Contacts of the helix formed by residues 439 - 458 (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 THR 439 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378B CYS* 4.4 12.1 - - - -
437B PRO 5.5 0.4 - - - +
438B PHE* 1.3 79.2 - - - +
440B GLU* 1.3 65.6 + - - +
441B GLU* 3.9 8.6 + - - +
442B ILE* 3.3 29.1 + - + +
443B LYS* 2.9 21.5 + - - +
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Residues in contact with GLU 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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438B PHE 4.0 0.5 + - - +
439B THR* 1.3 75.0 - - - +
441B GLU* 1.3 58.1 + - - +
443B LYS* 3.6 22.1 + - - +
444B ASN* 2.7 47.0 + - - +
447B ARG* 3.7 22.8 + - - -
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Residues in contact with GLU 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B THR* 3.2 10.6 + - - +
440B GLU* 1.3 79.2 - - - +
442B ILE* 1.3 60.6 + - + +
444B ASN* 3.3 13.7 + - - +
445B TYR* 3.2 21.8 + - - +
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Residues in contact with ILE 442 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
371B VAL* 6.2 0.2 - - + -
374B ALA* 4.0 28.5 - - + +
375B GLU* 3.6 21.5 - - + +
378B CYS* 3.4 32.3 - - - -
438B PHE* 3.4 31.6 - - + -
439B THR* 3.3 21.7 + - + +
441B GLU* 1.3 77.9 - - + +
443B LYS* 1.3 65.7 + - - +
445B TYR* 3.5 6.6 + - - +
446B ASN* 3.0 27.4 + - - +
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Residues in contact with LYS 443 (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* 3.6 56.1 - - + +
434B GLY 5.0 4.9 + - - -
436B VAL 4.3 8.3 + - - -
438B PHE* 3.6 27.8 + - + +
439B THR 2.9 17.9 + - - +
440B GLU* 3.7 24.6 + - - +
442B ILE* 1.3 77.1 - - - +
444B ASN* 1.3 63.0 + - - +
446B ASN* 3.2 4.7 + - - +
447B ARG* 3.0 45.7 + - - +
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Residues in contact with ASN 444 (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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440B GLU* 2.7 46.4 + - - +
441B GLU* 3.4 12.5 + - + +
443B LYS* 1.3 75.0 - - - +
445B TYR* 1.3 58.3 + - - +
447B ARG* 3.2 15.9 + - - +
448B GLU* 2.8 47.5 + - + +
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Residues in contact with TYR 445 (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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367B THR* 4.4 16.9 - - + +
368B GLU* 4.6 4.6 + - - -
371B VAL* 3.7 38.8 - - + -
429B ARG* 4.2 18.3 + - - -
441B GLU 3.2 10.8 + - - +
442B ILE* 3.8 9.6 - - - +
443B LYS 3.3 0.2 - - - -
444B ASN* 1.3 78.3 - - - +
446B ASN* 1.3 68.2 + - - +
448B GLU* 3.3 19.2 + - + +
449B ARG* 3.0 66.2 + - + +
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Residues in contact with ASN 446 (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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375B GLU* 3.1 24.2 + - - +
429B ARG* 3.4 23.5 - - - +
430B TYR* 3.0 41.5 + - - +
433B PHE* 3.7 21.3 - - + -
438B PHE* 4.8 0.2 - - - -
442B ILE* 3.0 25.1 + - - +
443B LYS 3.2 7.7 + - - +
445B TYR* 1.3 83.1 - - - +
447B ARG* 1.3 62.6 + - - +
449B ARG* 3.4 2.4 + - - +
450B LEU* 3.1 28.9 + - - +
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Residues in contact with ARG 447 (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 TYR 5.7 1.1 - - - +
431B LEU 6.1 0.7 - - - +
433B PHE* 4.0 28.3 - - + -
440B GLU* 3.7 21.4 + - - -
443B LYS* 3.0 32.5 + - - +
444B ASN* 3.6 20.9 + - - +
446B ASN* 1.3 75.6 - - - +
448B GLU* 1.3 57.6 + - + +
450B LEU* 3.2 8.2 + - + +
451B GLN* 2.9 31.6 + - - +
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Residues in contact with GLU 448 (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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444B ASN* 2.8 37.5 + - - +
445B TYR* 3.6 22.4 - - + +
447B ARG* 1.3 69.8 - - + +
449B ARG* 1.3 69.7 + - + +
451B GLN* 3.4 14.4 + - - +
452B GLU* 3.5 18.6 + - - +
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Residues in contact with ARG 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368B GLU* 5.3 1.2 + - - -
423B ASP* 3.0 51.7 + - + +
424B ASN 4.2 0.9 + - - -
425B LEU* 3.9 25.8 - - - +
427B CYS* 3.8 16.2 - - - -
429B ARG* 3.8 18.7 - - + +
445B TYR* 3.0 59.2 + - + +
446B ASN 3.7 3.6 - - - +
448B GLU* 1.3 78.2 - - + +
450B LEU* 1.3 64.4 + - - +
452B GLU* 3.3 37.0 + - - +
453B ARG 3.8 2.1 + - - -
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Residues in contact with LEU 450 (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* 3.5 26.0 - - + -
422B ARG 3.3 33.0 - - - +
423B ASP* 3.7 6.5 - - + +
429B ARG* 3.9 12.1 - - + -
430B TYR 3.5 26.7 - - - +
431B LEU* 3.9 15.5 - - + -
446B ASN 3.1 18.7 + - - +
447B ARG* 3.2 8.0 + - + +
449B ARG* 1.3 74.9 - - - +
451B GLN* 1.3 66.4 + - - +
453B ARG* 2.9 16.0 + - + +
454B ALA 3.1 9.4 + - - -
461B VAL* 3.5 22.2 - - + +
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Residues in contact with GLN 451 (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 ARG 2.9 17.7 + - - +
448B GLU* 3.7 8.7 - - - +
449B ARG 3.3 0.6 - - - -
450B LEU* 1.3 77.4 - - - +
452B GLU* 1.3 62.4 + - + +
454B ALA* 3.2 14.6 + - - +
455B LYS* 2.9 39.6 + - - +
461B VAL* 5.4 0.9 - - - -
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Residues in contact with GLU 452 (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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423B ASP* 6.0 0.2 - - - -
424B ASN* 3.8 16.8 + - + +
448B GLU* 3.5 14.0 - - - +
449B ARG* 3.3 35.9 + - - +
450B LEU 3.1 0.8 - - - -
451B GLN* 1.3 80.5 - - + +
453B ARG* 1.3 57.2 + - - +
455B LYS* 3.5 7.0 + - - +
456B PHE* 3.0 28.1 + - - +
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Residues in contact with ARG 453 (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* 3.9 2.0 - - - +
422B ARG* 2.9 30.1 + - - +
423B ASP* 3.9 9.6 - - - -
424B ASN* 3.6 28.1 - - - +
449B ARG 3.8 0.4 + - - -
450B LEU* 2.9 11.9 + - - +
452B GLU* 1.3 77.4 - - - +
454B ALA* 1.3 66.7 + - - +
457B GLU* 2.7 49.5 + - - +
461B VAL* 4.9 0.9 - - + -
465B MET* 3.7 34.5 + - + +
469B ASP* 2.8 42.3 + - - -
479B ILE* 3.7 7.8 - - - +
480B GLY 3.0 29.5 + - - +
481B ARG* 4.5 1.1 - - - +
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Residues in contact with ALA 454 (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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450B LEU 3.1 10.9 + - - +
451B GLN* 3.5 23.6 - - - +
453B ARG* 1.3 77.2 - - - +
455B LYS* 1.3 56.4 + - - +
458B GLY* 2.8 31.0 + - - -
459B ARG 3.1 26.0 + - - +
460B ASP* 4.4 2.2 - - - -
461B VAL* 4.3 14.7 - - + +
465B MET* 4.6 2.9 - - - -
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Residues in contact with LYS 455 (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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451B GLN* 2.9 30.4 + - - +
452B GLU* 3.8 6.5 - - - +
454B ALA* 1.3 79.4 - - - +
456B PHE* 1.3 63.6 + - - +
458B GLY* 3.5 7.8 + - - -
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Residues in contact with PHE 456 (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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424B ASN* 3.5 22.2 - - - +
452B GLU 3.0 19.3 + - - +
453B ARG 3.3 0.9 + - - +
455B LYS* 1.3 79.8 - - - +
457B GLU* 1.3 61.3 + - + +
481B ARG* 3.5 44.4 - - + -
355D GLU* 4.5 5.6 - - - -
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Residues in contact with GLU 457 (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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453B ARG* 2.7 51.4 + - - +
456B PHE* 1.3 79.9 - - + +
458B GLY* 1.3 61.9 + - - +
459B ARG* 2.8 45.5 + - + +
465B MET* 3.8 2.8 - - + +
481B ARG* 2.8 34.5 + - - +
482B PRO* 3.5 32.1 - - + +
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Residues in contact with GLY 458 (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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454B ALA 2.8 14.4 + - - -
455B LYS 3.5 5.9 + - - -
456B PHE 3.4 2.8 + - - -
457B GLU* 1.3 77.8 - - - +
459B ARG* 1.3 55.3 - - - +
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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
------------------------------------------------------------
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