP* 1.3 56.7 + - - +
337A ALA 3.4 0.3 + - - -
338A ARG* 2.9 25.6 + - - +
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Residues in contact with TRP 335 (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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21A ALA 4.0 7.6 - - - -
24A ARG* 4.0 22.9 - - + -
25A ALA* 3.6 33.9 - - + -
28A SER* 3.7 23.9 - - - -
88A ASP* 4.5 6.7 - - + -
115A ARG* 4.7 0.4 - - - -
331A ASP* 2.8 43.8 + - - +
332A ALA 3.8 3.6 - - - +
334A ALA* 1.3 76.2 - - - +
336A TYR* 1.3 62.9 + - - +
338A ARG* 3.2 29.6 - - - +
339A ASP* 3.2 25.8 + - - +
388A THR* 3.7 13.5 - - - +
389A ASP* 3.0 30.7 + - - -
390A TYR* 3.4 50.7 - + + +
391A PRO* 5.4 0.9 - - + +
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Residues in contact with TYR 336 (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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304A TYR* 3.5 23.9 - - - -
305A LYS* 3.8 26.2 - - + +
307A VAL* 3.8 15.0 - - + -
308A VAL* 4.0 13.9 - - + -
332A ALA 3.1 17.4 + - - +
333A GLN 3.6 2.7 - - - +
335A TRP* 1.3 78.3 - - - +
337A ALA* 1.3 65.0 + - - +
339A ASP* 3.2 3.3 + - - -
340A VAL* 3.1 39.3 + - + +
345A LEU* 3.5 33.2 - - + +
347A LEU* 4.0 12.3 - - - +
384A LEU* 4.1 16.4 - - + +
387A MET* 3.8 28.4 - - + -
388A THR* 3.9 10.0 - - + +
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Residues in contact with ALA 337 (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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22A GLN* 3.5 22.9 - - - +
164A VAL* 5.2 0.2 - - + -
307A VAL* 4.4 2.9 - - + -
316A PHE* 4.1 24.4 - - + -
318A ILE* 4.2 9.0 - - + -
333A GLN 2.8 15.7 + - - +
334A ALA 3.4 0.4 + - - +
336A TYR* 1.3 79.0 - - - +
338A ARG* 1.4 62.6 + - - +
340A VAL* 3.2 10.5 + - - +
341A ILE* 3.0 32.6 + - + +
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Residues in contact with ARG 338 (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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22A GLN* 4.0 2.1 - - - +
25A ALA* 2.9 43.6 + - + -
26A PHE* 3.6 35.7 - - + +
28A SER* 4.3 1.8 - - - -
29A ALA* 4.0 14.4 - - - +
334A ALA 2.9 19.5 + - - +
335A TRP* 3.2 36.8 - - - +
336A TYR 3.3 0.2 - - - -
337A ALA* 1.4 72.3 - - - +
339A ASP* 1.3 86.7 + - - +
341A ILE* 3.2 1.8 + - - +
342A MET* 2.7 48.4 + - - +
344A ARG* 3.3 19.4 - - - +
389A ASP* 2.9 27.5 + - - -
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Residues in contact with ASP 339 (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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335A TRP 3.2 11.0 + - - +
336A TYR 3.2 4.9 + - - +
338A ARG* 1.3 116.6 + - - +
340A VAL* 1.3 61.4 + - - +
343A GLY 3.3 1.9 + - - -
344A ARG* 2.8 56.6 + - + +
345A LEU* 3.3 26.3 + - + +
387A MET 4.3 3.5 - - - +
388A THR* 3.5 23.7 - - + +
389A ASP 4.7 0.7 + - - -
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Residues in contact with VAL 340 (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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162A TYR* 5.5 1.9 + - + -
308A VAL* 4.8 0.2 - - + -
313A PRO 5.2 0.4 - - - +
316A PHE* 3.7 27.4 - - + -
336A TYR* 3.1 49.5 + - + +
337A ALA* 3.2 6.9 + - - +
339A ASP* 1.3 74.1 - - - +
341A ILE* 1.3 66.8 + - - +
343A GLY* 3.2 12.3 + - - -
345A LEU* 3.6 20.6 - - + +
347A LEU* 4.1 25.4 - - + -
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Residues in contact with ILE 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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6A MET* 4.9 2.1 - - - +
8A THR* 5.3 1.2 + - - +
10A ILE* 3.8 25.4 - - + -
22A GLN* 5.5 0.2 - - - +
26A PHE* 4.1 25.4 - - + -
37A PRO* 4.3 10.5 - - + -
162A TYR* 3.9 39.9 + - + -
164A VAL* 4.0 22.0 - - + -
316A PHE* 3.7 30.1 - - + -
337A ALA* 3.0 23.5 + - + +
338A ARG* 3.6 4.5 - - - +
340A VAL* 1.3 76.8 - - - +
342A MET* 1.3 61.6 - - - +
343A GLY* 3.2 1.8 + - - -
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Residues in contact with MET 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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6A MET* 3.3 28.0 - - + +
26A PHE* 4.2 16.4 - - + -
29A ALA* 4.3 4.9 - - - -
34A ALA* 4.0 12.1 - - + -
35A GLU 3.7 22.9 - - - +
36A ILE* 4.3 7.4 - - + -
37A PRO* 4.5 0.7 - - + -
338A ARG* 2.7 44.4 + - - +
339A ASP 3.6 3.6 + - - +
341A ILE* 1.3 73.3 - - - +
343A GLY* 1.3 58.8 + - - +
344A ARG* 3.5 40.7 + - + +
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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