Contacts of the helix formed by residues 419 - 425 (chain U) in PDB entry 2GLJ
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 ILE 419 (chain U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103U GLY* 5.5 1.6 - - - -
104U ALA* 4.8 8.5 - - - +
105U HIS* 4.8 18.8 - - + +
292U VAL* 4.3 23.8 - - + -
295U GLU* 3.6 20.8 - - + +
299U SER* 3.2 29.6 - - - +
338U MET* 4.9 3.5 - - - +
340U SER* 3.8 14.6 + - - +
341U SER 6.0 1.8 - - - +
417U GLY 5.7 0.4 - - - +
418U THR* 1.3 71.7 - - - +
420U ALA* 1.3 60.8 + - - +
421U TYR* 3.4 1.8 - - - -
422U ILE* 3.5 34.9 + - + +
423U LEU* 4.2 4.5 + - - +
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Residues in contact with ALA 420 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338U MET* 4.0 2.2 - - - +
340U SER* 3.7 19.6 + - - +
382U ASN* 4.0 12.1 - - + +
418U THR* 2.9 18.8 - - - +
419U ILE* 1.3 77.4 - - - +
421U TYR* 1.3 65.3 + - - +
422U ILE 3.4 0.2 + - - -
423U LEU 3.6 2.1 + - - -
424U ALA* 3.4 18.9 + - - +
430U VAL* 3.9 26.5 - - + +
431U ILE 5.3 0.4 - - - -
432U ASP* 3.7 14.1 - - - +
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Residues in contact with TYR 421 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300Q ILE* 4.2 31.2 - - + -
301Q GLY* 4.1 11.9 - - - +
305Q MET* 6.4 1.6 - - - -
298U GLY 5.5 2.4 + - - -
305U MET* 3.9 19.0 - - + +
380U GLY 5.5 3.4 - - - -
381U CYS* 4.7 9.9 - - - -
382U ASN* 3.6 28.1 - - + +
417U GLY* 5.6 3.4 - - - -
418U THR 3.3 26.9 + - - -
420U ALA* 1.3 76.7 - - - +
422U ILE* 1.3 86.9 + - + +
424U ALA* 3.7 6.2 - - - +
425U GLU* 3.2 26.8 + - - +
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Residues in contact with ILE 422 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298U GLY 5.5 0.2 - - - +
299U SER* 3.9 13.9 - - - -
304U GLY 5.2 4.0 - - - +
305U MET* 3.8 49.1 - - + +
419U ILE* 3.5 42.2 - - + +
420U ALA 3.2 0.4 - - - -
421U TYR* 1.3 105.1 - - + +
423U LEU* 1.3 67.8 + - + +
425U GLU* 3.6 20.2 - - - +
426U TYR* 4.9 3.1 - - - -
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Residues in contact with LEU 423 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101U ILE* 5.0 0.7 - - + -
103U GLY* 6.3 0.2 - - - -
290U ILE* 3.7 24.0 - - + -
309U PHE* 3.9 23.1 - - + -
338U MET* 3.3 42.2 - - + -
419U ILE 4.2 2.6 + - - +
420U ALA 3.6 2.4 + - - -
421U TYR 3.2 0.2 - - - -
422U ILE* 1.3 83.4 - - + +
424U ALA* 1.3 63.0 + - - +
425U GLU 2.9 7.0 + - - -
426U TYR* 3.1 48.2 + - + +
428U MET* 3.5 17.8 - - - +
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Residues in contact with ALA 424 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302Q ALA* 3.1 27.5 + - + +
382U ASN* 3.3 30.3 - - - +
420U ALA 3.4 10.9 + - - +
421U TYR* 3.2 5.8 + - - +
423U LEU* 1.3 74.1 - - - +
425U GLU* 1.3 53.3 + - - +
426U TYR 2.9 5.8 - - - -
427U GLY* 2.7 23.1 + - - -
428U MET 4.4 9.2 - - - +
430U VAL* 3.8 17.0 - - + +
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Residues in contact with GLU 425 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301Q GLY* 4.1 5.5 - - - -
302Q ALA 3.9 8.7 - - - +
305Q MET* 3.6 41.9 - - - +
306Q GLN* 3.3 5.9 - - - +
307Q SER* 2.9 37.1 + - - +
305U MET* 6.1 1.7 - - - +
421U TYR* 3.2 15.2 + - - +
422U ILE* 3.6 22.2 - - - +
423U LEU 2.9 0.4 - - - -
424U ALA* 1.3 76.9 - - - +
426U TYR* 1.3 61.5 + - + +
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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