Contacts of the helix formed by residues 428 - 436 (chain A) in PDB entry 1YQZ
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 ASP 428 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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395A ARG* 2.8 47.6 + - - -
415A PHE* 4.2 5.3 - - + -
417A VAL* 3.9 25.8 - - + +
424A SER* 3.5 9.4 - - - -
425A HIS* 3.3 13.3 + - - +
427A LYS* 1.3 77.2 - - - +
429A LEU* 1.3 76.2 + - - +
430A ILE* 3.1 20.8 + - - +
431A ASN* 2.9 27.9 + - - +
432A MET* 2.9 12.1 + - - +
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Residues in contact with LEU 429 (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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353A VAL* 4.5 10.2 - - + +
355A GLN* 4.0 21.0 + - + +
356A GLY 3.6 23.1 - - - +
368A LEU* 3.4 46.2 - - + +
370A LEU* 4.0 24.2 - - + -
395A ARG* 3.8 25.4 - - + +
425A HIS* 4.0 9.8 - - + -
428A ASP* 1.3 80.0 + - - +
430A ILE* 1.3 61.9 + - - +
432A MET* 3.2 11.8 + - - +
433A ILE* 3.1 24.8 + - - +
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Residues in contact with ILE 430 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A LEU* 4.0 20.0 - - + -
395A ARG* 3.8 28.0 - - + +
398A VAL* 3.4 37.9 - - + -
399A LEU* 4.4 8.1 - - + -
412A LEU* 3.5 34.4 - - + +
415A PHE* 3.6 31.6 - - + -
428A ASP* 3.1 9.6 + - - +
429A LEU* 1.3 77.7 - - - +
431A ASN* 1.3 64.0 + - - +
433A ILE* 3.3 13.0 + - - +
434A GLY 3.5 6.8 + - - -
401B MET* 5.1 0.2 - - + -
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Residues in contact with ASN 431 (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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412A LEU 2.9 26.4 + - - +
413A THR* 3.4 12.3 + - - +
415A PHE* 2.8 35.0 + - - +
417A VAL* 4.6 1.2 - - - +
426A PRO 3.9 1.0 - - - +
427A LYS* 3.7 8.0 - - - -
428A ASP* 2.9 34.7 + - - +
430A ILE* 1.3 76.6 - - - +
432A MET* 1.3 58.6 + - - +
434A GLY* 3.0 5.2 + - - -
435A TYR* 2.9 47.4 + - + -
296B TRP* 3.7 11.4 + - - -
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Residues in contact with MET 432 (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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353A VAL* 3.9 17.3 - - + -
355A GLN* 3.9 20.4 - - - +
427A LYS* 3.9 33.2 - - - +
428A ASP 2.9 17.0 + - - +
429A LEU* 3.2 9.4 + - - +
431A ASN* 1.3 73.5 - - - +
433A ILE* 1.3 66.3 + - - +
435A TYR* 3.2 13.0 + - + -
436A LYS* 2.9 35.9 + - + +
442B COA 3.5 49.4 - - + +
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Residues in contact with ILE 433 (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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351A VAL* 3.6 22.0 - - + +
352A GLU* 3.7 35.4 - - - +
353A VAL* 4.0 4.7 - - + +
370A LEU* 3.8 27.6 - - + +
372A VAL* 3.8 28.7 - - + -
409A VAL* 3.9 10.5 - - + -
412A LEU* 3.8 15.9 - - + -
429A LEU 3.1 14.5 + - - +
430A ILE* 3.5 8.3 - - - +
431A ASN 3.2 0.4 - - - -
432A MET* 1.3 74.1 - - - +
434A GLY* 1.3 62.4 + - - +
436A LYS 3.3 0.3 + - - -
437A ALA* 3.2 22.2 + - - +
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Residues in contact with GLY 434 (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 VAL 3.5 22.6 - - - +
410A ASP* 4.5 4.0 - - - -
412A LEU* 4.1 6.0 - - - +
413A THR* 3.4 17.9 - - - +
430A ILE 3.5 3.6 + - - -
431A ASN 3.0 8.7 + - - -
433A ILE* 1.3 80.9 - - - +
435A TYR* 1.3 61.2 + - - +
437A ALA* 3.3 16.0 + - - +
438A LYS* 4.6 8.7 + - - +
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Residues in contact with TYR 435 (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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413A THR* 3.5 16.7 + - + +
427A LYS* 3.6 22.9 - - + +
431A ASN* 2.9 40.9 + - + -
432A MET* 3.2 18.6 + - + +
434A GLY* 1.3 76.5 - - - +
436A LYS* 1.3 60.3 + - - +
437A ALA 3.3 1.0 + - - -
438A LYS* 4.2 11.1 + - - +
300B ARG* 3.0 48.3 + - - -
303B SER* 3.6 25.9 + - - -
307B GLU* 6.2 0.4 - - - -
442B COA 3.6 39.1 + - + +
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Residues in contact with LYS 436 (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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351A VAL* 3.8 20.1 - - + +
352A GLU 2.8 24.1 + - - +
353A VAL* 3.3 30.2 - - + +
432A MET* 2.9 22.1 + - + +
433A ILE 3.3 1.8 + - - -
434A GLY 3.2 0.4 - - - -
435A TYR* 1.3 75.9 - - - +
437A ALA* 1.3 59.9 + - - +
438A LYS* 3.3 6.4 + - - +
442B COA 4.0 19.1 - - + +
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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