Contacts of the helix formed by residues 326 - 342 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C CYS 5.6 2.0 + - - -
84C LEU* 4.1 9.5 - - - +
323C GLN* 4.7 8.3 - - - -
324C TRP 4.1 1.1 + - - -
325C TYR* 1.3 77.2 - - - +
327C PHE* 1.3 82.6 + - - +
328C ASN* 3.4 3.3 - - - +
329C MET* 2.9 16.6 + - - +
330C PHE* 3.1 33.8 + - - -
500C FAD 2.7 37.7 + - - -
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Residues in contact with PHE 327 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PRO* 3.8 32.3 - - + -
52C TRP* 3.9 27.4 - + - -
84C LEU* 3.5 56.6 - - + +
86C PHE* 3.8 31.4 - + + -
108C LEU* 5.4 2.2 - - + -
112C ILE* 4.3 22.7 - - + -
326C SER* 1.3 81.4 + - - +
328C ASN* 1.3 61.9 + - - +
330C PHE* 3.1 12.1 + + - +
331C ASP* 3.0 27.1 + - - +
500C FAD 3.8 17.3 - - - -
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Residues in contact with ASN 328 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83C CYS 3.6 22.0 + - - -
84C LEU* 4.3 8.6 + - - +
85C GLU 3.6 18.8 + - - +
86C PHE* 4.5 3.4 - - - -
87C ALA* 4.4 9.2 + - - +
325C TYR* 4.3 13.8 - - + -
326C SER 3.4 2.2 - - - +
327C PHE* 1.3 76.0 - - - +
329C MET* 1.3 64.5 + - - +
331C ASP* 3.5 8.7 + - - +
332C ALA* 3.1 22.0 + - - +
381C ILE* 4.6 3.5 - - + +
390C TYR* 4.8 9.8 + - + +
393C PHE* 3.7 45.0 - - + -
398C THR* 5.4 1.4 - - - +
425C MET* 5.1 0.5 - - - +
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Residues in contact with MET 329 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319C GLY* 5.7 0.9 - - - -
321C GLN* 4.6 9.6 - - + +
322C ASP 4.0 8.5 - - - +
323C GLN* 4.1 11.9 - - + -
325C TYR* 3.3 25.5 - - + +
326C SER 2.9 8.4 + - - +
328C ASN* 1.3 76.4 - - - +
330C PHE* 1.3 73.7 + - + +
332C ALA* 3.1 2.8 + - - +
333C GLN* 2.9 40.9 + - + +
377C GLN* 3.6 35.7 - - - +
380C TYR* 4.0 20.6 - - + -
381C ILE* 3.9 26.6 - - + +
384C LEU* 5.6 0.4 - - + -
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Residues in contact with PHE 330 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C PRO* 4.0 14.4 - - + +
18C SER* 3.6 29.8 - - - +
21C ALA* 4.2 7.9 - - + -
318C ILE* 4.2 3.8 - - + +
319C GLY* 3.8 18.8 - - - -
323C GLN* 3.5 41.3 - - + -
326C SER* 3.4 28.7 - - - -
327C PHE* 3.1 23.9 + + - +
329C MET* 1.3 81.9 - - + +
331C ASP* 1.3 59.6 + - - +
333C GLN* 3.2 8.4 + - - +
334C ALA* 2.8 32.1 + - - +
500C FAD 3.8 23.8 - - - -
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Residues in contact with ASP 331 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C ALA* 3.3 14.1 - - - +
86C PHE* 4.3 5.1 - - - -
115C ARG* 2.8 42.4 + - - -
327C PHE 3.0 16.8 + - - +
328C ASN* 3.8 6.6 - - - +
329C MET 3.3 0.2 - - - -
330C PHE* 1.3 76.4 - - - +
332C ALA* 1.3 63.9 + - - +
335C TRP* 2.9 38.0 + - + +
390C TYR* 2.7 42.9 + - + +
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Residues in contact with ALA 332 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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328C ASN 3.1 17.7 + - - +
329C MET* 3.1 4.0 + - - +
331C ASP* 1.3 76.9 - - - +
333C GLN* 1.3 61.8 + - - +
335C TRP* 4.0 4.9 - - - +
336C TYR* 3.1 23.2 + - - +
381C ILE* 4.1 9.4 - - + -
384C LEU* 3.9 25.4 - - + +
385C ILE* 3.7 30.7 - - + +
388C THR* 5.5 0.2 - - - +
390C TYR* 4.9 5.4 - - + -
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Residues in contact with GLN 333 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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306C GLY 3.9 5.5 + - - -
307C VAL* 3.8 13.1 - - + +
318C ILE* 3.7 20.0 - - + +
319C GLY* 2.9 28.4 + - - +
321C GLN* 2.7 31.9 + - - +
329C MET* 2.9 27.5 + - + +
330C PHE* 3.6 8.1 - - - +
332C ALA* 1.3 77.2 - - - +
334C ALA* 1.3 58.5 + - - +
336C TYR* 3.1 4.7 + - - +
337C ALA* 2.8 29.8 + - - +
380C TYR* 3.1 30.1 + - - +
384C LEU* 3.9 9.6 - - + -
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Residues in contact with ALA 334 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18C SER 4.9 1.3 - - - +
21C ALA* 3.8 11.7 - - + +
22C GLN* 3.1 53.7 + - + +
25C ALA* 4.1 3.4 - - + -
318C ILE* 3.8 5.8 - - + +
330C PHE 2.8 17.5 + - - +
331C ASP* 3.8 3.4 - - - +
333C GLN* 1.3 78.0 - - - +
335C TRP* 1.3 55.3 + - - +
337C ALA 3.4 0.3 + - - -
338C ARG* 2.9 26.0 + - - +
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Residues in contact with TRP 335 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21C ALA 4.1 5.4 - - - -
24C ARG* 4.0 22.2 - - + -
25C ALA* 3.4 35.4 - - + -
28C SER* 3.7 24.9 + - - -
88C ASP* 4.8 4.7 - - - -
331C ASP* 2.9 45.4 + - - +
332C ALA* 4.0 3.1 - - - +
334C ALA* 1.3 73.5 - - + +
336C TYR* 1.3 67.0 + - - +
338C ARG* 3.4 29.6 + - - +
339C ASP* 3.2 25.5 + - - +
388C THR* 3.7 14.6 - - - +
389C ASP* 3.1 29.8 + - - -
390C TYR* 3.4 48.9 - + + +
391C PRO* 5.5 1.1 - - + +
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Residues in contact with TYR 336 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304C TYR* 3.5 26.2 - - - -
305C LYS* 3.6 21.0 - - + +
307C VAL* 3.8 14.4 - - + -
308C VAL* 4.0 14.1 - - + +
332C ALA 3.1 14.6 + - - +
333C GLN 3.4 6.3 - - - +
335C TRP* 1.3 79.0 - - - +
337C ALA* 1.3 61.8 + - - +
339C ASP* 3.2 3.1 + - - +
340C VAL* 3.0 41.0 + - + +
345C LEU* 3.5 29.6 - - + +
347C LEU* 4.1 11.8 - - - +
384C LEU* 4.0 21.1 - - + +
387C MET* 3.7 28.3 - - + -
388C THR* 4.0 10.0 - - + +
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Residues in contact with ALA 337 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22C GLN* 3.6 19.5 - - - +
164C VAL* 5.2 0.9 - - + -
307C VAL* 4.2 7.2 - - + -
316C PHE* 4.0 26.0 - - + -
318C ILE* 4.3 5.4 - - + -
333C GLN 2.8 19.4 + - - +
335C TRP 3.3 0.2 - - - -
336C TYR* 1.3 73.2 - - - +
338C ARG* 1.3 66.0 + - - +
340C VAL* 3.2 9.7 + - - +
341C ILE* 3.0 30.2 + - + +
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Residues in contact with ARG 338 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C GLN* 3.9 2.7 - - - +
25C ALA* 2.7 44.6 + - + -
26C PHE* 3.5 36.6 - - + +
28C SER* 4.3 1.6 - - - -
29C ALA* 3.8 23.3 - - - +
334C ALA 2.9 19.7 + - - +
335C TRP* 3.4 34.5 - - - +
337C ALA* 1.3 71.2 - - - +
339C ASP* 1.3 79.5 + - - +
341C ILE* 3.1 2.6 + - - +
342C MET* 2.7 44.6 + - - +
344C ARG* 3.3 18.1 - - - +
389C ASP* 2.7 29.3 + - - -
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Residues in contact with ASP 339 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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335C TRP 3.2 14.5 + - - +
337C ALA 3.2 0.2 - - - -
338C ARG* 1.3 115.7 + - - +
340C VAL* 1.3 62.5 + - - +
342C MET* 3.5 0.4 + - - -
343C GLY 3.2 3.6 + - - -
344C ARG* 2.9 57.1 + - + +
345C LEU* 3.3 26.0 + - + +
387C MET 4.2 3.3 - - - +
388C THR* 3.6 23.0 - - - +
389C ASP 4.8 0.9 + - - -
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Residues in contact with VAL 340 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162C TYR* 5.6 1.8 + - + -
308C VAL* 4.8 0.4 - - + -
313C PRO 5.1 0.4 - - - +
316C PHE* 3.8 26.7 - - + -
336C TYR* 3.0 49.9 + - + +
337C ALA* 3.8 6.3 - - - +
339C ASP* 1.3 77.3 - - - +
341C ILE* 1.3 63.2 + - - +
343C GLY* 3.1 12.0 + - - -
345C LEU* 3.6 20.5 - - + +
347C LEU* 4.0 27.6 - - + -
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Residues in contact with ILE 341 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C MET* 4.5 4.9 - - - +
8C THR* 5.2 1.2 + - - +
10C ILE* 3.9 22.7 - - + -
22C GLN* 5.5 0.4 - - - +
26C PHE* 4.1 26.2 - - + -
37C PRO* 4.3 11.4 - - + -
162C TYR* 4.0 40.0 + - + -
164C VAL* 4.1 21.1 - - + -
316C PHE* 3.7 29.6 - - + -
337C ALA* 3.0 20.8 + - + +
338C ARG* 3.5 6.1 - - - +
340C VAL* 1.3 77.5 - - - +
342C MET* 1.3 59.9 + - - +
343C GLY* 3.1 4.5 + - - -
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Residues in contact with MET 342 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6C MET* 3.8 29.0 - - + +
26C PHE* 4.1 20.4 - - + -
29C ALA* 4.5 2.9 - - + -
34C ALA* 4.1 10.8 - - + -
35C GLU 3.5 24.5 - - - +
36C ILE* 4.3 6.5 - - + -
37C PRO* 4.4 1.6 - - + -
338C ARG* 2.7 43.1 + - - +
339C ASP 4.1 3.1 - - - +
341C ILE* 1.3 73.4 - - + +
343C GLY* 1.3 59.4 + - - +
344C ARG* 3.5 40.1 + - + +
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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