Contacts of the helix formed by residues 412 - 417 (chain D) in PDB entry 1Z10
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 ASN 412 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358D GLU* 2.7 17.3 + - - +
406D SER* 4.6 2.4 + - - -
407D ASN* 4.6 10.5 - - + +
410D ASP* 3.4 8.9 + - + +
411D PHE* 1.3 75.1 - - - +
413D PRO* 1.3 61.7 - - - +
414D GLN* 3.0 37.2 + - - +
415D HIS* 2.9 57.1 + - - +
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Residues in contact with PRO 413 (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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323D VAL* 4.1 22.9 - - + -
351D TYR* 3.8 32.5 - - + +
354D ALA* 3.5 8.7 - - + +
355D VAL* 3.9 28.9 - - + +
358D GLU* 4.0 11.4 - - + -
411D PHE* 4.2 16.4 - - + +
412D ASN* 1.3 85.7 - - - +
414D GLN* 1.3 62.1 + - + +
415D HIS 2.9 2.7 + - - -
416D PHE* 3.0 12.1 + - - +
417D LEU* 3.4 12.2 - - - +
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Residues in contact with GLN 414 (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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326D LYS* 5.0 6.8 + - - -
351D TYR* 4.3 10.9 + - - -
412D ASN* 2.9 27.6 + - - +
413D PRO* 1.3 77.7 - - + +
415D HIS* 1.3 61.1 + - - +
416D PHE 3.0 1.8 + - - -
417D LEU* 3.1 48.0 + - - +
418D ASN 4.5 7.5 + - - -
421D GLY* 6.1 0.4 - - - -
424D LYS* 5.0 2.3 + - - -
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Residues in contact with HIS 415 (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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358D GLU* 3.1 28.3 - - - +
361D ARG* 3.7 10.7 + - - -
404D PHE 5.4 1.0 - - - +
405D PHE* 3.8 31.0 - + + +
406D SER* 3.6 21.3 + - - -
407D ASN* 3.1 49.5 + - - -
408D PRO 4.2 0.2 - - - -
410D ASP 3.9 2.8 + - - -
412D ASN* 2.9 38.8 + - + +
413D PRO 2.9 0.2 - - - -
414D GLN* 1.3 78.2 - - - +
416D PHE* 1.3 63.2 + - + +
417D LEU 3.7 0.4 - - - -
424D LYS* 4.1 15.3 + - - +
426D SER* 5.6 1.7 - - - -
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Residues in contact with PHE 416 (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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354D ALA* 3.8 18.4 - - + -
357D HIS* 3.8 16.8 - + + -
358D GLU* 3.2 51.8 - - + -
361D ARG* 4.1 6.5 - - + -
405D PHE* 3.9 22.7 - + - -
413D PRO 3.0 3.7 + - - -
414D GLN 3.0 0.6 - - - -
415D HIS* 1.3 83.2 - - + +
417D LEU* 1.3 67.3 + - - +
423D PHE* 3.5 13.6 - + + -
424D LYS* 2.8 43.4 + - - +
426D SER* 4.3 7.6 - - - -
429D PHE* 3.7 41.1 - + + -
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Residues in contact with LEU 417 (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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350D PRO 3.7 15.7 - - - +
351D TYR* 3.9 22.4 - - + -
354D ALA* 3.5 19.1 - - + -
413D PRO 3.4 25.6 - - - +
414D GLN* 3.1 39.9 + - - +
415D HIS 3.7 0.4 - - - -
416D PHE* 1.3 89.0 - - - +
418D ASN* 1.3 65.0 + - - +
419D GLU* 5.0 0.9 - - - +
421D GLY* 4.0 16.2 - - - +
422D GLN 3.2 17.3 - - - +
423D PHE* 4.2 0.2 - - - -
424D LYS* 3.6 20.0 + - - +
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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