Contacts of the helix formed by residues 462 - 473 (chain B) in PDB entry 1CCW
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 462 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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431B LEU* 3.7 14.6 - - - +
459B ARG* 5.6 2.1 + - - -
460B ASP* 3.7 10.8 + - - -
461B VAL* 1.3 79.0 - - - +
463B PHE* 1.3 59.9 + - - +
464B GLN* 3.3 18.8 + - - +
465B MET* 3.0 31.7 + - - +
466B VAL* 3.3 8.5 + - - +
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Residues in contact with PHE 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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21A LYS* 6.1 4.9 - - + -
22A ILE* 5.4 6.5 - - + -
25A HIS* 4.4 20.6 - + + -
408B PHE* 5.0 13.9 - + - -
419B MET* 3.6 35.6 - - + -
431B LEU* 4.4 1.6 - - - +
432B GLU* 6.0 0.2 - - - +
462B SER* 1.3 71.3 - - - +
464B GLN* 1.3 65.8 + - - +
466B VAL* 3.0 24.8 + - + +
467B ILE* 2.9 47.9 + - + +
470B ILE* 6.0 1.1 - - + -
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Residues in contact with GLN 464 (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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25A HIS* 4.5 8.1 + - - -
459B ARG* 4.1 15.3 - - - +
462B SER* 3.2 10.5 + - - +
463B PHE* 1.3 78.1 - - - +
465B MET* 1.3 57.9 + - - +
467B ILE* 3.3 28.3 + - - +
468B ASP* 2.9 54.1 + - - +
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Residues in contact with MET 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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421B VAL* 3.7 11.7 - - + -
422B ARG 5.0 0.2 - - - +
453B ARG* 3.7 33.7 - - + +
454B ALA* 4.6 3.1 - - - -
457B GLU* 3.8 15.3 - - - +
459B ARG* 3.4 37.8 - - + +
460B ASP 3.6 8.7 - - - +
461B VAL* 3.5 46.4 - - + +
462B SER* 3.0 16.4 + - - +
464B GLN* 1.3 77.5 - - - +
466B VAL* 1.3 57.5 + - - +
468B ASP* 3.3 9.6 + - - +
469B ASP* 2.9 32.6 + - - +
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Residues in contact with VAL 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223B LEU* 4.3 7.6 - - + -
408B PHE* 4.1 26.2 - - + -
419B MET* 3.9 10.8 - - + -
420B PRO 3.2 28.3 - - - +
421B VAL* 3.5 16.4 - - + -
431B LEU* 3.9 10.3 - - + -
462B SER 3.7 9.6 - - - +
463B PHE* 3.0 21.7 + - + +
465B MET* 1.3 76.3 - - - +
467B ILE* 1.3 62.4 + - - +
469B ASP* 3.1 5.9 + - - +
470B ILE* 2.9 26.8 + - + +
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Residues in contact with ILE 467 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A ILE* 4.1 17.3 - - + -
25A HIS* 3.5 37.7 - - + +
463B PHE* 2.9 40.9 + - + +
464B GLN* 3.5 28.3 - - - +
466B VAL* 1.3 75.3 - - - +
468B ASP* 1.3 64.6 + - - +
470B ILE* 3.1 17.6 + - + +
471B PHE* 3.1 38.2 + - + -
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Residues in contact with ASP 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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459B ARG* 2.6 37.5 + - - -
464B GLN* 2.9 35.3 + - - +
465B MET 3.5 6.7 - - - +
467B ILE* 1.3 76.6 - - - +
469B ASP* 1.3 57.5 + - - +
471B PHE* 3.3 6.8 + - - +
472B ALA* 3.0 28.6 + - - +
480B GLY* 3.4 23.4 - - - +
481B ARG 4.8 4.4 - - - +
482B PRO* 5.1 1.2 - - - +
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Residues in contact with ASP 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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223B LEU* 3.9 20.9 - - + +
293B TRP* 5.4 6.6 - - - -
421B VAL* 3.6 6.6 - - - +
422B ARG* 3.0 38.7 + - - +
453B ARG* 2.8 32.3 + - - -
465B MET 2.9 16.0 + - - +
466B VAL* 3.1 4.9 + - - +
468B ASP* 1.3 73.0 - - - +
470B ILE* 1.3 66.2 + - - +
471B PHE 3.3 0.3 + - - -
472B ALA* 3.3 14.9 + - - +
473B VAL* 4.6 2.6 + - - +
478B LEU 4.8 2.1 - - - +
479B ILE 4.0 0.3 - - - -
480B GLY 2.9 23.0 + - - -
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Residues in contact with ILE 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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18A VAL* 3.9 28.5 - - + -
22A ILE* 4.6 10.8 - - + -
800A CNC 4.1 25.0 - - + -
222B THR* 4.0 18.4 - - + -
223B LEU* 4.1 9.6 - - + -
293B TRP* 5.7 3.5 - - - -
296B GLY* 4.9 12.6 + - - +
408B PHE* 3.8 28.7 - - + -
463B PHE* 5.9 1.1 - - + -
466B VAL* 2.9 25.7 + - + +
467B ILE* 3.1 12.3 + - + +
469B ASP* 1.3 76.2 - - - +
471B PHE* 1.3 66.0 + - + +
473B VAL* 5.0 1.7 + - - +
474B GLY 5.4 1.0 + - - -
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Residues in contact with PHE 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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22A ILE* 3.8 27.8 - - + -
123A PRO* 5.3 5.6 - - + -
800A CNC 3.3 44.9 - - + -
467B ILE* 3.1 39.5 + - + +
468B ASP* 3.9 5.2 - - - +
470B ILE* 1.3 81.8 - - + +
472B ALA* 1.3 64.7 + - - +
473B VAL 3.4 1.3 - - - -
474B GLY* 3.2 6.6 + - - +
475B LYS* 3.1 49.1 + - + +
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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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468B ASP 3.0 16.9 + - - +
469B ASP* 3.3 8.8 + - - +
471B PHE* 1.3 75.9 - - - +
473B VAL* 1.3 65.4 + - - +
475B LYS* 2.9 18.6 + - - +
476B GLY 3.0 8.7 + - - -
477B ARG* 2.9 22.8 + - + +
478B LEU 3.5 16.4 - - - +
479B ILE 3.8 2.7 - - - +
480B GLY* 3.6 19.3 - - - +
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Residues in contact with VAL 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B TRP* 3.6 42.2 - - + +
296B GLY 3.5 19.1 - - - +
298B PRO* 3.8 9.0 - - + +
307B VAL* 4.0 15.9 - - + -
422B ARG* 5.1 0.2 - - - +
469B ASP 4.6 2.3 + - - +
470B ILE 5.0 1.2 + - - +
471B PHE 3.4 0.6 - - - -
472B ALA* 1.3 74.4 - - + +
474B GLY* 1.3 63.1 + - - +
476B GLY 3.0 11.1 + - - -
477B ARG 3.1 15.5 - - - +
478B LEU* 4.2 10.5 - - + +
349D MET* 3.4 10.4 - - + +
353D MET* 3.8 28.9 - - + -
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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