Contacts of the helix formed by residues 435 - 454 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60B TYR 5.1 0.4 - - - -
65B GLN* 3.8 9.6 - - - +
172B CYS* 5.1 4.7 + - - -
188B TYR* 3.4 21.0 - + - -
192B CYS* 3.5 17.0 - - - -
198B ILE* 3.3 29.6 + - - +
205B GLY* 5.4 1.3 - - - -
206B GLN* 4.6 13.8 + - - -
398B TYR* 6.3 2.0 - + - -
426B THR* 2.7 22.3 + - - -
432B TRP* 3.1 50.2 + + + +
433B SER 3.6 4.5 - - - -
434B GLY* 1.3 82.1 - - - +
436B MET* 1.3 66.0 + - - +
437B GLU* 3.2 8.7 - - + +
438B GLY 3.1 1.0 + - - -
439B ALA* 3.1 6.1 + - - +
1500B FAD 3.3 41.7 + + - +
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Residues in contact with MET 436 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B ILE* 3.7 29.3 - - + +
43B THR* 3.8 13.7 - - + -
58B GLY 4.3 0.7 - - - +
59B SER* 3.6 25.1 - - - +
60B TYR 3.4 25.6 - - - +
61B VAL* 3.6 14.6 - - + -
68B ILE* 4.1 14.1 - - + -
210B PHE* 4.5 6.3 - - + -
214B SER* 3.7 24.7 - - - -
217B VAL* 5.9 0.2 - - - -
435B TYR* 1.3 70.5 - - - +
437B GLU* 1.3 62.3 + - - +
439B ALA* 3.1 20.0 + - - +
440B VAL* 3.1 17.2 + - - +
1500B FAD 2.8 29.0 + - + +
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Residues in contact with GLU 437 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B THR 4.4 2.6 - - - +
65B GLN* 3.0 34.2 + - + +
66B ASN 3.7 2.6 + - - -
67B ARG* 3.0 42.3 + - - +
68B ILE* 2.9 37.5 + - + +
431B HIS* 4.2 5.2 + - - +
432B TRP* 3.6 35.4 - - + -
435B TYR* 3.2 2.0 - - + +
436B MET* 1.3 76.6 - - - +
438B GLY* 1.3 58.3 + - - +
440B VAL* 3.1 6.4 + - - +
441B GLU* 3.0 24.5 + - + +
1500B FAD 4.5 0.6 + - - -
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Residues in contact with GLY 438 (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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426B THR* 3.4 9.0 - - - -
429B ALA* 3.4 22.2 - - - +
431B HIS 3.8 4.7 - - - -
432B TRP 3.1 23.1 + - - -
435B TYR 3.1 1.2 + - - -
437B GLU* 1.3 76.1 - - - +
439B ALA* 1.3 65.7 + - - +
441B GLU* 4.3 1.3 - - - -
442B ALA* 2.9 27.5 + - - +
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Residues in contact with ALA 439 (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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14B ILE* 3.8 8.1 - - + -
15B SER* 2.8 45.4 + - - +
426B THR* 3.3 8.9 + - - +
435B TYR 3.1 10.2 + - - +
436B MET* 3.1 12.7 + - - +
438B GLY* 1.3 76.5 - - - +
440B VAL* 1.3 59.0 + - - +
443B GLY 3.0 13.2 + - - -
1500B FAD 3.6 25.8 - - - +
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Residues in contact with VAL 440 (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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14B ILE* 3.6 18.4 - - + -
18B ALA* 4.2 6.5 - - + -
67B ARG* 3.8 27.1 - - + +
68B ILE* 3.8 22.4 - - + -
70B ARG* 4.4 0.9 - - - +
71B LEU* 3.8 16.8 - - + -
436B MET 3.1 13.9 + - - +
437B GLU 3.1 5.6 + - - +
439B ALA* 1.3 74.6 - - - +
441B GLU* 1.3 67.0 + - - +
443B GLY 3.3 0.3 + - - -
444B GLU* 3.1 50.5 + - + +
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Residues in contact with GLU 441 (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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67B ARG* 3.7 37.9 + - - +
429B ALA* 3.4 8.5 - - - +
430B THR* 2.9 32.0 + - - -
431B HIS* 3.1 36.3 + - - +
437B GLU* 3.0 12.6 + - - +
438B GLY* 3.4 7.6 + - - +
440B VAL* 1.3 75.6 - - - +
442B ALA* 1.3 58.4 + - - +
444B GLU* 3.9 2.7 - - - +
445B ARG* 2.9 31.7 + - + +
448B ARG* 5.1 1.7 + - - +
463B TRP* 3.5 22.6 - - + -
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Residues in contact with ALA 442 (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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15B SER* 4.0 0.7 - - - +
424B ALA* 3.7 3.1 - - - +
425B GLY 3.1 34.8 - - - +
428B THR* 3.2 15.0 - - - +
429B ALA 4.2 6.7 - - - +
438B GLY 2.9 15.4 + - - +
441B GLU* 1.3 78.2 - - - +
443B GLY* 1.3 60.7 + - - +
445B ARG* 3.9 10.8 + - - +
446B ALA* 2.9 30.8 + - - +
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Residues in contact with GLY 443 (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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15B SER* 3.3 29.8 + - - -
18B ALA* 4.9 0.7 - - - -
19B ALA* 3.2 21.3 - - - +
424B ALA* 3.8 8.5 - - - -
439B ALA 3.0 12.9 + - - -
440B VAL 4.0 0.2 - - - -
442B ALA* 1.3 75.6 - - - +
444B GLU* 1.3 57.7 + - - +
446B ALA* 4.0 0.5 - - - +
447B ALA 3.0 22.9 + - - -
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Residues in contact with GLU 444 (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 ALA* 4.1 18.9 - - + +
19B ALA* 4.9 0.2 - - - +
22B LEU* 3.7 21.7 - - + +
67B ARG* 5.1 3.5 - - - -
70B ARG* 2.8 45.4 + - - -
71B LEU* 4.9 4.0 - - - +
440B VAL* 3.1 27.1 + - + +
441B GLU* 4.1 2.5 - - - +
443B GLY* 1.3 78.9 - - - +
445B ARG* 1.3 56.0 + - - +
447B ALA* 3.3 3.1 + - - +
448B ARG* 2.9 56.8 + - - +
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Residues in contact with ARG 445 (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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415B ARG* 3.7 19.8 + - - +
423B PHE 2.9 24.4 + - - +
428B THR* 2.9 38.2 + - - -
441B GLU* 2.9 20.5 + - + +
442B ALA* 3.9 11.3 + - - +
444B GLU* 1.3 73.9 - - - +
446B ALA* 1.3 69.8 + - - +
448B ARG* 3.2 15.5 + - - +
449B GLU* 2.8 69.7 + - - +
462B ILE* 3.9 11.7 - - + +
463B TRP* 3.7 54.9 - - + -
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Residues in contact with ALA 446 (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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261B ILE* 4.2 14.8 - - + -
422B TYR* 4.4 5.8 - - + +
423B PHE 3.8 12.3 - - - +
424B ALA* 3.9 13.5 - - + -
442B ALA 2.9 21.6 + - - +
443B GLY 4.0 1.6 - - - +
445B ARG* 1.3 90.5 - - - +
447B ALA* 1.3 65.1 + - - +
449B GLU* 3.2 16.8 + - - +
450B ILE* 3.3 17.3 + - - +
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Residues in contact with ALA 447 (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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19B ALA* 3.8 13.7 - - - +
22B LEU* 4.0 14.1 - - + -
23B LEU* 3.6 28.0 - - + +
261B ILE* 3.9 10.4 - - - +
443B GLY 3.0 19.1 + - - +
444B GLU 3.5 4.7 - - - +
445B ARG 3.3 0.2 - - - -
446B ALA* 1.3 76.6 - - - +
448B ARG* 1.3 56.8 + - - +
450B ILE* 3.1 8.4 + - - +
451B LEU* 2.9 28.4 + - - +
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Residues in contact with ARG 448 (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 LEU* 4.0 24.7 - - + +
67B ARG* 6.0 1.4 - - - +
441B GLU* 5.1 1.8 + - - +
444B GLU* 2.9 47.8 + - - +
445B ARG* 3.2 14.9 + - - +
447B ALA* 1.3 72.1 - - - +
449B GLU* 1.3 60.8 + - - +
451B LEU* 4.1 6.1 - - + -
452B HIS* 2.8 30.5 + - - +
457B ILE* 3.5 22.3 - - + +
461B GLU* 3.1 14.6 + - - -
462B ILE* 2.8 40.2 + - - +
463B TRP* 3.9 2.0 - - - +
464B GLN* 3.3 50.2 + - - +
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Residues in contact with GLU 449 (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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415B ARG 4.7 5.6 - - - +
417B PRO* 3.9 14.7 - - - +
422B TYR* 3.5 34.0 - - + +
423B PHE 4.9 0.7 + - - -
445B ARG* 2.8 50.5 + - - +
446B ALA* 3.2 10.3 + - - +
448B ARG* 1.3 77.0 - - - +
450B ILE* 1.3 57.4 + - - +
452B HIS* 3.4 4.5 + - - +
453B ALA* 2.9 27.2 + - - +
462B ILE* 3.7 28.9 - - + +
463B TRP* 6.2 0.2 - - - -
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Residues in contact with ILE 450 (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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7B VAL* 4.0 17.3 - - + -
23B LEU* 4.6 6.5 - - + -
259B TYR* 3.6 40.4 - - + -
260B VAL 4.2 1.6 - - - +
261B ILE* 3.4 38.4 - - + -
422B TYR* 3.6 28.9 - - + -
446B ALA 3.3 4.7 + - - +
447B ALA* 3.1 9.0 + - - +
449B GLU* 1.3 72.7 - - - +
451B LEU* 1.3 68.6 + - - +
453B ALA* 3.1 7.3 + - - +
454B MET* 2.9 37.8 + - + +
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Residues in contact with LEU 451 (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 LEU* 3.7 28.7 - - + -
23B LEU* 4.0 4.5 - - + -
26B SER* 3.7 27.6 - - - +
28B LEU* 3.7 22.4 - - + -
447B ALA 2.9 15.7 + - - +
448B ARG* 3.3 15.7 + - + +
450B ILE* 1.3 75.9 - - - +
452B HIS* 1.3 59.3 + - - +
454B MET* 3.3 8.7 + - - +
456B LYS* 2.9 46.0 + - + +
457B ILE* 3.9 26.0 - - + -
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Residues in contact with HIS 452 (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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448B ARG 2.8 17.1 + - - +
449B GLU 3.6 4.7 - - - +
451B LEU* 1.3 73.9 - - - +
453B ALA* 1.3 62.9 + - - +
455B GLY* 2.9 20.5 + - - -
457B ILE* 3.1 30.4 + - + +
458B PRO* 4.1 1.6 - - + +
459B GLU* 3.4 36.1 + - + +
462B ILE* 3.9 29.6 - - + -
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Residues in contact with ALA 453 (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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259B TYR* 3.8 27.0 + - + +
422B TYR* 3.7 20.4 - - - +
449B GLU 2.9 14.2 + - - +
450B ILE* 3.1 9.2 + - - +
452B HIS* 1.3 79.9 - - - +
454B MET* 1.3 58.9 + - - +
455B GLY 3.4 1.0 + - - -
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Residues in contact with MET 454 (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 ASP* 4.6 3.6 - - + -
7B VAL* 4.3 6.5 - - + -
28B LEU* 3.8 34.3 - - + -
258B LYS* 4.4 17.0 - - + -
259B TYR* 3.5 39.7 - - + +
450B ILE* 2.9 27.7 + - + +
451B LEU* 3.6 7.2 - - - +
452B HIS 3.1 0.4 - - - -
453B ALA* 1.3 75.8 - - - +
455B GLY* 1.3 61.1 + - - +
456B LYS* 3.4 29.2 + - + +
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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