Contacts of the helix formed by residues 438 - 456 (chain B) in PDB entry 1ZKC
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 TYR 438 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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274B LEU* 3.4 33.9 - - + -
276B PRO* 3.6 27.9 - - + +
297B CYS* 4.0 1.4 - - + +
301B PRO* 2.5 32.3 + - - +
304B CYS* 3.4 13.1 - - + +
305B GLU* 3.1 42.9 + - + -
308B ILE* 4.2 17.0 - - + -
309B ARG* 4.2 9.9 - - + +
436B ASP* 3.0 17.2 + - - +
437B PRO* 1.3 83.6 - - + +
439B GLU* 1.3 58.8 + - - +
440B GLU 3.3 2.2 - - - -
441B ALA* 3.4 6.4 + - + -
442B ASP* 2.8 43.6 + - - +
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Residues in contact with GLU 439 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A ARG* 5.9 1.2 + - - -
436B ASP* 3.3 39.6 + - + +
437B PRO 3.3 1.4 - - - -
438B TYR* 1.3 77.6 - - - +
440B GLU* 1.3 58.1 + - - +
442B ASP* 3.4 5.5 + - - +
443B ALA* 2.8 31.8 + - - +
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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
----------------------------------------------------------
277B ARG* 3.3 48.2 + - + +
437B PRO 4.8 3.2 + - - +
438B TYR 3.3 0.2 - - - -
439B GLU* 1.3 78.1 - - - +
441B ALA* 1.3 58.5 + - - +
443B ALA* 3.2 7.0 + - - +
444B GLN* 2.9 31.2 + - + +
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Residues in contact with ALA 441 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 3.8 22.4 - - + -
275B VAL* 3.6 34.0 + - + +
277B ARG* 4.1 7.6 - - - +
437B PRO 5.4 0.4 + - - -
438B TYR* 3.4 9.1 + - - +
440B GLU* 1.3 78.4 - - - +
442B ASP* 1.3 62.6 + - - +
444B GLN* 3.2 9.7 + - - +
445B ILE* 3.0 27.0 + - - +
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Residues in contact with ASP 442 (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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274B LEU* 3.4 13.1 - - - +
309B ARG* 2.7 43.5 + - - -
312B LYS* 4.0 12.3 + - - -
436B ASP* 4.7 0.9 - - - +
438B TYR* 2.8 28.3 + - - +
439B GLU* 3.7 5.3 - - - +
441B ALA* 1.3 73.6 - - - +
443B ALA* 1.3 58.3 + - - +
445B ILE* 3.4 2.7 + - - +
446B ALA* 2.9 32.0 + - - +
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Residues in contact with ALA 443 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
439B GLU 2.8 21.6 + - - +
440B GLU* 3.6 8.1 - - - +
441B ALA 3.2 0.2 - - - -
442B ASP* 1.3 69.9 - - - +
444B GLN* 1.3 65.6 + - - +
446B ALA* 3.8 5.8 - - - +
447B GLN* 3.0 26.5 + - - +
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Residues in contact with GLN 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B ARG* 5.7 5.4 + - - -
440B GLU* 2.9 15.8 + - + +
441B ALA* 3.2 10.1 + - - +
443B ALA* 1.3 77.0 - - - +
445B ILE* 1.3 68.4 + - + +
447B GLN* 3.7 8.1 - - - +
448B GLU* 2.9 59.8 + - + +
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Residues in contact with ILE 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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273B GLY 5.4 5.2 - - - +
274B LEU* 3.7 22.0 - - + -
441B ALA 3.0 16.0 + - - +
442B ASP* 3.9 3.6 - - - +
444B GLN* 1.3 80.6 - - + +
446B ALA* 1.3 59.0 + - - +
448B GLU* 3.8 16.2 - - + +
449B ARG* 2.9 35.0 + - + +
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Residues in contact with ALA 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442B ASP 2.9 19.0 + - - +
443B ALA* 3.8 6.7 - - - +
445B ILE* 1.3 78.4 - - - +
447B GLN* 1.3 57.5 + - - +
449B ARG* 3.4 5.0 + - - +
450B LYS* 3.0 29.7 + - - +
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Residues in contact with GLN 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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443B ALA 3.0 18.3 + - - +
444B GLN* 3.7 7.9 - - - +
446B ALA* 1.3 73.8 - - - +
448B GLU* 1.3 80.0 + - - +
450B LYS* 3.2 8.7 + - + +
451B THR* 2.9 42.3 + - - +
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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
----------------------------------------------------------
444B GLN* 2.9 54.8 + - + +
445B ILE* 3.9 15.4 - - + +
447B GLN* 1.3 90.9 - - - +
449B ARG* 1.3 58.3 + - - +
451B THR* 3.5 5.5 + - - +
452B GLN* 3.0 32.7 + - - +
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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
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445B ILE* 2.9 24.5 + - + +
446B ALA* 3.8 5.6 - - - +
448B GLU* 1.3 76.4 - - - +
450B LYS* 1.3 56.2 + - - +
452B GLN* 3.4 7.7 + - - +
453B LEU* 3.0 60.5 + - + +
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Residues in contact with LYS 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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446B ALA 3.0 19.1 + - - +
447B GLN* 3.2 8.9 + - - +
449B ARG* 1.3 76.0 - - - +
451B THR* 1.3 64.8 + - - +
453B LEU* 3.4 7.6 + - - +
454B LYS* 3.1 24.4 + - + +
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Residues in contact with THR 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 GLN* 2.9 27.6 + - - +
448B GLU* 3.8 6.5 - - - -
450B LYS* 1.3 76.9 - - - +
452B GLN* 1.3 64.1 + - - +
454B LYS* 3.2 6.4 + - - +
455B VAL* 2.9 44.5 + - + +
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Residues in contact with GLN 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B GLU* 3.0 21.3 + - - +
449B ARG* 3.7 7.3 - - + +
451B THR* 1.3 78.2 - - - +
453B LEU* 1.3 62.3 + - + +
455B VAL* 4.6 1.3 - - - -
456B ALA* 2.7 59.9 + - + +
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Residues in contact with LEU 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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449B ARG* 3.0 47.0 + - + +
450B LYS* 3.9 6.7 - - - +
451B THR 3.3 0.2 - - - -
452B GLN* 1.3 81.2 - - + +
454B LYS* 1.3 63.5 + - - +
457B PRO* 4.0 23.9 - - + +
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Residues in contact with LYS 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 LYS* 3.1 19.4 + - + +
451B THR* 3.6 5.6 - - - +
453B LEU* 1.3 80.2 - - - +
455B VAL* 1.3 69.5 + - + +
457B PRO* 4.3 4.9 - - - +
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Residues in contact with VAL 455 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B THR* 2.9 37.7 + - + +
452B GLN* 4.6 0.9 - - - -
454B LYS* 1.3 89.0 - - + +
456B ALA* 1.3 65.8 + - + +
457B PRO* 3.4 9.8 - - - +
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Residues in contact with ALA 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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452B GLN* 2.7 44.4 + - + +
455B VAL* 1.3 78.3 - - + +
457B PRO* 1.3 64.7 - - - +
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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