Contacts of the helix formed by residues 439 - 458 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378D CYS* 4.5 13.7 - - - -
437D PRO 5.2 1.6 - - - +
438D PHE* 1.3 77.6 - - - +
440D GLU* 1.3 65.9 + - - +
441D GLU* 3.6 16.4 + - - +
442D ILE* 3.3 25.1 + - + +
443D LYS* 3.0 20.6 + - - +
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Residues in contact with GLU 440 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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438D PHE 5.6 0.2 - - - +
439D THR* 1.3 74.7 - - - +
441D GLU* 1.3 65.8 + - - +
443D LYS* 3.2 13.4 + - - +
444D ASN* 2.7 50.7 + - - +
447D ARG* 3.2 26.5 + - - -
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Residues in contact with GLU 441 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439D THR* 3.2 19.4 + - - +
440D GLU* 1.3 81.7 + - - +
442D ILE* 1.3 58.3 + - + +
444D ASN* 3.4 6.6 + - - +
445D TYR* 3.1 27.5 + - - +
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Residues in contact with ILE 442 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374D ALA* 4.0 27.1 - - + +
375D GLU* 3.6 23.8 - - + +
378D CYS* 3.4 33.0 - - - -
438D PHE* 3.4 31.9 - - + -
439D THR* 3.3 19.9 + - + +
441D GLU* 1.3 74.3 - - + +
443D LYS* 1.3 66.1 + - - +
445D TYR* 3.4 6.6 + - - +
446D ASN* 3.0 27.4 + - - +
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Residues in contact with LYS 443 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433D PHE* 3.6 55.6 - - + +
434D GLY 5.1 4.6 + - - -
436D VAL 4.3 7.6 + - - -
438D PHE* 3.4 30.1 + - + +
439D THR 3.0 17.8 + - - +
440D GLU* 3.7 17.1 + - - +
442D ILE* 1.3 78.1 - - - +
444D ASN* 1.3 59.4 + - - +
446D ASN* 3.2 6.1 + - - +
447D ARG* 2.9 48.7 + - - +
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Residues in contact with ASN 444 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440D GLU* 2.7 43.0 + - - +
441D GLU* 3.8 6.6 - - - +
443D LYS* 1.3 75.4 - - - +
445D TYR* 1.3 57.4 + - - +
447D ARG* 3.3 28.6 + - - +
448D GLU* 2.8 46.5 + - + +
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Residues in contact with TYR 445 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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367D THR* 4.4 16.6 - - + +
368D GLU* 4.7 4.8 + - - -
371D VAL* 3.7 38.4 - - + -
429D ARG* 4.1 18.2 + - - -
441D GLU 3.1 14.1 + - - +
442D ILE* 3.8 10.5 - - - +
443D LYS 3.2 0.2 - - - -
444D ASN* 1.3 75.4 - - - +
446D ASN* 1.3 68.5 + - - +
448D GLU* 3.2 17.1 + - + +
449D ARG* 3.0 64.8 + - + +
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Residues in contact with ASN 446 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375D GLU* 3.2 22.8 + - - +
429D ARG* 3.4 19.4 - - + +
430D TYR* 3.0 49.4 + - - +
433D PHE* 3.8 12.6 - - + -
442D ILE* 3.0 25.5 + - - +
443D LYS 3.2 7.9 + - - +
445D TYR* 1.3 84.3 - - - +
447D ARG* 1.3 62.1 + - - +
449D ARG* 3.3 5.7 + - - +
450D LEU* 3.1 29.4 + - - +
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Residues in contact with ARG 447 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430D TYR 5.8 1.1 - - - +
431D LEU 5.9 1.3 + - - +
433D PHE* 3.9 28.4 - - + -
440D GLU* 3.2 24.2 + - - -
443D LYS* 2.9 36.2 + - - +
444D ASN* 3.3 27.9 + - - +
446D ASN* 1.3 76.4 - - - +
448D GLU* 1.3 57.3 + - + +
450D LEU* 3.2 8.8 + - + +
451D GLN* 2.9 30.1 + - - +
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Residues in contact with GLU 448 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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444D ASN* 2.8 34.0 + - + +
445D TYR* 3.2 20.6 + - + +
447D ARG* 1.3 72.9 - - + +
449D ARG* 1.3 65.4 + - + +
451D GLN* 3.4 15.0 + - - +
452D GLU* 3.5 18.9 + - - +
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Residues in contact with ARG 449 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368D GLU* 5.3 1.4 + - - -
423D ASP* 2.9 54.6 + - + +
424D ASN 4.2 0.7 + - - -
425D LEU* 3.9 27.0 - - - +
427D CYS* 3.7 16.6 - - - -
429D ARG* 3.8 16.9 - - + +
445D TYR* 3.0 60.1 + - + +
446D ASN 3.7 4.5 - - - +
448D GLU* 1.3 76.5 - - + +
450D LEU* 1.3 63.9 + - - +
452D GLU* 3.2 37.5 + - - +
453D ARG 3.8 2.1 + - - -
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Residues in contact with LEU 450 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D VAL* 3.5 27.4 - - + -
422D ARG 3.4 28.0 - - - +
423D ASP* 3.7 13.0 - - + +
429D ARG* 3.9 11.2 - - + -
430D TYR 3.6 25.6 - - - +
431D LEU* 3.9 14.8 - - + +
446D ASN 3.1 20.0 + - - +
447D ARG* 3.2 7.4 + - + +
449D ARG* 1.3 75.9 - - - +
451D GLN* 1.3 66.6 + - - +
453D ARG* 2.9 16.5 + - - +
454D ALA 3.2 9.2 + - - -
461D VAL* 3.4 18.4 - - + +
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Residues in contact with GLN 451 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447D ARG 2.9 15.9 + - - +
448D GLU* 3.8 8.7 - - - +
449D ARG 3.3 0.2 - - - -
450D LEU* 1.3 76.6 - - - +
452D GLU* 1.3 63.7 + - + +
454D ALA* 3.2 15.7 + - - +
455D LYS* 2.9 39.8 + - + +
461D VAL* 4.6 2.1 - - - +
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Residues in contact with GLU 452 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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423D ASP* 5.9 0.2 - - - -
424D ASN* 3.8 14.9 + - + +
425D LEU* 5.0 8.0 - - - +
448D GLU* 3.5 15.2 + - - +
449D ARG* 3.2 34.0 + - - +
450D LEU 3.0 0.8 - - - -
451D GLN* 1.3 79.2 - - + +
453D ARG* 1.3 58.0 + - - +
455D LYS* 3.5 8.8 + - + +
456D PHE* 3.0 27.9 + - - +
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Residues in contact with ARG 453 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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421D VAL* 3.8 8.1 - - - +
422D ARG* 2.8 32.0 + - - +
423D ASP* 3.9 9.0 - - - -
424D ASN* 3.5 29.0 - - - +
449D ARG 3.8 0.6 + - - -
450D LEU* 2.9 12.3 + - - +
452D GLU* 1.3 77.8 - - - +
454D ALA* 1.3 60.4 + - - +
456D PHE 3.3 0.2 + - - -
457D GLU* 2.8 54.0 + - - +
459D ARG* 4.0 5.3 - - - +
461D VAL* 5.3 0.2 - - + -
465D MET* 3.7 22.8 + - + +
469D ASP* 2.9 41.5 + - - -
479D ILE* 3.8 7.2 - - - +
480D GLY 3.0 29.3 + - - +
481D ARG* 4.1 1.3 - - - +
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Residues in contact with ALA 454 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D LEU 3.2 6.6 + - - +
451D GLN* 3.2 23.1 + - - +
453D ARG* 1.3 76.5 - - - +
455D LYS* 1.3 59.3 + - - +
458D GLY* 2.7 27.7 + - - -
459D ARG 3.1 29.1 + - - +
460D ASP* 4.4 2.5 - - - +
461D VAL* 3.8 20.1 - - + +
465D MET* 4.4 3.8 - - - -
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Residues in contact with LYS 455 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451D GLN* 2.9 30.3 + - + +
452D GLU* 3.8 8.7 - - + +
454D ALA* 1.3 78.8 - - - +
456D PHE* 1.3 62.4 + - - +
458D GLY* 3.5 7.8 + - - -
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Residues in contact with PHE 456 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B GLU* 4.4 7.2 - - - -
424D ASN* 3.4 26.5 - - - +
452D GLU 3.0 14.0 + - - +
453D ARG 3.3 0.6 + - - +
455D LYS* 1.3 77.9 - - - +
457D GLU* 1.3 63.3 + - + +
481D ARG* 3.5 42.4 - - + -
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Residues in contact with GLU 457 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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453D ARG* 2.8 49.8 + - - +
456D PHE* 1.3 81.3 - - + +
458D GLY* 1.3 60.9 + - - +
459D ARG* 2.8 45.6 + - + +
465D MET* 3.6 3.3 - - - +
481D ARG* 2.9 34.6 + - - +
482D PRO* 3.6 29.4 - - + +
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Residues in contact with GLY 458 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D ALA 2.7 12.4 + - - -
455D LYS* 3.5 6.1 + - - -
456D PHE 3.4 3.2 + - - -
457D GLU* 1.3 79.3 - - - +
459D ARG* 1.3 57.0 + - - +
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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