Contacts of the helix formed by residues 467 - 482 (chain B) in PDB entry 2YWB
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 PRO 467 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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416B TRP* 5.8 5.8 - - + -
418B LEU* 4.1 31.6 - - + -
465B ARG 4.4 2.0 - - - +
466B LEU* 1.3 89.3 - - + +
468B LEU* 1.3 66.6 + - - +
469B GLU* 4.4 5.2 - - + +
470B PHE* 3.0 23.6 + - + +
471B LEU* 3.1 12.0 + - - +
468C LEU* 5.8 5.8 - - + -
465D ARG* 3.9 40.2 - - + +
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Residues in contact with LEU 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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463A TRP* 3.5 31.4 - - + -
465A ARG* 3.9 35.4 - - + +
466A LEU 3.6 24.0 - - - +
468A LEU* 3.4 35.0 - - + -
471A LEU* 5.4 2.2 - - + -
490A TYR* 6.1 0.4 - - + -
492A LEU* 5.6 0.2 - - + -
466B LEU 3.3 0.8 + - - -
467B PRO* 1.3 72.3 - - - +
469B GLU* 1.3 56.5 - - - +
471B LEU* 3.2 17.2 + - + +
472B ASP* 2.9 25.5 + - - +
467C PRO* 6.1 3.4 - - + -
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Residues in contact with GLU 469 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465A ARG* 4.2 9.3 - - - +
416B TRP* 2.6 41.3 - - + -
467B PRO* 3.1 4.4 - - + +
468B LEU* 1.3 78.1 - - - +
470B PHE* 1.3 63.1 + - - +
472B ASP* 3.3 6.6 + - + +
473B GLU* 3.0 29.3 + - - +
476B ARG* 4.9 6.4 + - - -
469C GLU* 3.5 38.7 - - + +
465D ARG* 4.6 12.6 - - - +
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Residues in contact with PHE 470 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B PHE* 4.0 17.9 - + - -
412B LEU* 3.6 38.4 - - + -
413B LEU* 3.3 41.5 - - + -
416B TRP* 4.1 18.8 - + + -
418B LEU* 3.6 26.5 - - + -
466B LEU* 4.3 11.7 - - + -
467B PRO* 3.0 18.2 + - + +
469B GLU* 1.3 84.1 + - - +
471B LEU* 1.3 78.6 + - + +
473B GLU* 3.1 8.6 + - + +
474B ALA* 2.9 24.4 + - + +
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Residues in contact with LEU 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A TRP* 4.6 0.2 - - - -
468A LEU* 5.6 2.2 - - + -
492A LEU* 3.9 29.5 - - + +
409B PHE* 5.4 1.1 - - + -
450B LEU* 4.7 7.6 - - + -
466B LEU* 4.0 32.3 - - + +
467B PRO 3.1 11.3 + - - +
468B LEU* 3.2 30.0 + - + +
470B PHE* 1.3 83.6 - - + +
472B ASP* 1.3 58.4 + - - +
474B ALA* 3.3 3.9 + - - +
475B ALA* 2.9 30.5 + - - +
490B TYR* 3.8 42.0 - - + -
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Residues in contact with ASP 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
463A TRP* 3.0 31.1 + - + +
465A ARG* 3.3 27.3 + - - +
492A LEU 4.7 1.2 - - - +
494A SER* 4.8 2.9 + - - -
468B LEU 2.9 13.4 + - - +
469B GLU* 3.5 12.3 - - - +
470B PHE 3.2 0.2 - - - -
471B LEU* 1.3 77.0 - - - +
473B GLU* 1.3 56.2 + - - +
475B ALA* 3.2 3.3 + - - +
476B ARG* 2.9 64.6 + - - +
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Residues in contact with GLU 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
412B LEU* 4.0 15.9 - - + +
415B GLU* 4.6 0.2 - - - +
416B TRP* 2.9 47.2 + - - -
469B GLU* 3.0 17.7 + - - +
470B PHE* 3.5 11.0 - - + +
472B ASP* 1.3 78.4 + - - +
474B ALA* 1.3 57.9 + - - +
476B ARG* 3.7 23.2 + - - +
477B ARG* 2.9 53.7 + - - +
102D LYS* 4.2 11.3 + - - -
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Residues in contact with ALA 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409B PHE* 4.5 13.2 - - + -
412B LEU* 3.4 21.7 - - + +
450B LEU* 4.0 20.4 - - + -
470B PHE* 2.9 23.2 + - + +
471B LEU* 3.6 6.1 - - - +
473B GLU* 1.3 76.0 - - - +
475B ALA* 1.3 59.1 + - - +
477B ARG* 3.9 0.3 - - - +
478B ILE* 3.0 39.7 + - + +
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Residues in contact with ALA 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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492A LEU* 3.5 35.4 - - + +
493A THR* 5.4 1.3 - - + -
471B LEU 2.9 17.7 + - - +
472B ASP* 3.6 4.9 - - - +
474B ALA* 1.3 78.2 - - - +
476B ARG* 1.3 62.5 + - + +
478B ILE* 3.9 0.7 - - - +
479B THR* 3.1 31.6 + - + +
488B VAL* 3.9 23.3 - - + +
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Residues in contact with ARG 476 (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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492A LEU 6.0 0.4 - - - +
494A SER* 6.4 2.9 - - - -
469B GLU* 4.9 5.7 + - - -
472B ASP* 2.9 45.5 + - - +
473B GLU* 3.7 28.8 + - - +
475B ALA* 1.3 76.2 - - + +
477B ARG* 1.3 65.5 + - - +
479B THR* 3.2 7.0 + - - -
480B ARG* 3.1 28.1 + - - +
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Residues in contact with ARG 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
408B ILE* 3.7 16.4 - - + -
412B LEU* 3.4 36.3 - - + +
415B GLU* 4.1 4.2 + - - -
473B GLU* 2.9 34.2 + - - +
474B ALA 3.9 2.9 - - - +
476B ARG* 1.3 78.0 - - - +
478B ILE* 1.3 57.7 + - - +
480B ARG* 3.8 6.0 - - - +
481B ARG* 3.0 63.5 + - - +
102D LYS* 4.7 5.7 - - - +
104D LEU* 5.9 0.2 - - - +
119D GLU* 3.4 25.1 + - - -
121D GLN* 3.1 28.6 + - - +
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Residues in contact with ILE 478 (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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405B ALA* 4.2 15.3 - - + +
408B ILE* 3.9 26.5 - - + -
409B PHE* 4.6 6.1 - - + +
448B LEU* 3.8 21.8 - - + -
450B LEU* 3.9 20.6 - - + -
474B ALA* 3.0 26.5 + - + +
475B ALA 3.9 3.1 - - - +
477B ARG* 1.3 74.3 - - - +
479B THR* 1.3 59.9 + - - +
482B VAL* 2.8 32.7 + - + +
485B ILE* 3.8 28.3 - - + -
488B VAL* 4.0 16.4 - - + -
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Residues in contact with THR 479 (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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493A THR* 4.8 11.0 - - + -
497A PRO* 4.5 19.1 - - + +
475B ALA* 3.1 18.8 + - + +
476B ARG* 3.2 9.9 + - - -
478B ILE* 1.3 74.5 - - - +
480B ARG* 1.3 63.2 + - - +
482B VAL 3.9 10.3 - - - +
483B PRO* 4.0 7.1 - - - +
485B ILE* 3.8 23.1 - - + +
486B GLY 4.4 13.2 - - - +
487B ARG* 4.7 1.6 - - - -
488B VAL* 3.7 20.6 - - + +
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Residues in contact with ARG 480 (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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476B ARG* 3.1 20.2 + - - +
477B ARG* 3.8 6.5 - - - +
478B ILE 3.1 0.6 - - - -
479B THR* 1.3 80.0 + - - +
481B ARG* 1.3 80.7 + - + +
483B PRO* 4.3 9.5 - - - +
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Residues in contact with ARG 481 (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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404B ARG* 3.7 9.4 + - - -
408B ILE* 3.8 17.9 - - + -
477B ARG* 3.0 48.2 + - - +
480B ARG* 1.3 93.5 - - + +
482B VAL* 1.3 61.6 + - + +
483B PRO* 3.2 12.0 - - - +
104D LEU* 3.4 32.9 - - - +
119D GLU* 2.5 37.9 + - - -
121D GLN* 5.4 1.4 + - - -
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Residues in contact with VAL 482 (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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401B ILE* 3.9 11.9 - - + +
404B ARG* 3.8 24.9 - - + +
405B ALA* 4.3 8.7 - - - +
408B ILE* 3.9 21.8 - - + -
478B ILE* 2.8 18.3 + - + +
479B THR 3.9 2.4 - - - +
481B ARG* 1.3 84.5 - - - +
483B PRO* 1.3 53.0 - - - +
484B GLU* 3.1 25.4 - - + +
485B ILE* 2.8 52.6 + - + +
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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