Contacts of the helix formed by residues 419 - 439 (chain I) in PDB entry 1DE4
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 419 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155I ARG* 2.8 20.1 + - - -
408I GLN* 2.9 11.5 + - - +
409I ARG* 2.6 34.5 + - - -
410I ASP 3.4 15.7 - - - -
411I ALA* 4.0 5.2 - - - -
415I GLY 2.7 12.7 + - - -
417I ALA 3.3 0.2 - - - -
418I LYS* 1.3 77.3 - - - +
420I GLY* 1.3 62.0 + - - -
421I VAL 3.6 0.9 - - - -
422I GLY* 3.5 3.7 + - - +
423I THR* 3.0 25.1 + - - -
485I ASP* 5.3 0.4 - - - -
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Residues in contact with GLY 420 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144I ILE* 4.8 5.2 - - - -
147I LEU* 3.7 15.2 - - - +
148I ASN* 4.9 1.8 - - - -
155I ARG* 3.8 16.2 - - - +
415I GLY 2.8 7.2 + - - -
416I ALA* 2.8 18.4 + - - -
419I SER* 1.3 68.3 - - - +
421I VAL* 1.3 54.6 + - - -
423I THR* 3.1 3.5 + - - -
424I ALA* 2.7 37.1 + - - +
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Residues in contact with VAL 421 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144I ILE* 4.0 20.3 - - + +
416I ALA 2.9 15.4 + - - +
417I ALA* 4.1 14.1 - - - +
419I SER 3.6 0.2 - - - -
420I GLY* 1.3 71.6 - - - +
422I GLY* 1.3 65.2 + - - +
424I ALA* 3.2 7.1 + - - +
425I LEU* 2.8 37.2 + - + +
487I ALA* 4.9 2.9 - - + +
488I VAL* 3.9 43.3 - - + +
576I LEU* 3.6 31.9 - - + -
583I LEU* 5.1 0.4 - - + -
587I ALA* 5.4 1.1 - - + -
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Residues in contact with GLY 422 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407I ALA* 3.6 17.6 - - - +
417I ALA 4.9 2.6 + - - -
418I LYS 5.6 0.2 + - - -
419I SER* 3.5 6.7 + - - -
420I GLY 3.2 0.8 - - - -
421I VAL* 1.3 78.2 - - - +
423I THR* 1.3 62.3 + - - +
425I LEU* 3.0 7.4 + - - +
426I LEU 2.9 18.7 + - - -
484I LEU* 3.5 26.9 + - - +
485I ASP* 4.6 5.2 - - - -
486I LYS 5.2 1.6 - - - +
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Residues in contact with THR 423 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147I LEU* 3.8 20.4 - - + -
155I ARG* 6.1 0.2 - - - -
165I LEU* 4.9 7.6 - - + -
169I VAL* 4.2 25.4 - - + -
407I ALA* 3.8 8.6 - - - +
408I GLN 3.1 22.0 + - - -
409I ARG* 3.8 12.5 - - + +
419I SER* 3.0 12.9 + - - -
420I GLY* 3.7 2.5 - - - -
422I GLY* 1.3 74.4 - - - +
424I ALA* 1.3 63.1 + - - +
426I LEU* 3.3 6.8 + - + +
427I LEU* 3.0 25.2 + - + +
452I SER* 4.4 7.5 + - - +
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Residues in contact with ALA 424 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I PHE* 4.7 5.4 - - + +
143I THR* 4.0 27.1 - - + +
144I ILE* 3.6 29.2 - - + +
147I LEU* 3.8 4.4 - - + +
420I GLY 2.7 20.4 + - - +
421I VAL 3.4 4.7 - - - +
423I THR* 1.3 72.0 - - - +
425I LEU* 1.3 64.4 + - + +
427I LEU* 3.2 4.2 + - - +
428I LYS* 3.1 27.5 + - - +
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Residues in contact with LEU 425 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140I PHE* 4.1 12.3 - - + -
421I VAL* 2.8 25.1 + - + +
422I GLY 3.0 6.7 + - - +
424I ALA* 1.3 78.8 - - + +
426I LEU* 1.3 57.6 + - - +
428I LYS* 3.9 3.9 - - - +
429I LEU* 2.9 40.2 + - + +
484I LEU* 4.0 26.5 - - + +
487I ALA* 3.7 30.1 - - + -
587I ALA* 3.5 31.0 - - + +
590I ALA* 4.0 11.4 - - + -
591I ALA* 4.0 17.9 - - + +
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Residues in contact with LEU 426 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169I VAL* 4.9 3.1 - - + -
173I PHE* 4.1 18.6 - - + -
405I VAL* 3.5 33.4 - - + +
406I GLY* 3.9 7.9 - - - -
407I ALA* 4.3 6.7 - - + +
422I GLY 2.9 12.4 + - - +
423I THR* 3.5 13.0 - - + +
424I ALA 3.2 0.2 - - - -
425I LEU* 1.3 76.7 - - - +
427I LEU* 1.3 63.5 + - - +
429I LEU* 3.9 2.6 - - - +
430I ALA* 3.0 24.3 + - - +
450I PHE* 4.0 13.9 - - + -
451I ALA 3.4 32.5 - - - +
452I SER* 3.9 17.3 - - - +
484I LEU* 3.7 9.1 - - + +
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Residues in contact with LEU 427 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143I THR* 3.9 18.6 - - + -
147I LEU* 4.6 4.0 - - + -
168I TYR* 3.8 25.8 - - + +
169I VAL* 3.9 26.0 - - + -
172I GLN* 3.7 32.3 - - + +
173I PHE* 4.3 6.5 - - + -
176I PHE* 3.1 17.0 - - + -
423I THR* 3.0 31.5 + - + +
424I ALA 3.6 5.6 - - - +
426I LEU* 1.3 77.8 - - + +
428I LYS* 1.3 74.1 + - - +
430I ALA* 3.3 1.9 + - - +
431I GLN* 3.1 16.5 + - - +
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Residues in contact with LYS 428 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I THR* 3.6 18.4 - - + -
139I ASP 4.4 4.2 + - - +
140I PHE* 3.5 39.7 - - + -
143I THR* 3.8 25.9 + - - +
172I GLN* 5.6 2.2 + - - -
176I PHE* 5.0 3.4 - - - -
424I ALA 3.1 16.1 + - - +
425I LEU 3.9 1.6 - - - +
427I LEU* 1.3 86.1 - - - +
429I LEU* 1.3 67.3 + - - +
431I GLN* 2.7 42.9 + - - +
432I MET* 2.8 24.4 + - + +
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Residues in contact with LEU 429 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I LEU* 5.8 0.9 - - + -
405I VAL* 4.5 6.7 - - + -
425I LEU* 2.9 28.3 + - + +
426I LEU 3.9 3.1 - - - +
428I LYS* 1.3 73.0 - - - +
430I ALA* 1.3 63.7 + - - +
432I MET* 3.4 9.8 + - + -
433I PHE* 3.0 52.9 + - + -
450I PHE* 3.7 12.3 - - + -
484I LEU* 3.4 29.4 - - + -
591I ALA* 3.5 35.2 - - + +
594I ALA* 3.9 15.7 - - + -
595I GLY* 3.9 7.0 - - - +
598I VAL* 5.7 1.6 - - + -
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Residues in contact with ALA 430 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173I PHE* 3.9 20.4 - - + -
176I PHE* 3.8 8.3 - - + -
178I LEU* 3.7 11.4 - - + +
393I ILE* 4.4 1.2 - - - +
426I LEU 3.0 18.1 + - - +
427I LEU 3.6 4.7 - - - +
429I LEU* 1.3 76.9 - - - +
431I GLN* 1.3 60.1 + - - +
433I PHE 4.2 0.4 - - - -
434I SER* 3.3 22.5 + - - -
450I PHE* 3.3 34.7 - - + -
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Residues in contact with GLN 431 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I THR* 5.4 2.1 - - - +
172I GLN* 5.4 0.6 + - - -
176I PHE* 3.3 38.7 - - + -
427I LEU 3.1 11.9 + - - +
428I LYS* 2.7 39.9 + - - +
430I ALA* 1.3 74.7 - - - +
432I MET* 1.3 68.9 + - + +
434I SER* 2.8 15.7 + - - -
435I ASP* 3.0 24.5 + - - +
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Residues in contact with MET 432 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I LEU* 4.4 6.7 - - + -
134I LYS* 4.2 16.7 - - + -
135I LEU* 3.3 44.9 - - + -
138I THR* 4.1 18.8 - - + +
140I PHE* 3.9 13.9 - - + -
428I LYS* 2.8 42.6 + - + +
429I LEU* 4.0 11.4 - - + +
431I GLN* 1.3 75.1 - - + +
433I PHE* 1.3 60.7 + - + +
435I ASP* 3.4 9.1 + - - +
436I MET* 3.0 42.7 + - + +
591I ALA* 4.5 3.8 - - + -
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Residues in contact with PHE 433 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131I LEU* 4.4 4.0 - - + -
393I ILE* 3.6 20.0 - - + +
429I LEU* 3.0 56.3 + - + +
430I ALA 4.5 0.2 - - - +
432I MET* 1.3 77.3 - - + +
434I SER* 1.3 64.1 + - - +
436I MET* 3.9 19.6 - - + +
437I VAL* 3.2 28.8 + - + +
442I PHE* 4.0 18.8 - + + -
448I ILE* 4.3 3.6 - - + -
450I PHE* 4.4 11.0 - + + -
595I GLY* 3.4 28.5 - - - -
598I VAL* 3.7 25.6 - - + -
599I ILE* 3.3 27.4 - - + -
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Residues in contact with SER 434 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176I PHE* 2.4 35.3 + - - -
177I LYS 3.3 10.2 + - - -
178I LEU* 3.5 10.2 - - - +
393I ILE* 4.0 7.1 - - - +
430I ALA 3.3 15.6 + - - -
431I GLN* 2.8 10.1 + - - -
433I PHE* 1.3 74.2 - - - +
435I ASP* 1.3 62.6 + - - +
437I VAL* 3.3 3.1 + - - +
438I LEU* 2.8 40.1 + - - +
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Residues in contact with ASP 435 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134I LYS* 2.9 30.7 + - - +
431I GLN* 3.0 26.4 + - - +
432I MET* 3.6 8.4 - - - +
434I SER* 1.3 73.7 - - - +
436I MET* 1.3 62.6 + - - +
438I LEU* 2.6 5.9 + - - +
439I LYS* 2.5 58.8 + - + +
440I ASP* 4.2 2.0 - - - -
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Residues in contact with MET 436 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127I LEU* 4.7 5.6 - - - +
130I LYS* 4.2 9.2 - - + -
131I LEU* 3.5 54.7 - - + -
134I LYS* 4.2 10.1 - - + -
432I MET* 3.0 23.9 + - + +
433I PHE* 3.9 30.3 - - + +
435I ASP* 1.3 78.7 - - - +
437I VAL* 1.3 51.0 + - - +
440I ASP* 3.3 22.5 + - + +
441I GLY 3.1 11.8 + - - -
442I PHE* 2.6 46.7 + - + +
599I ILE* 4.4 9.6 - - + -
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Residues in contact with VAL 437 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393I ILE* 4.1 22.2 - - + -
396I PHE* 4.0 24.5 - - + -
433I PHE 3.2 19.3 + - - +
434I SER* 3.6 4.5 - - - +
435I ASP 2.7 4.6 + - - -
436I MET* 1.3 77.9 - - - +
438I LEU* 1.3 73.2 + - + +
439I LYS 3.8 0.2 + - - -
441I GLY* 3.9 9.0 - - - -
442I PHE* 3.6 36.6 - - + +
444I PRO* 4.0 9.4 - - + -
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Residues in contact with LEU 438 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176I PHE 4.1 4.0 - - - +
177I LYS* 3.9 36.6 - - + +
434I SER* 2.8 26.2 + - - +
435I ASP* 2.6 10.3 + - - +
437I VAL* 1.3 86.0 - - + +
439I LYS* 1.3 62.5 + - + +
441I GLY* 5.4 0.2 - - - -
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Residues in contact with LYS 439 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134I LYS* 4.2 13.4 - - - +
435I ASP* 2.5 42.8 + - - +
438I LEU* 1.3 78.6 - - + +
440I ASP* 1.3 59.8 + - - +
441I GLY* 2.6 18.8 + - - -
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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