Contacts of the helix formed by residues 461 - 475 (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 SER 461 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460B LEU* 1.3 77.5 - - - +
462B ALA* 1.3 65.8 + - - +
463B TRP* 3.3 43.9 + - - -
464B ASP* 3.0 18.4 + - - +
465B ILE* 3.0 20.6 + - - +
66C LYS* 5.9 2.6 - - - -
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Residues in contact with ALA 462 (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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449B TYR* 3.8 25.7 - - + -
460B LEU 3.7 1.0 + - - -
461B SER* 1.3 72.0 - - - +
463B TRP* 1.3 75.0 + - + +
465B ILE* 3.4 13.8 + - - +
466B GLU 3.3 15.2 + - - -
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Residues in contact with TRP 463 (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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461B SER* 3.3 29.2 + - - -
462B ALA* 1.3 88.4 - - + +
464B ASP* 1.3 81.2 + - - +
465B ILE 3.1 0.4 - - - -
466B GLU* 3.3 6.0 + - - +
467B LYS* 3.0 14.4 + - - +
66C LYS 5.6 0.4 - - - -
69C LYS* 3.8 30.8 - - + +
70C ASP* 4.1 34.3 - - + -
73C HIS* 3.4 57.6 - + + +
167C ASP* 4.2 15.0 - - + +
170C ARG* 2.9 31.3 + - - +
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Residues in contact with ASP 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B LEU* 3.7 30.8 - - + +
461B SER* 3.0 27.4 + - - +
463B TRP* 1.3 89.8 + - - +
465B ILE* 1.3 59.4 + - - +
467B LYS* 3.3 17.7 + - - +
468B SER* 3.0 30.7 + - - -
163C ARG* 6.0 0.5 + - - -
167C ASP* 4.2 9.7 - - - +
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Residues in contact with ILE 465 (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* 4.0 11.7 - - + -
433B PHE* 3.5 19.3 - - + -
449B TYR* 3.4 42.2 - - + +
452B ALA* 4.0 8.7 - - + +
453B THR* 3.2 28.9 - - - +
460B LEU* 3.8 27.8 - - + +
461B SER 3.0 13.1 + - - +
462B ALA* 3.5 12.3 - - - +
463B TRP 3.1 0.2 - - - -
464B ASP* 1.3 74.9 - - - +
466B GLU* 1.3 65.1 + - - +
468B SER* 3.2 8.4 + - - -
469B LEU* 3.0 19.1 + - - +
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Residues in contact with GLU 466 (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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445B GLN* 3.4 14.6 + - - -
449B TYR* 3.2 34.6 + - + +
462B ALA 3.3 5.0 + - - +
463B TRP* 3.3 11.1 + - - +
465B ILE* 1.3 76.5 - - - +
467B LYS* 1.3 65.9 + - - +
469B LEU* 3.2 5.5 + - + +
470B LEU* 3.0 40.6 + - + +
482B ILE* 3.6 14.4 - - + +
484B HIS* 3.7 16.6 + - - -
77C LYS* 5.4 1.2 + - - -
170C ARG* 4.2 18.0 + - - +
216C GLN* 5.5 0.5 + - - -
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Residues in contact with LYS 467 (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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463B TRP 3.0 9.4 + - - +
464B ASP* 3.3 24.1 + - - +
466B GLU* 1.3 76.1 - - - +
468B SER* 1.3 57.8 + - - +
470B LEU* 3.3 8.8 + - - +
471B GLN* 3.0 32.7 + - - +
163C ARG* 5.7 5.1 - - - +
167C ASP* 4.1 18.6 + - - +
170C ARG* 3.5 29.2 - - - +
205C MET* 4.8 14.5 - - - +
208C GLN* 3.1 34.1 + - + +
209C HIS* 5.6 3.8 - - - -
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Residues in contact with SER 468 (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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426B ASP* 5.5 2.8 + - - -
429B MET* 4.4 10.2 - - - +
430B ARG* 4.7 3.5 + - - +
433B PHE* 3.5 16.8 - - - -
460B LEU* 4.2 13.2 - - - +
464B ASP 3.0 13.0 + - - -
465B ILE 3.4 9.0 - - - -
467B LYS* 1.3 77.3 - - - +
469B LEU* 1.3 58.2 + - - +
471B GLN* 3.2 12.6 + - - +
472B ALA* 2.9 29.8 + - - +
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Residues in contact with LEU 469 (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* 3.3 39.9 - - + -
448B LEU* 3.9 24.2 - - + -
449B TYR* 4.0 22.0 - - + +
465B ILE 3.0 12.4 + - - +
466B GLU* 3.2 8.9 + - - +
468B SER* 1.3 78.2 - - - +
470B LEU* 1.3 59.2 + - + +
472B ALA* 3.4 2.9 + - - +
473B ALA* 3.1 20.4 + - - +
478B VAL* 4.2 3.9 - - + +
480B ILE* 3.7 32.1 - - + -
482B ILE* 5.7 2.7 - - + -
489B VAL* 4.3 10.5 - - + -
491B PHE* 4.6 8.5 - - + -
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Residues in contact with LEU 470 (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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466B GLU* 3.0 34.9 + - + +
467B LYS* 3.7 9.2 - - - +
469B LEU* 1.3 74.3 - - + +
471B GLN* 1.3 61.5 + - - +
473B ALA* 3.0 4.8 + - - +
474B VAL* 2.8 36.8 + - + +
480B ILE* 3.7 21.5 - - + -
482B ILE* 4.5 10.3 - - + -
170C ARG* 6.0 3.4 - - - +
171C ASN* 5.6 1.3 - - - +
212C ALA* 4.1 24.9 - - + -
215C TYR* 4.6 17.7 - - + -
216C GLN* 4.0 28.0 - - + +
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Residues in contact with GLN 471 (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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336B GLN* 5.7 3.8 - - - +
426B ASP* 5.5 4.8 + - - -
430B ARG* 4.2 13.1 - - - +
467B LYS* 3.0 19.9 + - + +
468B SER* 3.5 14.3 + - - +
470B LEU* 1.3 77.4 - - - +
472B ALA* 1.3 59.9 + - - +
474B VAL* 3.2 7.2 + - + +
475B GLU* 3.1 52.3 + - + +
208C GLN* 4.5 24.4 + - - +
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Residues in contact with ALA 472 (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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430B ARG* 3.4 39.6 - - - +
433B PHE* 4.4 11.0 - - + -
468B SER 2.9 15.2 + - - +
469B LEU 3.5 7.0 - - - +
471B GLN* 1.3 76.8 - - - +
473B ALA* 1.3 56.7 + - - +
475B GLU 3.7 0.9 + - - -
476B ASP 3.3 2.6 + - - -
477B TYR* 2.8 33.3 + - + +
478B VAL* 3.7 15.0 - - + -
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Residues in contact with ALA 473 (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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469B LEU 3.1 13.4 + - - +
470B LEU* 3.0 10.2 + - - +
472B ALA* 1.3 75.8 - - - +
474B VAL* 1.3 60.0 + - - +
476B ASP* 3.0 25.1 + - - +
478B VAL* 3.2 19.0 - - + +
480B ILE* 3.9 12.3 - - + -
215C TYR* 3.4 40.9 - - + +
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Residues in contact with VAL 474 (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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343B ILE* 5.6 4.4 - - + +
470B LEU* 2.8 26.2 + - + +
471B GLN* 3.2 8.0 + - + +
473B ALA* 1.3 73.3 - - - +
475B GLU* 1.3 61.9 + - + +
476B ASP* 3.0 11.0 + - - +
211C ASP* 3.9 42.0 - - + +
212C ALA* 4.8 4.5 - - - +
215C TYR* 4.0 21.1 - - + -
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Residues in contact with GLU 475 (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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336B GLN* 5.2 7.1 + - - -
340B ILE* 3.9 7.1 - - - +
341B PRO 5.0 1.4 - - - +
343B ILE* 5.6 13.0 - - + -
430B ARG* 2.7 29.3 + - - -
471B GLN* 3.1 39.3 + - + +
472B ALA 4.2 1.1 - - - +
473B ALA 3.3 0.2 - - - -
474B VAL* 1.3 78.6 - - + +
476B ASP* 1.3 68.8 + - - +
477B TYR* 3.4 23.6 + - + -
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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