Contacts of the helix formed by residues 435 - 454 (chain A) in PDB entry 2XFN
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 TYR 435 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60A TYR* 5.2 0.4 - - + -
65A GLN* 3.8 13.9 - - - +
172A CYS* 5.1 4.4 + - - -
188A TYR* 3.4 20.6 - + - -
192A CYS* 3.5 17.3 - - - -
198A ILE* 3.3 28.8 + - - +
205A GLY* 5.4 1.3 - - - -
206A GLN* 4.5 15.2 + - - -
398A TYR* 6.2 3.1 - + - -
426A THR* 2.8 16.8 + - - -
432A TRP* 3.1 41.7 + + + +
433A SER 3.5 10.5 - - - -
434A GLY* 1.3 80.9 - - - +
436A MET* 1.3 66.5 - - - +
437A GLU* 3.9 8.3 - - + +
438A GLY 3.1 1.2 + - - -
439A ALA* 3.0 7.1 + - - +
1500A FAD 3.3 41.9 + + - +
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Residues in contact with MET 436 (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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14A ILE* 3.7 28.7 - - + +
43A THR* 3.8 13.2 - - + -
58A GLY* 4.3 1.1 - - - +
59A SER* 3.6 23.3 - - - +
60A TYR 3.4 26.5 - - - +
61A VAL* 3.6 15.9 - - + -
68A ILE* 4.1 13.0 - - + -
210A PHE* 4.5 7.0 - - + -
214A SER* 3.8 24.9 - - - -
435A TYR* 1.3 69.9 - - - +
437A GLU* 1.3 62.5 + - - +
439A ALA* 3.1 10.6 + - - +
440A VAL* 3.1 24.6 + - - +
1500A FAD 2.7 30.3 + - + +
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Residues in contact with GLU 437 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A THR 4.2 2.8 - - - +
65A GLN* 3.1 35.3 + - + +
66A ASN 3.5 4.0 + - - -
67A ARG* 3.0 39.2 + - - +
68A ILE* 2.8 37.7 + - + +
431A HIS* 4.1 6.7 + - - +
432A TRP* 3.6 33.4 - - + -
435A TYR* 3.9 1.9 - - + +
436A MET* 1.3 76.6 - - - +
438A GLY* 1.4 61.6 + - - +
440A VAL* 3.1 6.8 + - - +
441A GLU* 3.0 20.0 + - + +
1500A FAD 4.5 0.8 + - - -
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Residues in contact with GLY 438 (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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426A THR* 3.5 7.4 - - - -
429A ALA* 3.4 26.1 - - - +
431A HIS 3.7 5.6 - - - -
432A TRP 3.1 24.0 + - - -
435A TYR 3.1 1.2 + - - -
437A GLU* 1.4 74.5 - - - +
439A ALA* 1.3 65.8 + - - +
441A GLU* 4.3 1.3 - - - -
442A ALA* 2.9 23.0 + - - +
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Residues in contact with ALA 439 (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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14A ILE* 3.9 7.2 - - + -
15A SER* 2.8 44.9 + - - +
426A THR* 3.3 10.9 + - - +
435A TYR 3.0 12.4 + - - +
436A MET* 3.1 11.9 + - - +
438A GLY* 1.3 75.9 - - - +
440A VAL* 1.3 61.6 + - - +
443A GLY* 3.0 8.8 + - - -
1500A FAD 3.6 26.2 - - - +
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Residues in contact with VAL 440 (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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14A ILE* 3.6 19.1 - - + -
18A ALA* 4.2 9.8 - - + +
67A ARG* 3.8 27.6 - - + +
68A ILE* 3.8 17.9 - - + +
70A ARG* 4.4 1.3 - - - +
71A LEU* 3.8 17.9 - - + -
436A MET 3.1 13.1 + - - +
437A GLU 3.1 7.0 + - - +
439A ALA* 1.3 74.6 - - - +
441A GLU* 1.3 65.1 + - - +
443A GLY* 3.3 0.5 + - - -
444A GLU* 3.1 50.7 + - + +
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Residues in contact with GLU 441 (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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67A ARG* 3.6 38.4 + - - +
429A ALA* 3.4 8.9 - - - -
430A THR* 2.9 30.9 + - - -
431A HIS* 3.0 38.5 + - - +
437A GLU* 3.0 11.3 + - - +
438A GLY* 3.7 7.0 - - - +
440A VAL* 1.3 76.6 - - - +
442A ALA* 1.3 58.9 + - - +
444A GLU* 3.9 2.5 - - - +
445A ARG* 3.0 31.4 + - + +
448A ARG* 5.1 1.8 + - - +
463A TRP* 3.5 22.3 - - + -
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Residues in contact with ALA 442 (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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15A SER* 4.0 0.7 - - - +
424A ALA* 3.7 2.4 - - - +
425A GLY 3.1 35.0 - - - +
428A THR* 3.2 15.3 - - - +
429A ALA 4.2 7.4 - - - +
438A GLY 2.9 14.4 + - - +
441A GLU* 1.3 79.1 - - - +
443A GLY* 1.3 59.4 + - - +
445A ARG* 3.9 12.1 + - - +
446A ALA* 2.9 32.1 + - - +
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Residues in contact with GLY 443 (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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15A SER* 3.3 29.8 + - - -
18A ALA* 4.9 0.2 - - - -
19A ALA* 3.2 21.3 - - - +
424A ALA* 3.8 8.1 - - - -
439A ALA 3.0 12.7 + - - -
440A VAL 3.9 0.7 - - - -
442A ALA* 1.3 75.7 - - - +
444A GLU* 1.3 56.7 + - - +
446A ALA* 3.9 0.5 - - - +
447A ALA 3.0 23.6 + - - -
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Residues in contact with GLU 444 (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 ALA* 4.2 20.3 - - + +
19A ALA* 4.9 0.4 - - - +
22A LEU* 3.7 20.2 - - + +
67A ARG* 5.0 4.3 + - - -
70A ARG* 2.8 45.3 + - - -
71A LEU* 5.0 3.5 - - - +
440A VAL* 3.1 26.1 + - - +
441A GLU* 4.1 2.7 - - - +
443A GLY* 1.3 75.7 - - - +
445A ARG* 1.3 57.8 + - - +
447A ALA* 3.4 3.0 + - - +
448A ARG* 2.9 55.6 + - - +
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Residues in contact with ARG 445 (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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415A ARG* 3.7 18.4 + - - +
423A PHE 2.9 23.8 + - - +
428A THR* 2.8 38.8 + - - -
441A GLU* 3.0 21.4 + - + +
442A ALA* 3.9 15.6 + - - +
444A GLU* 1.3 76.4 - - - +
446A ALA* 1.3 63.8 + - - +
448A ARG* 3.2 16.8 + - - +
449A GLU* 2.8 68.4 + - - +
462A ILE* 4.0 9.3 - - + +
463A TRP* 3.7 53.5 - - + -
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Residues in contact with ALA 446 (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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261A ILE* 4.2 15.7 - - + -
422A TYR* 4.4 4.9 - - + +
423A PHE 3.9 11.7 - - - +
424A ALA* 3.9 11.9 - - + -
442A ALA 2.9 18.7 + - - +
443A GLY 3.9 3.4 - - - +
445A ARG* 1.3 96.0 - - - +
447A ALA* 1.3 62.0 + - - +
449A GLU* 3.2 10.5 + - - +
450A ILE* 3.2 24.4 + - - +
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Residues in contact with ALA 447 (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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19A ALA* 3.8 13.0 - - + +
22A LEU* 3.9 13.7 - - + -
23A LEU* 3.6 28.5 - - + +
261A ILE* 3.9 10.2 - - - +
443A GLY 3.0 18.4 + - - +
444A GLU 3.6 5.2 - - - +
445A ARG 3.3 0.2 - - - -
446A ALA* 1.3 76.0 - - - +
448A ARG* 1.3 58.5 + - - +
450A ILE* 3.2 7.0 + - - +
451A LEU* 3.0 29.0 + - - +
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Residues in contact with ARG 448 (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 LEU* 4.0 24.0 - - + +
67A ARG* 6.0 1.0 - - - +
441A GLU* 5.1 1.4 + - - +
444A GLU* 2.9 46.4 + - - +
445A ARG* 3.2 18.2 + - - +
447A ALA* 1.3 73.3 - - - +
449A GLU* 1.3 60.0 + - - +
451A LEU* 4.1 5.4 - - + -
452A HIS* 2.9 30.3 + - - +
457A ILE* 3.5 21.4 - - + +
461A GLU* 3.0 16.1 + - - -
462A ILE* 2.8 36.9 + - - +
463A TRP* 3.9 1.8 - - - +
464A GLN* 3.3 49.7 + - - +
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Residues in contact with GLU 449 (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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415A ARG* 4.6 10.1 - - - +
417A PRO* 4.6 6.7 - - - +
422A TYR* 3.6 34.8 - - + +
423A PHE 4.9 0.7 + - - -
445A ARG* 2.8 51.3 + - - +
446A ALA* 3.2 10.3 + - - +
448A ARG* 1.3 77.3 - - - +
450A ILE* 1.3 57.7 + - - +
452A HIS* 3.4 4.9 + - - +
453A ALA* 2.9 26.5 + - - +
462A ILE* 3.6 28.4 - - + +
463A TRP* 5.3 3.6 + - - -
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Residues in contact with ILE 450 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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7A VAL* 3.9 22.9 - - + -
23A LEU* 4.6 5.6 - - + -
259A TYR* 3.7 39.7 - - + -
260A VAL 4.2 2.0 - - - +
261A ILE* 3.5 36.6 - - + -
422A TYR* 3.5 28.9 - - + -
446A ALA 3.2 3.8 + - - +
447A ALA* 3.2 9.7 + - - +
449A GLU* 1.3 73.2 - - - +
451A LEU* 1.3 66.7 + - - +
453A ALA* 3.1 7.1 + - - +
454A MET* 2.9 32.5 + - + +
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Residues in contact with LEU 451 (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 LEU* 3.6 30.3 - - + -
23A LEU* 4.1 3.4 - - + -
26A SER* 3.6 30.1 - - - +
28A LEU* 3.8 22.2 - - + -
447A ALA 3.0 15.0 + - - +
448A ARG* 3.3 15.0 + - + +
450A ILE* 1.3 74.7 - - - +
452A HIS* 1.3 60.6 + - - +
454A MET* 3.3 4.1 + - - +
455A GLY 3.3 3.8 + - - -
456A LYS* 2.9 48.0 + - + +
457A ILE* 3.9 24.7 - - + -
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Residues in contact with HIS 452 (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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448A ARG 2.9 17.4 + - - +
449A GLU 3.6 4.9 - - - +
451A LEU* 1.3 74.7 - - - +
453A ALA* 1.3 62.6 + - - +
455A GLY* 2.9 19.8 + - - -
457A ILE* 3.2 27.2 + - + +
458A PRO* 4.7 1.1 - - + +
459A GLU* 3.5 33.6 + - + +
462A ILE* 3.9 28.0 - - + -
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Residues in contact with ALA 453 (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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259A TYR* 3.8 28.2 + - + +
422A TYR* 3.7 20.2 - - - +
449A GLU 2.9 14.4 + - - +
450A ILE* 3.1 9.6 + - - +
452A HIS* 1.3 80.2 - - - +
454A MET* 1.3 60.0 + - - +
455A GLY 3.4 0.5 + - - -
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Residues in contact with MET 454 (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 ASP* 4.3 9.2 - - + -
7A VAL* 4.4 1.3 - - + -
28A LEU* 3.6 44.2 - - + -
258A LYS* 4.0 19.7 - - + -
259A TYR* 3.6 39.0 - - + +
450A ILE* 2.9 23.6 + - + +
451A LEU* 3.7 5.6 - - - +
452A HIS 3.1 0.4 - - - -
453A ALA* 1.3 76.0 - - - +
455A GLY* 1.3 61.6 + - - +
456A LYS* 3.6 23.6 + - + +
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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
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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