Contacts of the helix formed by residues 410 - 420 (chain A) in PDB entry 3ZFW
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 PRO 410 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393A LEU 4.6 1.3 - - - +
394A THR* 3.9 25.6 - - + +
397A HIS* 3.9 20.6 - - + -
404A VAL* 3.9 20.0 - - + -
409A LYS* 1.4 89.5 - - + +
411A ILE* 1.4 68.0 + - - +
412A TRP* 3.3 33.9 - - + +
413A MET* 3.1 28.2 + - + +
414A HIS* 3.3 10.1 + - - -
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Residues in contact with ILE 411 (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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393A LEU* 4.1 19.3 + - + +
397A HIS* 4.8 3.6 + - - +
409A LYS 3.9 0.8 + - - -
410A PRO* 1.4 70.3 - - - +
412A TRP* 1.3 60.3 + - - +
414A HIS* 3.1 18.9 + - + +
415A ALA* 3.0 25.5 + - - +
440A ALA 6.1 0.2 - - - -
441A CYS* 4.2 22.4 - - + -
443A VAL* 6.3 2.9 - - + -
452A LEU* 3.8 22.9 - - + -
470A THR* 4.3 19.3 - - + -
471A LEU* 3.9 16.8 - - + -
474A CYS* 4.3 18.4 - - + -
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Residues in contact with TRP 412 (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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390A LYS* 3.4 37.6 + - + -
393A LEU* 3.7 27.1 - - + -
394A THR* 3.0 29.3 + - + -
410A PRO* 3.4 17.5 - - + +
411A ILE* 1.3 79.5 - - - +
413A MET* 1.4 100.3 + - + +
415A ALA* 3.3 8.5 + - - +
416A GLU* 3.0 60.8 + - + +
455A LEU* 3.8 15.9 - - + -
459A TYR* 3.5 13.2 - - + +
471A LEU* 4.4 3.8 - - + -
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Residues in contact with MET 413 (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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404A VAL* 5.1 9.2 - - + -
409A LYS* 4.1 24.7 - - + -
410A PRO* 3.1 31.4 + - + +
412A TRP* 1.4 109.5 - - + +
414A HIS* 1.3 60.7 + - - +
416A GLU* 3.3 4.9 + - - +
417A GLU* 3.0 40.3 + - + +
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Residues in contact with HIS 414 (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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397A HIS* 5.7 0.2 - - - -
407A GLU 4.2 11.2 + - - -
409A LYS* 3.4 50.2 + - + +
410A PRO 3.3 10.0 + - - -
411A ILE* 3.1 22.3 + - + +
413A MET* 1.3 78.0 - - - +
415A ALA* 1.4 56.4 + - - +
417A GLU* 3.6 13.8 + - - +
418A ARG* 3.1 32.4 + - - +
470A THR* 5.0 3.1 - - + -
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Residues in contact with ALA 415 (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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411A ILE 3.0 12.9 + - - +
412A TRP* 3.4 13.9 - - - +
413A MET 3.2 0.2 - - - -
414A HIS* 1.4 73.9 - - - +
416A GLU* 1.3 58.2 + - - +
418A ARG* 3.4 5.1 - - - +
419A GLU 3.2 20.8 + - - -
459A TYR* 4.4 5.8 - - + -
467A ALA* 3.5 40.0 - - + +
470A THR* 3.9 19.9 - - + +
471A LEU* 4.5 4.5 - - + -
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Residues in contact with GLU 416 (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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390A LYS* 2.8 24.1 + - - -
412A TRP* 3.0 30.6 + - - +
413A MET* 3.9 6.1 - - - +
415A ALA* 1.3 76.1 - - - +
417A GLU* 1.4 56.7 + - + +
419A GLU* 3.4 7.8 + - - +
420A GLU* 3.2 32.6 + - + +
459A TYR* 2.7 35.1 + - + +
464A LYS* 3.4 26.1 + - + +
467A ALA* 4.7 2.7 - - + -
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Residues in contact with GLU 417 (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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409A LYS* 3.4 40.3 + - - +
413A MET* 3.0 24.5 + - - +
414A HIS* 3.9 12.6 + - - +
416A GLU* 1.4 72.8 - - + +
418A ARG* 1.3 63.2 + - - +
420A GLU* 3.4 19.5 + - - +
421A SER* 3.7 10.7 + - - -
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Residues in contact with ARG 418 (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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414A HIS* 3.1 17.5 + - - +
415A ALA* 3.4 8.3 - - - +
416A GLU 3.4 0.2 - - - -
417A GLU* 1.3 73.1 - - - +
419A GLU* 1.4 62.0 + - - +
421A SER* 3.4 23.4 + - - -
466A GLU* 3.3 34.9 + - + +
470A THR* 3.3 43.5 + - - +
473A ASP* 5.0 5.9 + - - -
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Residues in contact with GLU 419 (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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415A ALA 3.2 10.1 + - - +
416A GLU* 3.6 10.8 - - - +
417A GLU 3.4 0.4 - - - -
418A ARG* 1.4 70.1 - - - +
420A GLU* 1.4 60.4 + - + +
421A SER 2.9 19.7 + - - +
463A GLY 4.1 3.5 - - - +
464A LYS* 3.4 37.0 - - + +
465A LEU* 3.1 7.6 + - - +
466A GLU* 2.9 29.5 + - + +
467A ALA* 3.4 24.7 - - + +
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Residues in contact with GLU 420 (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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416A GLU 3.2 18.7 + - - +
417A GLU* 3.6 14.4 - - + +
418A ARG 3.4 1.0 - - - -
419A GLU* 1.4 74.9 - - - +
421A SER* 1.4 56.3 + - - +
464A LYS* 5.6 6.2 + - - -
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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