Contacts of the helix formed by residues 442 - 457 (chain A) in PDB entry 1ZD4
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 442 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437A LEU* 4.0 7.4 - - - -
441A VAL* 1.3 77.5 - - - +
443A GLU* 1.3 65.4 + - - +
444A GLU* 3.2 17.2 + - - +
445A GLU* 3.0 37.4 + - + +
446A ILE* 3.3 20.6 + - - +
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Residues in contact with GLU 443 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A SER* 4.9 0.2 + - - -
404A LYS* 2.9 35.2 + - - -
437A LEU* 3.9 23.6 - - + +
442A THR* 1.3 75.8 - - - +
444A GLU* 1.3 76.9 + - - +
446A ILE* 3.4 5.7 + - - +
447A GLN* 3.2 48.7 + - + +
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Residues in contact with GLU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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442A THR* 3.2 15.4 + - - +
443A GLU* 1.3 85.2 + - - +
445A GLU* 1.3 70.2 + - + +
446A ILE 3.0 2.0 - - - -
447A GLN* 2.8 22.0 + - - +
448A PHE* 3.1 9.6 + - - +
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Residues in contact with GLU 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229A SER* 4.3 3.5 + - - -
270A TYR* 3.9 24.9 + - + +
273A ARG* 2.6 36.1 + - - +
274A TYR* 3.5 13.9 + - - -
440A MET 3.6 6.6 - - - +
441A VAL* 3.1 17.7 - - + -
442A THR* 3.0 41.8 + - + +
444A GLU* 1.3 79.6 - - + +
446A ILE* 1.3 61.9 + - - +
448A PHE* 3.3 11.4 + - - +
449A TYR* 3.1 22.3 - - + -
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Residues in contact with ILE 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A SER 4.4 5.2 - - - +
403A PHE* 4.0 19.5 - - + +
404A LYS* 4.0 27.8 - - + +
407A PHE* 3.9 24.9 - - + -
437A LEU* 4.7 4.0 - - + -
441A VAL* 3.5 34.3 - - + -
442A THR 3.3 7.7 + - - +
443A GLU* 3.4 9.4 - - - +
444A GLU 3.0 0.8 - - - -
445A GLU* 1.3 72.5 - - - +
447A GLN* 1.3 83.1 + - - +
448A PHE 3.0 1.6 - - - -
449A TYR* 2.9 20.2 + - + +
450A VAL* 3.1 16.2 + - + +
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Residues in contact with GLN 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400A SER* 3.6 22.5 + - - -
443A GLU* 3.2 35.3 + - + +
444A GLU* 2.8 15.0 + - - +
446A ILE* 1.3 86.3 - - - +
448A PHE* 1.3 61.4 + - - +
449A TYR 3.2 0.2 - - - -
450A VAL* 3.4 22.1 - - - +
451A GLN* 2.9 25.6 + - - +
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Residues in contact with PHE 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232A PRO* 3.8 27.8 - - + -
268A SER* 3.9 6.3 - - - -
269A TRP* 4.0 25.8 - + - -
270A TYR* 3.4 46.0 - + + -
444A GLU 3.1 7.4 + - - +
445A GLU* 3.3 13.7 - - - +
446A ILE 3.0 0.8 - - - -
447A GLN* 1.3 76.5 - - - +
449A TYR* 1.3 66.2 + + - +
451A GLN* 3.0 33.4 - - - +
452A GLN* 3.0 55.8 - - + +
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Residues in contact with TYR 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A PRO 4.5 0.2 - - - -
267A GLU* 4.0 10.1 - - - -
268A SER* 4.2 9.2 - - - -
270A TYR* 3.6 22.4 - + + -
271A SER* 3.1 27.0 + - - -
273A ARG* 3.0 27.6 + - - -
403A PHE* 3.9 20.0 - + + -
407A PHE* 3.5 38.6 - + - -
441A VAL* 5.6 1.3 - - + -
445A GLU* 3.1 28.7 - - + -
446A ILE* 2.9 9.7 + - - +
448A PHE* 1.3 79.7 - + - +
450A VAL* 1.3 63.8 + - - +
452A GLN* 3.1 7.5 + - - -
453A PHE* 3.0 44.8 + + - +
527A MET* 3.6 7.9 - - + +
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Residues in contact with VAL 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A LEU* 3.4 25.2 - - + +
400A SER* 3.9 28.9 - - - +
403A PHE* 4.0 15.5 - - + -
446A ILE* 3.1 16.5 + - + +
447A GLN* 3.4 32.1 - - - +
449A TYR* 1.3 76.9 - - - +
451A GLN* 1.3 63.3 + - - +
453A PHE 3.6 0.3 + - - -
454A LYS* 3.2 35.1 + - - +
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Residues in contact with GLN 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A GLN 2.9 12.8 + - - +
448A PHE* 3.0 43.0 - - - +
450A VAL* 1.3 73.8 - - - +
452A GLN* 1.3 81.2 + - - +
454A LYS* 3.3 24.4 - - + +
455A LYS* 4.0 3.1 + - - +
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Residues in contact with GLN 452 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268A SER* 4.9 8.6 - - - +
269A TRP* 5.2 3.8 + - - -
290A ASP* 5.2 1.2 - - - +
295A GLY* 4.0 31.2 + - - +
296A GLU* 4.5 13.4 + - - +
448A PHE* 3.0 56.2 - - + +
449A TYR* 3.1 7.7 + - - +
451A GLN* 1.3 101.5 + - - +
453A PHE* 1.3 69.3 + - + +
454A LYS 2.9 9.8 + - - -
455A LYS* 3.0 23.6 + - - +
456A SER 4.2 1.2 + - - -
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Residues in contact with PHE 453 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A PRO* 3.4 30.1 - - + -
267A GLU 3.0 30.5 - - - -
268A SER* 4.9 1.3 - - - -
294A TYR* 3.6 23.8 - + + -
295A GLY 5.8 2.7 - - - +
399A LEU* 4.3 10.5 - - + +
403A PHE* 3.3 23.8 - + + -
449A TYR* 3.0 26.3 + + - +
450A VAL 3.9 2.0 - - - +
452A GLN* 1.3 87.1 - - + +
454A LYS* 1.3 57.8 + - - +
455A LYS 3.1 0.7 - - - -
456A SER 5.0 0.2 - - - +
457A GLY* 3.0 40.0 + - - +
458A PHE* 3.5 32.1 - + + -
461A PRO* 4.5 4.3 - - + -
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Residues in contact with LYS 454 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399A LEU* 3.5 15.9 - - + -
450A VAL* 3.2 32.3 + - - +
451A GLN* 3.3 20.4 - - + +
452A GLN 2.9 1.2 + - - -
453A PHE* 1.3 78.1 - - - +
455A LYS* 1.3 64.6 + - - +
457A GLY* 4.8 0.6 + - - -
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Residues in contact with LYS 455 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247A ARG* 6.2 1.6 - - - +
295A GLY 3.3 23.8 + - - +
296A GLU* 4.5 11.1 - - + +
297A SER 3.7 12.9 + - - -
298A SER* 5.1 3.0 - - - +
299A ALA 5.2 0.4 - - - +
451A GLN 4.0 3.3 + - - +
452A GLN 3.0 14.0 + - - +
454A LYS* 1.3 83.0 - - - +
456A SER* 1.3 78.1 + - - +
457A GLY 3.8 0.2 + - - -
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Residues in contact with SER 456 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A GLY 4.2 10.3 - - - -
294A TYR* 5.7 1.1 - - - -
295A GLY 4.1 5.9 + - - -
297A SER 4.3 0.3 + - - -
299A ALA* 3.4 32.0 - - - +
452A GLN 4.2 2.0 + - - -
453A PHE* 4.2 0.4 + - - +
455A LYS* 1.3 102.7 + - - +
457A GLY* 1.3 63.1 + - - +
458A PHE 4.0 0.2 + - - -
459A ARG* 4.3 11.6 + - - +
460A GLY 4.9 1.9 + - - -
461A PRO* 6.1 0.2 - - - -
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Residues in contact with GLY 457 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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293A GLY 4.5 3.1 - - - +
396A GLU* 3.6 19.7 - - - -
453A PHE* 3.0 33.3 + - - +
454A LYS 4.6 0.4 - - - -
455A LYS 3.5 1.4 + - - -
456A SER* 1.3 81.9 - - - +
458A PHE* 1.3 65.7 + - - -
461A PRO* 3.6 14.7 - - - +
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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