Contacts of the helix formed by residues 471 - 488 (chain B) in PDB entry 4CCN
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 ASP 471 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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461B TYR* 3.6 17.6 - - + +
469B SER* 3.1 14.5 + - - +
470B LYS* 1.3 77.0 - - - +
472B PRO* 1.3 72.8 - - - +
473B ARG* 2.7 53.9 + - - +
474B ARG* 3.0 26.9 + - + +
475B THR* 3.7 4.9 + - - +
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Residues in contact with PRO 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B LYS 3.1 8.5 - - - +
471B ASP* 1.3 87.5 - - - +
473B ARG* 1.3 65.1 + - + +
474B ARG 3.1 2.5 - - - -
475B THR* 2.7 29.8 + - + +
476B ALA* 3.0 10.7 + - - +
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Residues in contact with ARG 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457B ASP* 3.1 23.9 + - - -
460B ASP* 4.7 8.7 - - - +
461B TYR* 3.5 43.5 + - + +
471B ASP* 2.7 33.5 + - - +
472B PRO* 1.3 80.4 - - + +
474B ARG* 1.3 57.1 - - - +
476B ALA* 3.3 8.2 + - - +
477B PHE* 2.9 28.6 + - - +
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Residues in contact with ARG 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A ASP* 2.6 43.2 + - - -
461B TYR* 3.0 39.9 + - + +
462B MET* 3.8 13.3 - - - +
466B HIS 3.5 19.3 + - - -
467B SER* 3.4 25.2 + - - +
469B SER* 4.3 17.9 + - - -
471B ASP* 3.0 18.0 + - + +
473B ARG* 1.3 79.3 - - - +
475B THR* 1.3 60.0 + - + +
477B PHE* 3.1 3.6 + - - +
478B MET* 2.9 52.0 + - + +
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Residues in contact with THR 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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470B LYS 5.2 3.6 - - - +
471B ASP 4.3 9.4 - - - +
472B PRO* 2.7 24.8 + - + +
474B ARG* 1.3 79.0 - - + +
476B ALA* 1.3 58.4 + - - +
478B MET* 3.7 9.2 - - - +
479B GLU* 3.0 27.7 + - - +
482B ARG* 5.1 0.5 + - - -
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Residues in contact with ALA 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472B PRO 3.0 12.7 + - - +
473B ARG* 3.6 9.0 - - - +
475B THR* 1.3 78.9 + - - +
477B PHE* 1.3 61.0 + - - +
479B GLU* 3.4 5.5 + - - +
480B LYS* 2.9 30.5 + - - +
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Residues in contact with PHE 477 (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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428A TRP* 3.4 27.4 - + - -
431A PHE* 3.7 28.0 - + - -
494A VAL* 3.5 23.1 - - + -
454B LEU* 4.4 4.5 - - + -
455B PRO* 4.2 7.2 - - + -
458B PHE* 3.7 27.4 - + + -
461B TYR* 4.0 13.9 - + + +
462B MET* 3.6 32.3 - - + -
473B ARG 2.9 14.3 + - - +
474B ARG 3.1 9.2 + - - +
476B ALA* 1.3 78.6 - - - +
478B MET* 1.3 56.0 + - - +
480B LYS* 3.2 7.7 + - - +
481B VAL* 2.9 44.2 + - + +
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Residues in contact with MET 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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492A ALA 6.0 0.4 - - - +
494A VAL* 4.3 20.2 - - + -
495A ASP* 5.3 2.7 - - - +
462B MET* 3.9 25.4 - - - -
474B ARG* 2.9 47.8 + - + +
475B THR* 3.7 8.5 - - - +
477B PHE* 1.3 76.5 - - - +
479B GLU* 1.3 61.0 + - - +
481B VAL* 3.3 7.3 + - - +
482B ARG* 3.1 56.9 + - - +
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Residues in contact with GLU 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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475B THR 3.0 18.2 + - - +
476B ALA* 3.8 7.6 - - - +
477B PHE 3.3 0.2 - - - -
478B MET* 1.3 73.6 - - - +
480B LYS* 1.3 65.1 + - - +
482B ARG* 3.5 12.3 + - - +
483B VAL* 3.0 34.1 + - + +
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Residues in contact with LYS 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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428A TRP* 3.4 58.0 - - + +
449B GLU* 5.3 10.9 + - - -
452B ARG* 5.9 4.4 - - - +
476B ALA 2.9 20.1 + - - +
477B PHE 3.4 5.2 - - - +
479B GLU* 1.3 75.9 - - - +
481B VAL* 1.3 61.6 + - - +
483B VAL* 3.4 9.5 + - + +
484B LEU* 2.9 47.6 + - + +
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Residues in contact with VAL 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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428A TRP* 4.0 8.1 - - + -
431A PHE* 4.4 7.2 - - + -
432A LEU* 4.7 9.0 - - + -
435A ILE* 5.0 5.6 - - + -
489A GLY 5.6 0.9 - - - +
492A ALA* 4.5 12.3 - - + -
494A VAL* 4.3 23.8 - - + -
477B PHE* 2.9 45.2 + - + +
478B MET* 3.6 7.9 - - - +
479B GLU 3.3 0.2 - - - -
480B LYS* 1.3 76.8 - - - +
482B ARG* 1.3 60.0 + - + +
484B LEU* 3.2 9.6 + - - +
485B VAL* 2.8 47.8 + - + +
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Residues in contact with ARG 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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486A ALA 5.4 1.7 - - - +
489A GLY* 4.2 31.7 + - - +
490A HIS* 4.8 9.0 - - - +
475B THR 5.1 0.2 + - - -
478B MET* 3.1 62.6 + - - +
479B GLU* 3.6 11.6 - - - +
480B LYS 3.4 0.2 - - - -
481B VAL* 1.3 76.0 - - + +
483B VAL* 1.3 65.5 + - + +
485B VAL* 3.1 9.0 + - - +
486B ALA* 2.9 26.1 + - - +
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Residues in contact with VAL 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B GLU* 3.0 22.5 + - + +
480B LYS* 3.6 9.9 - - + +
482B ARG* 1.3 78.9 - - + +
484B LEU* 1.3 66.0 + - + +
486B ALA* 3.3 6.5 + - - +
487B ARG* 3.2 37.5 + - - +
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Residues in contact with LEU 484 (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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428A TRP* 3.5 48.2 - - + -
432A LEU* 4.0 24.2 - - + -
449B GLU* 4.4 12.3 - - + +
450B PHE* 3.8 26.3 - - + -
480B LYS* 2.9 36.1 + - + +
481B VAL* 3.6 3.6 - - - +
483B VAL* 1.3 77.7 - - + +
485B VAL* 1.3 63.1 + - - +
487B ARG* 3.1 32.6 + - - +
488B LEU* 3.3 15.1 + - - +
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Residues in contact with VAL 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432A LEU* 4.6 7.9 - - + -
435A ILE* 5.2 2.2 - - + -
436A LEU* 4.3 18.8 - - + -
485A VAL* 3.2 30.2 - - + +
486A ALA 4.7 0.9 - - - +
488A LEU* 4.0 8.7 - - + -
489A GLY* 3.9 19.1 - - - +
492A ALA* 5.6 2.0 - - + -
481B VAL* 2.8 40.4 + - + +
482B ARG* 3.5 7.4 - - - +
484B LEU* 1.3 72.2 - - - +
486B ALA* 1.3 59.1 + - - +
488B LEU* 3.0 39.3 + - + +
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Residues in contact with ALA 486 (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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482A ARG* 5.3 3.8 - - - +
485A VAL* 4.8 1.0 - - - +
486A ALA* 4.0 32.6 + - + +
482B ARG 2.9 16.5 + - - +
483B VAL* 3.7 6.3 - - - +
485B VAL* 1.3 74.1 - - - +
487B ARG* 1.3 64.6 + - - +
488B LEU 3.3 0.3 + - - -
489B GLY* 3.5 9.9 + - - -
490B HIS 4.8 0.2 + - - -
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Residues in contact with ARG 487 (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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447B ASN* 3.5 31.3 + - - +
449B GLU* 3.6 26.4 - - - +
450B PHE* 4.0 20.6 - - + -
483B VAL* 3.2 26.6 + - - +
484B LEU* 3.1 23.0 + - - +
486B ALA* 1.3 79.7 - - - +
488B LEU* 1.3 65.2 + - - +
489B GLY 3.0 0.7 - - - -
490B HIS* 3.1 23.0 + - + +
491B PHE* 3.6 14.9 - - + -
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Residues in contact with LEU 488 (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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432A LEU* 4.1 9.0 - - + -
436A LEU* 3.4 35.9 - - + -
485A VAL* 3.9 9.4 - - + -
436B LEU* 4.9 4.3 - - + -
439B ALA* 4.1 11.4 - - + +
440B VAL* 3.9 29.6 - - - +
443B ALA* 4.2 6.5 - - + -
450B PHE* 3.8 22.4 - - + -
484B LEU 3.5 5.8 - - - +
485B VAL* 3.0 32.5 + - + +
487B ARG* 1.3 78.7 - - - +
489B GLY* 1.3 56.4 + - - +
491B PHE* 2.8 27.7 + - - +
492B ALA* 3.3 8.2 + - - +
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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