Contacts of the helix formed by residues 427 - 436 (chain A) in PDB entry 2XGZ
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 GLY 427 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148A VAL* 3.3 20.1 - - - +
174A THR* 3.2 22.6 - - - -
176A ALA 4.6 1.6 - - - -
425A PHE* 3.3 21.3 - - - -
426A ALA* 1.3 75.4 - - - +
428A GLU* 1.3 62.6 + - - -
429A ASN 3.0 1.4 + - - -
430A PHE* 3.3 13.9 + - - -
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Residues in contact with GLU 428 (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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174A THR* 3.4 18.6 + - - +
426A ALA 3.4 0.6 + - - -
427A GLY* 1.3 70.5 - - - -
429A ASN* 1.3 64.7 + - - +
430A PHE* 3.3 16.2 + - - -
431A HIS* 5.0 1.0 + - - +
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Residues in contact with ASN 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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426A ALA* 2.9 16.4 + - - +
428A GLU* 1.3 85.1 - - - +
430A PHE* 1.3 62.8 + - - +
431A HIS 3.2 3.0 + - - -
432A HIS* 3.3 8.9 + - + +
433A GLY* 3.2 18.0 + - - -
436A LEU* 3.7 31.7 - - + +
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Residues in contact with PHE 430 (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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148A VAL* 3.7 8.3 - - + -
150A PHE* 3.8 15.0 - + - -
174A THR* 3.9 20.0 - - + -
292A VAL* 3.7 37.5 - - + -
316A GLN* 3.7 26.5 - - + -
392A THR 3.1 21.8 - - - +
393A GLY 3.4 22.9 - - - +
394A GLN* 3.5 22.9 - - + +
426A ALA* 3.8 6.7 + - - -
427A GLY 3.3 18.9 + - - +
428A GLU* 3.3 12.2 - - - -
429A ASN* 1.3 75.8 - - - +
431A HIS* 1.3 83.0 + - + +
433A GLY 3.1 1.9 + - - -
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Residues in contact with HIS 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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316A GLN* 2.8 32.3 + - + +
340A ASP* 3.2 50.5 + - - +
363A PHE* 5.6 0.2 - - - -
366A GLY 4.1 5.3 + - - -
368A GLY* 3.2 34.6 - - - -
369A VAL 4.6 0.2 + - - -
392A THR 4.7 0.9 - - - +
394A GLN* 3.8 4.5 - - - +
428A GLU 5.9 0.4 - - - +
429A ASN 3.3 0.8 - - - -
430A PHE* 1.3 97.2 - - + +
432A HIS* 1.3 91.3 + + - +
433A GLY 3.8 0.9 + - - -
434A ASP* 4.6 0.7 - - - +
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Residues in contact with HIS 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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366A GLY* 3.2 31.5 + - - -
367A TRP 4.6 4.5 - - - -
429A ASN* 3.3 10.1 + - + +
431A HIS* 1.3 100.6 + + - +
433A GLY* 1.3 64.6 + - - +
434A ASP* 3.1 13.5 - - - +
435A LYS* 3.0 31.0 + - + -
436A LEU* 3.4 8.7 + - - +
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Residues in contact with GLY 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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145A VAL* 3.6 9.0 - - - +
391A ARG* 3.1 23.4 + - - +
392A THR 3.4 17.6 + - - -
393A GLY* 4.1 6.1 - - - -
426A ALA* 4.8 1.6 - - - -
429A ASN 3.2 10.2 + - - -
430A PHE 3.1 10.0 + - - -
431A HIS 3.5 0.4 + - - -
432A HIS* 1.3 75.8 - - - +
434A ASP* 1.3 61.4 + - - +
435A LYS 3.3 0.5 + - - -
436A LEU* 3.3 13.8 + - - +
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Residues in contact with ASP 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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140A LYS* 5.4 2.6 - - - +
363A PHE* 3.3 50.4 - - + +
367A TRP 4.5 2.6 - - - +
390A LEU 4.6 2.0 - - - +
391A ARG* 3.0 39.0 + - + +
392A THR 4.0 1.6 + - - -
431A HIS 4.6 0.3 - - - +
432A HIS* 3.6 16.3 - - - +
433A GLY* 1.3 77.1 + - - +
435A LYS* 1.3 95.4 + - - +
437A LEU* 5.7 0.3 - - - +
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Residues in contact with LYS 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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363A PHE* 3.1 29.4 + - - +
366A GLY* 4.5 11.1 - - - -
367A TRP 5.0 0.6 + - - -
391A ARG* 4.0 0.2 - - - -
432A HIS* 3.0 25.8 + - + +
434A ASP* 1.3 103.2 + - - +
436A LEU* 1.3 64.4 + - - +
437A LEU* 3.4 18.4 + - - +
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Residues in contact with LEU 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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143A PRO* 6.0 0.2 - - - -
145A VAL* 4.3 8.5 - - + -
391A ARG* 2.7 33.4 + - - +
424A VAL* 4.2 24.0 - - + -
425A PHE 4.4 2.7 - - - +
426A ALA* 3.8 35.0 - - + +
429A ASN* 3.7 34.3 - - + +
432A HIS 3.4 6.2 + - - +
433A GLY* 3.3 15.8 + - - +
435A LYS* 1.3 76.4 - - - +
437A LEU* 1.3 72.0 + - - +
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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