Contacts of the helix formed by residues 428 - 437 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B GLN* 4.7 0.2 - - - -
395B ARG* 2.8 47.6 + - - -
415B PHE* 4.2 4.6 - - + -
417B VAL* 4.0 26.4 - - + +
424B SER* 3.5 9.4 - - - -
425B HIS* 3.3 12.3 + - - +
427B LYS* 1.3 78.0 - - - +
429B LEU* 1.3 75.9 + - - +
430B ILE* 3.0 22.8 + - - +
431B ASN* 2.9 28.8 + - - +
432B MET* 2.9 11.9 + - - +
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Residues in contact with LEU 429 (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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353B VAL* 3.9 13.8 - - + +
355B GLN* 3.9 29.1 - - + +
356B GLY 3.7 23.1 - - - +
357B ALA 4.9 0.2 - - - +
368B LEU* 3.4 46.9 - - + +
370B LEU* 4.0 25.6 - - + -
395B ARG* 3.9 15.3 - - + +
425B HIS* 5.4 3.4 - - + +
428B ASP* 1.3 90.2 + - - +
430B ILE* 1.3 63.4 + - - +
432B MET* 3.2 4.6 + - - +
433B ILE* 3.0 25.6 + - - +
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Residues in contact with ILE 430 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370B LEU* 4.0 20.4 - - + -
395B ARG* 3.9 23.1 - - + +
398B VAL* 3.4 37.5 - - + -
399B LEU* 4.4 11.4 - - + -
412B LEU* 3.5 34.5 - - + +
415B PHE* 3.7 30.1 - - + -
428B ASP* 3.0 12.6 + - - +
429B LEU* 1.3 78.0 - - - +
431B ASN* 1.3 63.0 + - - +
433B ILE* 3.3 12.7 + - - +
434B GLY 3.5 6.2 + - - -
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Residues in contact with ASN 431 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A TRP* 3.5 18.9 + - - -
412B LEU 3.0 26.0 + - - -
413B THR* 3.5 11.7 + - - +
415B PHE* 2.8 29.7 + - - +
417B VAL* 4.5 0.9 - - - +
427B LYS* 3.7 7.1 - - - -
428B ASP* 2.9 34.1 + - - +
430B ILE* 1.3 76.7 - - - +
432B MET* 1.3 64.0 + - - +
434B GLY* 2.9 13.3 + - - -
435B TYR* 3.0 35.3 + - + -
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Residues in contact with MET 432 (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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441A COA 3.4 55.0 - - + +
353B VAL* 3.9 16.8 - - + -
355B GLN* 4.0 16.4 - - - +
427B LYS* 3.8 41.3 - - - +
428B ASP 2.9 16.1 + - - +
429B LEU* 3.5 8.7 - - - +
431B ASN* 1.3 74.5 - - - +
433B ILE* 1.3 65.1 + - - +
435B TYR* 3.7 6.6 - - + -
436B LYS* 2.8 35.3 + - + +
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Residues in contact with ILE 433 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B VAL* 3.7 34.0 - - + +
352B GLU* 3.8 8.7 - - - +
353B VAL* 4.1 7.6 - - + -
370B LEU* 3.7 35.4 - - + +
372B VAL* 3.8 24.9 - - + -
399B LEU* 6.5 0.2 - - + -
409B VAL* 3.8 10.8 - - + -
412B LEU* 3.8 20.9 - - + -
429B LEU 3.0 19.3 + - - +
430B ILE* 3.5 8.3 - - - +
431B ASN 3.2 0.4 - - - -
432B MET* 1.3 74.9 - - - +
434B GLY* 1.3 63.7 + - - +
436B LYS 3.4 0.2 + - - -
437B ALA* 3.0 22.5 + - - +
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Residues in contact with GLY 434 (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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409B VAL 3.4 24.5 - - - -
410B ASP* 4.6 6.2 - - - +
412B LEU* 4.1 4.9 - - - +
413B THR* 3.4 17.0 - - - +
430B ILE 3.5 4.2 + - - -
431B ASN 2.9 8.2 + - - -
433B ILE* 1.3 80.8 - - - +
435B TYR* 1.3 61.8 + - - +
437B ALA* 3.4 14.8 + - - +
438B LYS 5.0 0.3 + - - -
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Residues in contact with TYR 435 (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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300A ARG* 3.0 47.9 + - - -
303A SER* 3.6 26.9 + - - -
307A GLU* 6.1 1.3 - - - -
441A COA 3.6 37.7 + - + +
413B THR* 3.5 16.0 + - + -
427B LYS* 3.5 29.9 - - + +
431B ASN* 3.0 41.8 + - + -
432B MET* 3.2 12.3 + - + +
434B GLY* 1.3 76.2 - - - +
436B LYS* 1.3 61.7 + - - +
437B ALA 3.5 1.4 + - - -
438B LYS* 5.2 6.9 + - - +
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Residues in contact with LYS 436 (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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441A COA 3.7 28.3 - - + +
351B VAL* 3.6 17.5 - - + +
352B GLU 2.7 24.9 + - - +
353B VAL* 3.2 25.9 - - + +
432B MET* 2.8 20.6 + - + +
435B TYR* 1.3 75.3 - - - +
437B ALA* 1.3 69.4 + - - +
438B LYS* 4.6 1.5 - - - +
3004B CL 3.6 18.6 - - - +
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Residues in contact with ALA 437 (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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351B VAL* 3.8 16.4 - - + +
374B TYR* 4.2 4.4 + - + -
379B ARG* 3.6 13.5 - - - +
409B VAL* 3.8 23.1 - - + -
410B ASP* 3.9 3.4 - - - +
433B ILE 3.0 13.1 + - - +
434B GLY* 3.6 14.1 - - - +
435B TYR 3.3 3.2 - - - -
436B LYS* 1.3 83.9 - - - +
438B LYS* 1.3 79.6 - - - +
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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