Contacts of the helix formed by residues 412 - 433 (chain O) 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 O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M LEU* 3.6 23.4 - - - +
406O THR 4.3 3.8 - - - -
409O HIS* 3.1 18.0 + - - +
410O PRO 3.5 0.6 - - - -
411O TRP* 1.3 79.9 - - - +
413O ASN* 1.3 60.9 + - - -
414O ALA 3.5 2.2 - - - -
415O PRO* 3.4 3.3 - - - +
416O GLY 3.0 23.0 + - - -
70V TRP* 3.9 6.3 - - - -
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Residues in contact with ASN 413 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78M LEU* 4.9 0.6 - - - +
188O ALA* 3.1 40.0 + - - +
191O GLU* 3.6 10.5 - - + +
192O CYS* 3.5 29.1 - - - +
406O THR* 3.5 8.6 - - - +
407O LEU* 3.3 23.2 - - - +
412O GLY* 1.3 70.0 - - - -
414O ALA* 1.3 60.7 + - - +
416O GLY 3.2 0.3 + - - -
417O ALA* 2.8 31.2 + - - +
70V TRP* 2.8 34.3 + - + +
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Residues in contact with ALA 414 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191O GLU* 3.1 24.5 + - - +
194O ARG* 3.6 38.4 - - + +
195O GLY* 3.4 13.0 - - - -
413O ASN* 1.3 78.1 - - - +
415O PRO* 1.3 65.5 - - + +
417O ALA 3.3 0.7 + - - -
418O ALA* 2.9 27.1 + - - +
4T TRP* 3.9 10.0 - - + -
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Residues in contact with PRO 415 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409O HIS* 3.8 10.9 + - + -
411O TRP* 3.5 39.0 - - + +
412O GLY* 3.4 11.4 - - - +
414O ALA* 1.3 95.2 - - + +
416O GLY* 1.3 55.3 + - - +
418O ALA* 3.2 3.4 + - + +
419O ALA* 2.9 29.6 + - - +
454O GLU* 3.6 23.6 - - + +
2T MET 3.8 14.4 - - - +
3T VAL* 5.4 0.4 - - - -
4T TRP* 4.6 11.2 - - + +
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Residues in contact with GLY 416 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
405O GLY 4.4 1.7 - - - +
406O THR* 3.9 14.4 - - - -
409O HIS* 3.5 29.3 - - - -
412O GLY 3.0 12.4 + - - -
413O ASN 3.2 4.0 + - - -
415O PRO* 1.3 75.2 - - - +
417O ALA* 1.3 60.9 + - - +
419O ALA* 3.4 3.1 + - - +
420O ASN* 3.1 28.1 + - - +
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Residues in contact with ALA 417 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
192O CYS 3.1 28.3 - - - +
195O GLY* 3.4 12.8 - - - -
196O GLY 4.7 0.2 - - - -
197O LEU* 3.6 27.1 - - + +
406O THR* 3.7 3.4 - - - +
413O ASN 2.8 17.0 + - - +
414O ALA 3.5 4.7 - - - +
416O GLY* 1.3 71.5 - - - +
418O ALA* 1.3 59.4 + - - +
420O ASN* 3.2 4.3 + - - +
421O ARG* 2.9 30.0 + - - +
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Residues in contact with ALA 418 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195O GLY 3.0 17.1 + - - +
414O ALA 2.9 15.2 + - - +
415O PRO* 3.5 6.3 - - + +
417O ALA* 1.3 77.1 - - - +
419O ALA* 1.3 58.0 + - - +
421O ARG* 3.8 2.6 - - - +
422O VAL* 2.8 38.5 + - + +
454O GLU* 4.3 5.4 - - + -
4T TRP* 3.6 37.9 - - + -
17T TYR* 4.8 1.8 - - + -
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Residues in contact with ALA 419 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384O VAL* 4.1 5.2 - - + -
409O HIS* 4.1 2.9 - - + -
415O PRO 2.9 15.1 + - - +
416O GLY 3.7 5.4 - - - +
417O ALA 3.2 0.2 - - - -
418O ALA* 1.3 76.9 - - - +
420O ASN* 1.3 57.4 + - - +
422O VAL* 3.5 2.0 + - - +
423O ALA* 2.9 30.3 + - - +
454O GLU* 3.5 27.3 - - - +
455O LEU* 3.7 21.5 - - - +
458O ALA* 3.8 16.4 - - + -
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Residues in contact with ASN 420 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170O LEU* 4.0 4.0 - - + +
197O LEU* 4.5 9.1 - - + +
384O VAL* 3.4 25.7 - - - +
387O MET* 3.4 12.8 - - + +
402O PHE* 3.5 43.6 - - + +
405O GLY 3.2 13.5 + - - +
406O THR* 3.1 19.9 + - - -
416O GLY 3.1 15.9 + - - +
417O ALA 3.7 6.7 - - - +
419O ALA* 1.3 77.4 - - - +
421O ARG* 1.3 56.3 + - - +
423O ALA 3.4 0.3 + - - -
424O LEU* 3.0 27.0 + - - +
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Residues in contact with ARG 421 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167O ARG* 3.5 28.5 - - - +
170O LEU* 3.5 18.5 - - + +
196O GLY* 2.9 33.6 + - - +
198O ASP* 4.5 0.6 + - - -
234O GLU* 2.8 41.2 + - - -
417O ALA 2.9 17.0 + - - +
418O ALA 3.8 3.1 - - - +
420O ASN* 1.3 73.1 - - - +
422O VAL* 1.3 66.7 + - - +
424O LEU* 3.4 1.7 + - - +
425O GLU* 2.8 58.5 + - - +
13T GLU 3.3 16.6 + - - -
17T TYR* 3.4 39.0 - - + -
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Residues in contact with VAL 422 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
418O ALA* 2.8 26.8 + - + +
419O ALA* 3.7 4.3 - - - +
421O ARG* 1.3 71.9 - - - +
423O ALA* 1.3 63.7 + - - +
425O GLU* 3.3 3.1 + - - +
426O ALA* 2.9 23.4 + - - +
448O ALA* 4.2 1.6 - - + -
451O TRP* 3.4 28.3 - - + -
452O SER* 3.9 22.2 - - - +
454O GLU* 6.1 0.2 - - + -
455O LEU* 3.8 21.8 - - + -
4T TRP* 5.7 3.4 - - + -
17T TYR* 3.7 33.9 - - + +
18T LEU* 4.3 1.1 - - - +
138T ARG* 5.4 1.6 - - - +
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Residues in contact with ALA 423 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
384O VAL* 4.3 7.9 - - + +
387O MET* 3.7 17.7 - - + -
419O ALA 2.9 17.0 + - - +
420O ASN 3.4 4.2 + - - +
422O VAL* 1.3 76.1 - - - +
424O LEU* 1.3 62.9 + - - +
426O ALA* 3.5 2.8 + - - +
427O CYS* 3.1 30.1 + - - -
445O ILE* 3.9 23.6 - - + -
455O LEU* 4.1 16.4 - - + -
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Residues in contact with LEU 424 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167O ARG* 4.0 15.3 - - + +
168O GLY* 3.2 39.0 - - - +
170O LEU* 3.6 26.5 - - + -
387O MET* 3.7 14.5 - - + +
391O VAL* 3.7 24.2 - - + -
400O LEU* 4.1 16.6 - - + -
420O ASN 3.0 17.4 + - - +
421O ARG* 3.7 4.9 - - - +
423O ALA* 1.3 77.8 - - - +
425O GLU* 1.3 54.7 + - - +
427O CYS* 3.3 2.6 + - - +
428O THR* 2.7 44.8 + - - +
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Residues in contact with GLU 425 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167O ARG* 3.9 11.4 - - - -
421O ARG* 2.8 57.1 + - - +
422O VAL* 4.0 0.9 - - - +
424O LEU* 1.3 76.5 - - + +
426O ALA* 1.3 57.0 + - - +
428O THR* 3.3 7.3 + - - -
429O GLN* 2.8 31.9 + - - +
13T GLU 3.5 0.9 - - - +
14T THR* 3.6 3.7 - - + -
15T PHE* 2.9 36.2 + - + +
17T TYR* 2.8 33.6 + - - +
18T LEU* 3.7 17.5 + - + -
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Residues in contact with ALA 426 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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422O VAL 2.9 18.3 + - - +
423O ALA* 3.8 4.7 - - - +
425O GLU* 1.3 76.6 - - - +
427O CYS* 1.3 57.2 + - - +
429O GLN* 3.4 8.8 + - - +
430O ALA* 2.9 29.5 + - - +
444O VAL* 3.6 16.4 - - + +
445O ILE* 5.5 1.1 - - + -
448O ALA* 3.9 25.1 - - + -
451O TRP* 5.1 0.9 - - + -
18T LEU* 3.6 14.7 - - + +
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Residues in contact with CYS 427 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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387O MET* 3.8 7.0 - - + -
388O PRO* 3.6 42.2 - - - -
391O VAL* 4.1 17.0 - - + -
423O ALA 3.1 23.9 + - - +
424O LEU 3.7 3.6 - - - +
426O ALA* 1.3 75.4 - - - +
428O THR* 1.3 58.0 + - - +
430O ALA* 3.6 1.2 - - - +
431O ARG* 2.9 30.8 + - - +
437O LEU* 3.7 17.4 - - + +
444O VAL* 4.0 9.9 - - - -
445O ILE* 3.9 10.1 - - - -
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Residues in contact with THR 428 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166O GLY 3.3 26.2 - - - +
167O ARG* 4.1 9.6 - - + +
391O VAL* 4.8 7.1 - - - +
396O ASP* 4.3 2.8 + - - +
424O LEU* 2.7 36.0 + - - +
425O GLU* 3.6 6.7 - - - -
427O CYS* 1.3 73.8 - - - +
429O GLN* 1.3 67.4 + - - +
431O ARG* 3.4 24.2 + - - +
432O ASN* 2.9 31.7 + - - +
15T PHE* 4.1 15.0 - - + -
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Residues in contact with GLN 429 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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425O GLU 2.8 20.5 + - - +
426O ALA* 3.7 6.6 - - - +
428O THR* 1.3 72.0 - - - +
430O ALA* 1.3 58.6 + - - +
432O ASN* 3.2 3.8 + - - +
433O GLU* 2.9 48.5 + - - +
15T PHE* 3.7 18.7 - - + -
18T LEU* 3.6 19.7 - - + +
21T LEU* 3.4 29.9 - - - +
25T GLN* 3.6 23.5 + - - +
29T GLN* 3.9 11.5 + - - +
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Residues in contact with ALA 430 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426O ALA 2.9 17.5 + - - +
427O CYS* 3.6 4.5 - - - +
429O GLN* 1.3 75.6 - - - +
431O ARG* 1.3 62.8 + - - +
433O GLU* 3.1 18.6 + - - +
434O GLY 3.3 0.2 + - - -
435O ARG* 3.0 41.9 + - + +
437O LEU* 4.3 2.9 - - + -
444O VAL* 3.6 31.9 - - + -
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Residues in contact with ARG 431 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166O GLY 4.4 0.6 + - - -
391O VAL* 4.0 19.4 + - - +
395O GLY* 4.4 5.3 - - - -
396O ASP* 2.9 49.1 + - - +
427O CYS 2.9 18.0 + - - +
428O THR* 3.5 18.1 - - - +
430O ALA* 1.3 74.8 - - - +
432O ASN* 1.3 87.5 + - - +
434O GLY* 3.0 16.3 + - - -
435O ARG 3.9 13.8 + - - +
437O LEU* 3.9 17.8 - - + +
32T TYR* 3.6 16.3 + - + -
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Residues in contact with ASN 432 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166O GLY 5.0 2.1 - - - +
428O THR* 2.9 18.8 + - - +
429O GLN 3.4 4.9 - - - +
431O ARG* 1.3 111.4 + - - +
433O GLU* 1.3 59.5 + - - +
434O GLY 3.4 0.9 + - - -
15T PHE* 3.7 10.7 - - - -
28T ALA 4.2 4.2 - - - +
29T GLN* 2.9 34.9 + - - +
32T TYR* 3.2 55.3 - - + +
119T MET* 5.3 2.4 - - - +
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Residues in contact with GLU 433 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
429O GLN* 2.9 45.1 + - - +
430O ALA* 3.1 14.3 + - - +
432O ASN* 1.3 75.2 - - - +
434O GLY* 1.3 57.4 + - - +
435O ARG* 3.5 14.8 + - + +
25T GLN* 3.9 20.3 - - - +
28T ALA* 3.9 26.0 - - + +
29T GLN* 4.3 5.9 - - - +
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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