Contacts of the helix formed by residues 412 - 433 (chain E) in PDB entry 1UW9
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 GLY 412 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406E THR 4.3 3.6 - - - -
409E HIS* 3.3 14.5 + - - +
410E PRO 3.5 1.2 + - - -
411E TRP* 1.3 80.2 - - - +
413E ASN* 1.3 60.7 + - - -
414E ALA 3.5 2.0 - - - -
415E PRO* 3.3 3.1 - - - +
416E GLY* 3.0 25.8 + - - -
77J LYS 5.4 0.2 - - - -
78J LEU* 3.7 24.3 - - - +
70K TRP* 3.9 6.5 - - - -
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Residues in contact with ASN 413 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188E ALA* 3.1 34.6 + - - +
191E GLU* 3.6 10.7 - - + +
192E CYS* 3.5 29.5 - - - +
406E THR* 3.5 9.1 - - - +
407E LEU* 3.4 28.3 - - - +
412E GLY* 1.3 70.0 - - - -
414E ALA* 1.3 57.8 + - - +
417E ALA* 2.8 36.2 + - - +
78J LEU* 5.0 0.2 - - - +
70K TRP* 2.8 34.5 + - - +
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Residues in contact with ALA 414 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191E GLU* 3.1 26.3 + - - +
194E ARG* 3.6 38.6 - - + +
195E GLY* 3.4 13.5 - - - -
413E ASN* 1.3 76.0 - - - +
415E PRO* 1.3 64.4 - - + +
417E ALA 3.3 0.7 + - - -
418E ALA* 2.9 27.0 + - - +
4F TRP* 3.8 9.4 - - + -
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Residues in contact with PRO 415 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
194E ARG* 5.7 0.2 - - - +
409E HIS* 3.8 10.3 + - + -
411E TRP* 3.5 38.6 - - + +
412E GLY 3.3 12.6 - - - +
414E ALA* 1.3 93.4 - - + +
416E GLY* 1.3 58.4 + - - +
418E ALA* 3.3 3.6 + - + +
419E ALA* 2.9 30.1 + - - +
454E GLU* 3.6 24.1 - - + +
2F MET 3.8 14.8 - - - +
3F VAL* 5.4 0.4 - - - -
4F TRP* 4.7 10.7 - - + +
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Residues in contact with GLY 416 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405E GLY 4.3 1.7 - - - +
406E THR* 3.8 13.0 - - - -
409E HIS* 3.5 29.1 - - - -
412E GLY 3.0 12.4 + - - -
413E ASN 3.6 3.4 - - - -
415E PRO* 1.3 76.4 - - - +
417E ALA* 1.3 61.0 + - - +
419E ALA* 3.4 3.5 + - - +
420E ASN* 3.1 28.3 + - - +
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Residues in contact with ALA 417 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192E CYS 3.1 27.4 - - - +
195E GLY* 3.5 12.1 - - - -
196E GLY* 4.7 0.2 - - - -
197E LEU* 3.5 26.9 - - + +
406E THR* 3.7 3.2 - - - +
413E ASN 2.8 17.7 + - - +
414E ALA 3.6 4.7 - - - +
416E GLY* 1.3 69.6 - - - +
418E ALA* 1.3 60.4 + - - +
420E ASN* 3.3 4.5 + - - +
421E ARG* 2.9 30.1 + - - +
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Residues in contact with ALA 418 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195E GLY 3.1 15.3 + - - +
414E ALA 2.9 16.9 + - - +
415E PRO 3.6 4.7 - - - +
417E ALA* 1.3 76.2 - - - +
419E ALA* 1.3 53.4 + - - +
421E ARG* 3.3 3.1 + - - +
422E VAL* 2.8 42.0 + - + +
454E GLU* 4.2 6.7 - - + -
4F TRP* 3.6 38.6 - - + -
17F TYR* 4.8 2.5 - - + -
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Residues in contact with ALA 419 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384E VAL* 4.1 4.7 - - + -
409E HIS* 4.1 2.5 - - + -
415E PRO 2.9 16.9 + - - +
416E GLY 3.6 6.3 - - - +
417E ALA 3.3 0.2 - - - -
418E ALA* 1.3 77.0 - - - +
420E ASN* 1.3 55.7 + - - +
422E VAL* 3.8 1.0 - - - +
423E ALA* 2.9 30.7 + - - +
454E GLU* 3.6 24.3 - - - +
455E LEU* 3.7 21.8 - - - +
458E ALA* 3.8 16.6 - - + -
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Residues in contact with ASN 420 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170E LEU* 4.0 4.3 - - + -
197E LEU* 4.5 9.0 - - + -
384E VAL* 3.4 24.9 - - - +
387E MET* 3.4 12.7 - - + +
402E PHE* 3.5 42.9 - - + +
405E GLY 3.2 12.7 + - - +
406E THR* 3.1 25.1 + - - -
416E GLY 3.1 11.3 + - - +
417E ALA* 3.7 6.2 - - - +
419E ALA* 1.3 76.2 - - - +
421E ARG* 1.3 58.6 + - - +
423E ALA 3.4 0.2 + - - -
424E LEU* 3.0 26.2 + - - +
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Residues in contact with ARG 421 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ARG* 3.5 29.3 - - - +
170E LEU* 3.5 19.7 - - + +
196E GLY* 2.8 41.5 + - - +
198E ASP* 4.4 0.6 + - - -
234E GLU* 2.9 41.2 + - - -
417E ALA 2.9 17.6 + - - +
418E ALA 3.8 2.9 - - - +
420E ASN* 1.3 72.7 - - - +
422E VAL* 1.3 65.8 + - - +
424E LEU* 3.4 0.9 + - - +
425E GLU* 2.7 59.5 + - - +
13F GLU 3.2 16.0 + - - -
17F TYR* 3.5 35.1 - - + -
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Residues in contact with VAL 422 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418E ALA* 2.8 29.0 + - + +
419E ALA* 3.8 3.4 - - - +
421E ARG* 1.3 72.7 - - - +
423E ALA* 1.3 64.7 + - - +
425E GLU* 3.2 3.7 + - - +
426E ALA* 2.9 23.9 + - - +
448E ALA* 4.2 1.8 - - + -
451E TRP* 3.4 28.9 - - + -
452E SER* 3.9 22.4 - - - +
455E LEU* 3.9 20.6 - - + -
4F TRP* 5.7 3.6 - - + -
17F TYR* 3.7 33.7 - - + +
18F LEU* 4.3 0.9 - - - +
138F ARG* 5.5 1.1 - - - +
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Residues in contact with ALA 423 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384E VAL* 4.3 7.4 - - + -
387E MET* 3.8 17.3 - - + -
419E ALA 2.9 18.1 + - - +
420E ASN 3.7 4.5 - - - +
422E VAL* 1.3 77.5 - - - +
424E LEU* 1.3 63.4 + - - +
426E ALA* 3.5 3.6 + - - +
427E CYS* 3.1 29.1 + - - -
445E ILE* 3.9 23.3 - - + -
455E LEU* 4.0 13.9 - - + +
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Residues in contact with LEU 424 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ARG* 4.0 15.3 - - + +
168E GLY* 3.1 39.0 - - - +
170E LEU* 3.6 26.7 - - + -
387E MET* 3.7 13.8 - - + +
391E VAL* 3.7 24.9 - - + -
400E LEU* 4.1 15.9 - - + -
420E ASN 3.0 17.8 + - - +
421E ARG* 3.8 4.7 - - - +
423E ALA* 1.3 75.8 - - - +
425E GLU* 1.3 55.4 + - - +
427E CYS* 3.3 2.1 + - - +
428E THR* 2.7 44.5 + - - +
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Residues in contact with GLU 425 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167E ARG* 3.9 11.8 - - + +
421E ARG* 2.7 58.6 + - - +
422E VAL* 3.9 2.5 - - - +
424E LEU* 1.3 75.7 - - + +
426E ALA* 1.3 57.7 + - - +
428E THR* 3.6 6.9 - - - -
429E GLN* 2.8 31.5 + - - +
13F GLU 3.6 0.7 - - - +
14F THR* 3.7 4.0 - - + -
15F PHE* 3.0 35.7 + - + +
16F SER 4.0 0.2 + - - -
17F TYR* 2.9 33.4 + - - +
18F LEU* 3.8 16.0 + - + -
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Residues in contact with ALA 426 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422E VAL 2.9 16.8 + - - +
423E ALA* 3.7 5.2 - - - +
425E GLU* 1.3 76.1 - - - +
427E CYS* 1.3 56.7 + - - +
429E GLN* 3.4 9.1 + - - +
430E ALA* 2.9 30.1 + - - +
444E VAL* 3.6 16.5 - - + +
445E ILE* 5.5 1.1 - - + -
448E ALA* 4.0 26.2 - - + -
451E TRP* 5.1 0.7 - - + -
18F LEU* 3.7 13.5 - - + +
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Residues in contact with CYS 427 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387E MET* 3.9 5.4 - - + -
388E PRO* 3.6 43.3 - - - -
391E VAL* 4.1 18.6 - - + -
423E ALA 3.1 20.8 + - - +
424E LEU 3.7 3.4 - - - +
426E ALA* 1.3 76.9 - - - +
428E THR* 1.3 57.1 + - - +
430E ALA* 3.4 1.7 + - - +
431E ARG* 2.9 30.3 + - - +
437E LEU* 3.7 16.9 - - + +
444E VAL* 4.0 9.9 - - - -
445E ILE* 4.0 10.3 - - - -
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Residues in contact with THR 428 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E GLY 3.3 26.2 - - - +
167E ARG* 4.2 9.7 - - + +
168E GLY 5.0 0.3 + - - -
391E VAL* 4.8 6.8 - - - +
396E ASP* 4.3 2.3 + - - +
424E LEU* 2.7 35.6 + - - +
425E GLU* 3.6 7.9 - - - -
427E CYS* 1.3 73.9 - - - +
429E GLN* 1.3 66.5 + - - +
431E ARG* 3.4 24.4 + - - +
432E ASN* 3.0 33.9 + - - +
15F PHE* 4.2 12.1 - - + -
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Residues in contact with GLN 429 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425E GLU 2.8 17.4 + - - +
426E ALA* 3.7 6.6 - - - +
428E THR* 1.3 77.0 - - - +
430E ALA* 1.3 61.1 + - - +
432E ASN* 3.2 4.6 + - - +
433E GLU* 2.9 45.8 + - - +
15F PHE* 3.8 20.1 - - + -
18F LEU* 3.7 18.4 - - + +
21F LEU* 3.5 30.1 - - - +
25F GLN* 3.7 21.5 + - - +
29F GLN* 4.0 11.7 + - - +
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Residues in contact with ALA 430 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426E ALA 2.9 17.7 + - - +
427E CYS 3.7 4.3 - - - +
429E GLN* 1.3 77.1 - - - +
431E ARG* 1.3 62.2 + - - +
433E GLU* 3.1 18.4 + - - +
435E ARG* 3.0 41.8 + - + +
437E LEU* 4.4 3.4 - - + -
444E VAL* 3.6 31.4 - - + -
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Residues in contact with ARG 431 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166E GLY 4.4 0.8 + - - -
391E VAL* 4.0 18.7 + - + +
395E GLY* 4.4 5.5 - - - -
396E ASP* 2.8 48.8 + - - +
427E CYS 2.9 17.0 + - - +
428E THR* 3.6 16.6 - - - +
430E ALA* 1.3 76.5 - - - +
432E ASN* 1.3 89.4 + - - +
434E GLY* 3.0 15.9 + - - -
435E ARG 4.0 13.3 - - - +
437E LEU* 3.9 17.4 - - + +
32F TYR* 3.6 17.5 + - - -
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Residues in contact with ASN 432 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166E GLY 5.0 1.9 - - - +
428E THR* 3.0 15.5 + - - +
429E GLN 3.4 5.4 - - - +
431E ARG* 1.3 111.6 + - - +
433E GLU* 1.3 59.9 + - - +
434E GLY 3.2 0.7 + - - -
15F PHE* 3.8 10.2 - - - -
28F ALA 4.3 4.0 - - - +
29F GLN* 3.0 33.2 + - - +
32F TYR* 3.2 54.3 - - + +
119F MET* 5.4 2.6 - - - +
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Residues in contact with GLU 433 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429E GLN* 2.9 42.1 + - - +
430E ALA* 3.1 16.7 + - - +
432E ASN* 1.3 75.6 - - - +
434E GLY* 1.3 57.8 + - - +
435E ARG* 3.5 14.8 + - + +
25F GLN* 4.0 19.6 - - - +
28F ALA* 4.0 24.7 - - + +
29F GLN* 4.4 6.7 - - - +
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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
------------------------------------------------------------
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