Contacts of the helix formed by residues 420 - 442 (chain B) in PDB entry 3R29
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 LEU 420 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373A ILE* 3.8 13.7 - - + -
393A ARG* 3.8 23.6 + - - +
397A TYR* 3.3 42.0 - - + -
419A LEU* 4.1 19.7 - - + +
422A LEU* 3.6 30.7 - - + -
416B ALA 3.0 19.4 + - - +
417B LYS* 3.2 6.0 + - - +
418B LEU 3.1 1.0 - - - -
419B LEU* 1.3 79.6 - - - +
421B ARG* 1.3 77.7 + - - +
422B LEU 3.4 0.4 - - - -
423B PRO* 3.3 18.3 - - + +
424B ALA 4.5 1.9 + - - -
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Residues in contact with ARG 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
377A ASN* 5.6 0.2 + - - -
378A PRO* 5.0 7.5 - - - +
379A ASP* 2.5 40.5 + - - -
393A ARG* 4.2 14.3 - - - +
352B GLU 3.0 29.0 + - - -
353B LEU* 4.2 13.4 - - + +
356B LYS* 3.8 27.4 - - + +
357B MET* 5.6 1.8 - - + -
360B MET* 5.5 5.2 - - - -
362B MET* 4.7 20.9 - - + -
370B LEU* 5.2 4.5 - - + -
417B LYS 3.8 7.2 + - - +
418B LEU 3.2 12.3 + - - +
419B LEU 3.0 1.2 - - - -
420B LEU* 1.3 94.9 + - - +
422B LEU* 1.3 65.6 + - - +
423B PRO 3.3 1.1 - - - -
424B ALA* 3.2 14.3 + - - +
425B LEU* 3.0 21.2 + - - +
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Residues in contact with LEU 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
420A LEU* 3.4 32.1 - - + -
423A PRO* 3.6 19.0 - - + +
370B LEU* 3.8 35.2 - - + +
373B ILE* 3.9 18.6 - - + -
374B VAL* 4.2 21.8 - - + -
393B ARG* 5.7 1.3 - - - +
419B LEU* 3.0 25.6 + - + +
421B ARG* 1.3 76.6 - - - +
423B PRO* 1.3 70.4 - - - +
425B LEU* 2.8 21.9 + - + +
426B ARG* 2.9 12.1 + - - +
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Residues in contact with PRO 423 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
393A ARG* 6.1 0.9 - - - +
419A LEU 5.9 0.2 - - - +
422A LEU* 3.9 31.6 - - + +
423A PRO* 4.1 16.6 - - + -
426A ARG* 3.8 36.4 + - + +
419B LEU 3.5 6.5 - - - +
420B LEU* 3.3 25.8 - - + +
422B LEU* 1.3 90.6 - - + +
424B ALA* 1.3 64.1 + - - +
426B ARG* 3.1 3.6 + - + +
427B SER* 3.0 21.5 + - - -
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Residues in contact with ALA 424 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379A ASP* 4.8 2.2 - - - +
426A ARG* 3.8 12.9 - - - +
352B GLU* 4.0 21.1 - - - +
353B LEU* 4.1 6.7 - - + -
420B LEU 4.5 0.6 + - - -
421B ARG* 3.2 39.0 + - - +
422B LEU 3.1 0.4 - - - -
423B PRO* 1.3 82.5 - - - +
425B LEU* 1.3 60.8 + - - +
427B SER* 3.1 2.6 + - - -
428B ILE* 3.0 29.3 + - - +
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Residues in contact with LEU 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLU* 3.6 29.3 - - + +
310B ILE* 3.8 30.5 - - + -
311B ALA* 3.9 28.5 - - + +
353B LEU* 4.0 19.3 - - + -
370B LEU* 6.3 0.9 - - + -
374B VAL* 4.2 19.1 - - + -
421B ARG 3.0 11.6 + - - +
422B LEU* 2.8 24.2 + - + +
424B ALA* 1.3 68.0 - - - +
426B ARG* 1.3 65.1 + - - +
428B ILE* 3.4 1.0 + - - -
429B GLY* 2.8 20.3 + - - -
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Residues in contact with ARG 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352A GLU* 5.2 3.6 + - - -
423A PRO* 3.4 34.0 + - + +
424A ALA* 3.3 31.9 - - - +
426A ARG* 4.9 2.5 - - + -
427A SER* 3.9 23.3 + - - -
307B GLU* 3.1 37.2 + - - +
377B ASN* 3.1 30.3 - - - +
379B ASP* 5.6 4.4 + - - +
393B ARG* 5.5 1.8 - - - +
422B LEU 2.9 10.5 + - - +
423B PRO* 3.4 8.7 - - + +
425B LEU* 1.3 71.1 - - - +
427B SER* 1.3 58.6 + - - +
429B GLY* 2.6 24.3 + - - -
430B LEU* 3.0 19.4 + - - +
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Residues in contact with SER 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
426A ARG* 3.5 41.4 + - - -
430A LEU* 3.8 18.8 - - - +
352B GLU* 4.2 4.9 + - - -
423B PRO 3.0 4.8 + - - -
424B ALA* 3.1 11.8 + - - -
426B ARG* 1.3 80.8 - - - +
428B ILE* 1.3 60.8 + - - +
430B LEU* 3.3 4.3 + - - +
431B LYS* 2.9 43.8 + - - +
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Residues in contact with ILE 428 (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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310B ILE* 4.6 9.9 - - + -
345B ILE* 3.6 20.4 - - + +
348B ARG* 3.4 47.1 - - + +
349B VAL* 3.7 11.7 - - + +
352B GLU* 3.9 15.7 - - + +
353B LEU* 3.8 24.2 - - + -
424B ALA 3.0 18.1 + - - +
425B LEU 3.9 3.6 - - - +
426B ARG 3.0 0.6 - - - -
427B SER* 1.3 79.3 - - - +
429B GLY* 1.3 61.4 + - - +
431B LYS* 4.2 6.3 - - - -
432B CYS* 3.1 27.5 + - - -
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Residues in contact with GLY 429 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ASN* 3.3 21.5 + - - -
307B GLU* 4.7 11.4 - - - -
310B ILE* 4.3 15.2 - - - +
425B LEU 2.8 11.7 + - - -
426B ARG 2.6 14.8 + - - -
428B ILE* 1.3 73.9 - - - +
430B LEU* 1.3 59.9 + - - -
432B CYS* 3.7 0.7 - - - +
433B LEU* 3.3 16.8 + - - +
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Residues in contact with LEU 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427A SER* 3.5 37.2 - - - +
430A LEU* 4.7 16.2 - - + -
431A LYS* 3.8 30.1 - - - +
434A GLU* 4.8 9.2 - - - +
307B GLU* 5.9 0.4 - - - +
426B ARG* 3.0 20.3 + - - +
427B SER* 4.0 4.9 - - - +
429B GLY* 1.3 77.7 - - - +
431B LYS* 1.3 55.5 + - - +
432B CYS 3.2 0.2 - - - -
433B LEU* 3.0 18.7 + - + +
434B GLU* 2.7 40.7 + - + +
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Residues in contact with LYS 431 (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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430A LEU* 4.3 20.1 - - + +
345B ILE* 4.2 11.9 - - + -
348B ARG* 3.6 49.6 - - - +
427B SER* 2.9 43.3 + - - +
428B ILE* 3.9 8.3 - - - +
430B LEU* 1.3 75.4 - - - +
432B CYS* 1.3 62.7 + - - +
434B GLU* 2.9 29.7 + - - +
435B HIS* 3.0 24.9 + - + +
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Residues in contact with CYS 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ASN* 4.4 6.3 - - - +
310B ILE* 3.8 23.8 - - + -
313B PHE* 6.1 2.0 - - - -
345B ILE* 3.1 38.1 - - - +
349B VAL* 5.7 0.9 - - - -
428B ILE* 3.1 17.7 + - - +
429B GLY 3.7 6.1 - - - +
431B LYS* 1.3 77.2 - - - +
433B LEU* 1.3 63.9 + - - +
435B HIS* 3.2 9.4 + - - +
436B LEU* 3.0 26.2 + - + +
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Residues in contact with LEU 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
306B ASN* 3.9 20.6 - - + +
429B GLY 3.3 9.2 + - - +
430B LEU* 3.0 23.0 + - + +
432B CYS* 1.3 77.9 - - - +
434B GLU* 1.3 62.5 - - + +
436B LEU* 3.3 9.2 + - + +
437B PHE* 3.0 58.2 + - + -
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Residues in contact with GLU 434 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LEU* 5.0 6.3 - - - +
434A GLU* 2.8 39.3 - - + +
430B LEU* 2.7 21.5 + - - +
431B LYS* 2.9 26.5 + - - +
433B LEU* 1.3 73.6 - - + +
435B HIS* 1.3 58.5 + - + +
437B PHE* 3.2 7.7 + - - +
438B PHE* 2.8 28.0 + - - +
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Residues in contact with HIS 435 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
341B GLY 4.3 3.6 - - - -
342B VAL* 3.8 16.9 - - + +
344B ALA* 4.5 10.6 - - + +
345B ILE* 3.4 39.2 + - + +
431B LYS* 3.0 29.3 + - + +
432B CYS* 3.2 9.8 + - - +
434B GLU* 1.3 75.7 - - + +
436B LEU* 1.3 55.5 + - - +
438B PHE* 3.1 8.1 + - - +
439B PHE* 2.8 67.2 + + + -
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Residues in contact with LEU 436 (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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265B VAL* 6.1 5.2 - - + -
268B ILE* 5.9 6.1 - - + -
269B CYS* 4.9 19.3 - - - -
432B CYS* 3.0 11.4 + - + +
433B LEU* 3.4 15.5 - - + +
435B HIS* 1.3 79.1 - - - +
437B PHE* 1.3 69.0 + - + +
439B PHE* 3.5 8.2 + - + +
440B LYS* 3.3 31.0 + - + +
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Residues in contact with PHE 437 (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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433B LEU* 3.0 42.9 + - + +
434B GLU* 3.6 8.3 - - - +
436B LEU* 1.3 81.0 - - + +
438B PHE* 1.3 65.1 + - - +
440B LYS* 3.3 8.4 + - - +
441B LEU* 3.0 22.2 + - - +
450B PHE* 5.3 14.4 - + - -
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Residues in contact with PHE 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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434B GLU 2.8 13.7 + - - +
435B HIS* 3.1 11.9 + - - +
437B PHE* 1.3 77.6 - - - +
439B PHE* 1.3 71.9 - + - +
441B LEU* 2.8 25.2 + - + +
442B ILE* 1.9 66.5 + - + +
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Residues in contact with PHE 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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265B VAL* 4.6 23.6 - - + -
340B ALA 5.1 3.1 - - - -
341B GLY 3.3 26.0 - - - -
342B VAL* 3.8 16.6 - - + -
435B HIS* 2.8 46.5 + + + +
436B LEU* 4.2 7.6 - - + +
438B PHE* 1.3 95.8 - + - +
440B LYS* 1.3 62.9 + - - +
442B ILE* 2.9 21.1 - - + +
443B GLY* 3.2 12.6 + - - -
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Residues in contact with LYS 440 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
436B LEU* 3.3 23.6 + - + +
437B PHE* 3.4 11.2 - - - +
439B PHE* 1.3 79.9 - - - +
441B LEU* 1.3 53.6 + - - +
443B GLY* 2.8 26.5 + - - -
446B PRO 3.3 21.2 + - - +
447B ILE* 3.2 37.2 + - - +
449B THR* 4.2 15.0 + - - +
450B PHE* 5.2 13.7 - - - -
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Residues in contact with LEU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
437B PHE 3.0 13.2 + - - +
438B PHE* 2.8 23.9 + - + +
440B LYS* 1.3 74.0 - - - +
442B ILE* 1.3 58.8 + - + +
443B GLY 2.8 8.4 + - - +
447B ILE* 3.2 33.1 - - + +
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Residues in contact with ILE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
438B PHE* 1.9 82.3 + - + +
439B PHE* 2.9 22.0 - - + +
441B LEU* 1.3 74.1 - - + +
443B GLY* 1.3 67.1 + - - +
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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