Contacts of the helix formed by residues 420 - 440 (chain B) in PDB entry 4U1D
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 420 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B PHE* 4.0 16.6 - + - -
299B HIS* 2.6 30.2 + + - -
327B THR* 3.9 22.5 - - + +
330B LEU* 3.6 36.8 - - + -
331B SER* 3.3 28.0 - - - -
334B SER* 3.6 22.4 - - - +
416B TYR 3.8 5.6 - - - -
417B PHE* 3.4 3.4 + - - +
418B SER 3.3 0.2 - - - -
419B GLN* 1.3 114.0 + - + +
421B ILE* 1.3 65.1 + - - +
422B ALA 3.2 2.9 - - - -
423B PRO* 3.1 9.7 - - + +
424B LEU* 3.0 26.5 + - + +
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Residues in contact with ILE 421 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
417B PHE* 3.3 33.8 + - + +
418B SER* 3.5 22.4 + - - +
419B GLN 3.6 2.2 - - - -
420B TYR* 1.3 76.7 - - - +
422B ALA* 1.3 59.4 + - - +
424B LEU* 3.7 4.0 - - - +
425B ARG* 2.9 36.0 + - - +
457B PRO* 3.6 46.7 - - + +
458B LEU* 3.9 13.6 - - + +
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Residues in contact with ALA 422 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
419B GLN 5.4 0.2 - - - -
421B ILE* 1.3 81.0 - - - +
423B PRO* 1.3 70.7 - - + +
425B ARG* 3.2 25.9 + - - +
426B ASP* 2.9 29.3 + - - +
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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
----------------------------------------------------------
291B PHE* 6.0 4.5 - - + -
334B SER* 2.9 31.4 - - - +
336B GLN* 6.5 1.1 - - + -
419B GLN 4.6 3.6 - - - +
420B TYR* 3.1 29.2 - - + +
422B ALA* 1.3 90.5 - - + +
424B LEU* 1.3 59.4 + - - -
426B ASP* 3.2 12.5 + - + +
427B VAL* 2.9 25.8 + - - +
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Residues in contact with LEU 424 (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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330B LEU* 4.5 6.7 - - + -
333B ILE* 4.1 30.7 - - + +
334B SER* 3.4 13.3 + - - +
387B LEU* 4.1 19.7 - - + -
391B ILE* 4.2 5.8 - - + -
408B LEU* 5.8 0.4 - - + -
417B PHE* 3.8 31.2 - - + -
420B TYR* 3.0 20.5 + - + +
421B ILE 3.7 2.2 - - - +
423B PRO* 1.3 78.3 - - - +
425B ARG* 1.3 64.0 + - - +
427B VAL* 3.0 7.2 + - + +
428B ILE* 3.0 49.5 + - + +
458B LEU* 4.7 8.3 - - + -
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Residues in contact with ARG 425 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
421B ILE* 2.9 22.0 + - - +
422B ALA* 3.4 29.7 - - - +
424B LEU* 1.3 76.4 - - - +
426B ASP* 1.3 72.3 + - - +
428B ILE* 3.4 1.9 + - - +
429B MET* 2.9 36.6 + - + +
454B LEU* 4.2 10.3 - - + -
457B PRO 4.4 11.1 + - - -
458B LEU* 3.3 45.7 - - + +
459B ASP 4.5 3.4 + - - -
460B LEU* 3.8 34.6 - - - +
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Residues in contact with ASP 426 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336B GLN* 6.5 0.9 - - + -
422B ALA* 2.9 16.8 + - - +
423B PRO* 3.2 13.3 + - + +
425B ARG* 1.3 92.5 + - - +
427B VAL* 1.3 56.9 + - + +
429B MET* 3.9 4.2 - - - +
430B ARG* 2.9 35.2 + - - +
460B LEU* 5.7 1.4 - - - +
468B SER* 5.5 3.0 + - - -
471B GLN* 5.5 5.0 + - - -
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Residues in contact with VAL 427 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333B ILE 3.8 17.9 - - - +
334B SER* 4.0 5.8 - - - +
335B THR 3.3 27.1 - - - +
336B GLN* 4.6 4.0 - - - +
337B LEU* 3.6 24.4 - - + +
363B ARG* 4.3 6.7 - - - +
391B ILE* 4.5 16.4 - - + -
392B GLU* 4.6 0.2 - - - +
423B PRO 2.9 16.2 + - - +
424B LEU* 3.0 10.3 + - + +
426B ASP* 1.3 76.1 - - + +
428B ILE* 1.3 65.7 + - + +
430B ARG* 3.2 7.7 + - - +
431B ARG* 3.0 25.6 + - + +
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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
----------------------------------------------------------
391B ILE* 3.5 35.2 - - + -
395B PHE* 4.9 4.0 - - + -
400B VAL* 4.6 8.3 - - + -
404B LEU* 3.7 26.2 - - + -
424B LEU* 3.0 27.9 + - + +
425B ARG 3.8 3.1 - - - +
427B VAL* 1.3 77.2 - - + +
429B MET* 1.3 57.8 + - - +
431B ARG* 3.2 9.6 + - - +
432B VAL* 2.9 35.9 + - + +
454B LEU* 3.5 29.4 - - + -
458B LEU* 3.8 19.1 - - + -
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Residues in contact with MET 429 (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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425B ARG* 2.9 25.2 + - + +
426B ASP* 4.1 4.3 - - - +
428B ILE* 1.3 73.4 - - - +
430B ARG* 1.3 62.0 + - - +
432B VAL* 3.2 8.2 + - + +
433B PHE* 2.9 68.3 + - + -
452B ALA* 3.3 31.0 - - + +
454B LEU* 3.7 20.2 - - + -
458B LEU 5.1 0.7 - - - +
460B LEU* 3.5 31.6 - - - -
465B ILE* 4.0 13.9 - - + -
468B SER* 4.4 10.1 - - - +
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Residues in contact with ARG 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU* 3.9 24.6 + - + +
426B ASP* 2.9 23.0 + - - +
427B VAL* 3.4 6.7 - - - +
429B MET* 1.3 75.1 - - - +
431B ARG* 1.3 65.0 + - - +
433B PHE* 3.2 7.7 + - - +
434B VAL* 3.0 27.6 + - + +
468B SER* 4.7 2.4 + - - +
471B GLN* 4.2 15.8 - - - +
472B ALA* 3.4 41.5 - - - +
475B GLU* 2.7 33.1 + - - -
477B TYR* 3.8 38.5 - - + -
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Residues in contact with ARG 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337B LEU* 3.7 13.8 - - + +
339B GLU* 2.6 40.0 + - - -
363B ARG* 3.3 24.4 - - - +
391B ILE* 3.7 33.1 + - + +
392B GLU* 3.4 19.9 + - - -
395B PHE* 3.7 25.0 - - + -
427B VAL* 3.0 19.5 + - + +
428B ILE* 3.5 8.3 - - - +
430B ARG* 1.3 77.4 - - - +
432B VAL* 1.3 56.2 + - - +
434B VAL* 3.3 10.3 + - - +
435B ALA* 2.9 31.2 + - - +
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Residues in contact with VAL 432 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
395B PHE* 3.7 21.3 - - + -
397B VAL* 3.7 24.5 - - + +
400B VAL* 4.6 7.2 - - + -
428B ILE* 2.9 28.5 + - + +
429B MET* 3.2 11.0 + - + +
431B ARG* 1.3 75.4 - - - +
433B PHE* 1.3 59.0 + - + +
435B ALA* 3.4 2.9 + - - +
436B ALA* 2.9 29.0 + - + +
448B LEU* 6.0 0.7 - - + -
451B LEU* 4.0 14.1 - - + +
452B ALA* 3.9 25.6 - - + -
454B LEU* 4.9 7.9 - - + -
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Residues in contact with PHE 433 (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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429B MET* 2.9 44.2 + - + +
430B ARG* 3.6 6.7 - - - +
432B VAL* 1.3 77.0 - - - +
434B VAL* 1.3 58.8 + - + +
436B ALA* 3.5 4.1 + - - +
437B SER* 2.9 28.6 + - - -
448B LEU* 3.7 28.3 - - + -
452B ALA* 3.9 13.5 - - + -
465B ILE* 3.5 24.7 - - + -
468B SER* 3.5 17.7 - - - -
469B LEU* 3.3 50.3 - - + -
472B ALA* 4.4 13.7 - - + -
478B VAL* 4.5 5.6 - - + +
491B PHE* 4.3 5.7 - + - -
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Residues in contact with VAL 434 (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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337B LEU* 6.0 1.3 - - + -
339B GLU* 6.0 2.7 - - - +
430B ARG* 3.0 20.8 + - + +
431B ARG* 3.6 11.9 - - - +
433B PHE* 1.3 77.0 - - + +
435B ALA* 1.3 58.8 + - - +
437B SER* 3.0 12.0 + - - -
438B GLN* 3.0 35.8 + - + +
472B ALA* 6.4 0.2 - - + -
477B TYR* 3.5 44.9 - - + +
478B VAL* 5.2 1.1 - - + -
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Residues in contact with ALA 435 (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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395B PHE* 4.1 9.9 - - + -
397B VAL* 3.6 29.2 - - + -
431B ARG 2.9 17.3 + - - +
432B VAL 3.8 0.9 - - - +
434B VAL* 1.3 78.8 - - - +
436B ALA* 1.3 57.7 + - - +
438B GLN* 3.1 10.9 + - - +
439B LYS* 2.9 28.2 + - - +
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Residues in contact with ALA 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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397B VAL* 5.0 1.5 - - - +
432B VAL* 2.9 18.6 + - + +
433B PHE* 3.8 7.0 - - - +
435B ALA* 1.3 74.0 - - - +
437B SER* 1.3 60.7 + - - +
439B LYS* 4.3 2.5 - - - -
440B PHE* 3.0 52.8 + - + +
448B LEU* 4.8 11.7 - - + -
451B LEU* 4.3 18.2 - - + -
491B PHE* 3.9 12.1 - - + -
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Residues in contact with SER 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 PHE 2.9 14.7 + - - -
434B VAL* 3.1 14.6 - - - -
436B ALA* 1.3 77.4 - - - +
438B GLN* 1.3 69.6 + - - +
440B PHE 3.4 13.9 - - - +
477B TYR 5.4 0.6 + - - -
478B VAL* 3.6 19.0 - - - +
479B SER 5.1 0.7 + - - -
491B PHE* 3.5 34.2 - - - +
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Residues in contact with GLN 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 VAL* 3.0 25.6 + - + +
435B ALA* 3.1 10.3 + - - +
437B SER* 1.3 92.4 + - - +
439B LYS* 1.3 60.4 + - - +
440B PHE 4.5 1.6 - - - +
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Residues in contact with LYS 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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397B VAL* 6.1 6.5 - - + -
398B ASP* 3.9 27.6 + - - +
435B ALA 2.9 14.4 + - - +
436B ALA* 3.1 2.4 + - - -
438B GLN* 1.3 79.2 - - - +
440B PHE* 1.3 98.7 + - + +
451B LEU* 5.6 3.4 - - + -
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Residues in contact with PHE 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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436B ALA* 3.0 30.6 + - + +
437B SER 3.4 16.5 - - - +
438B GLN 4.5 2.1 - - - +
439B LYS* 1.3 118.9 - - + +
441B THR* 1.3 65.6 + - - +
442B THR 4.5 1.8 - - - +
443B VAL* 3.6 48.5 - - + -
447B GLU* 5.0 10.8 - - + -
448B LEU* 6.4 0.2 - - + -
451B LEU* 4.2 23.8 - - + -
491B PHE* 4.1 9.0 - - + +
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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