Contacts of the helix formed by residues 419 - 425 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103T GLY* 5.5 0.9 - - - -
104T ALA* 4.8 8.7 - - - +
105T HIS* 4.7 20.0 - - + +
292T VAL* 4.3 24.7 - - + -
295T GLU* 3.6 20.8 - - + +
299T SER* 3.1 29.6 - - - +
338T MET* 4.9 3.6 - - - +
340T SER* 3.9 14.8 + - - +
341T SER 6.0 1.1 - - - +
342T ASP* 6.5 0.7 - - + -
418T THR* 1.3 71.8 - - - +
420T ALA* 1.3 62.4 + - - +
421T TYR* 3.4 1.8 - - - -
422T ILE* 3.5 33.6 + - + +
423T LEU* 4.2 4.2 + - - +
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Residues in contact with ALA 420 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338T MET* 4.0 2.5 - - - +
340T SER* 3.7 19.6 + - - +
382T ASN* 4.0 12.3 - - + +
418T THR* 2.9 19.7 + - - +
419T ILE* 1.3 77.6 - - - +
421T TYR* 1.3 65.1 + - - +
422T ILE 3.4 0.5 + - - -
423T LEU 3.6 2.1 + - - -
424T ALA* 3.4 18.7 + - - +
430T VAL* 3.8 25.0 - - + +
431T ILE 5.3 0.4 - - - -
432T ASP* 3.7 13.5 - - - +
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Residues in contact with TYR 421 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300S ILE* 4.2 30.1 - - + -
301S GLY* 4.2 10.5 - - - +
305S MET* 6.5 1.3 - - - -
298T GLY 5.4 2.6 + - - -
305T MET* 3.9 18.5 - - + +
380T GLY 5.6 3.6 - - - -
381T CYS* 4.8 9.2 - - - -
382T ASN* 3.6 26.5 - - + +
417T GLY* 5.6 2.9 - - - -
418T THR 3.2 27.4 - - - -
420T ALA* 1.3 75.9 - - - +
422T ILE* 1.3 88.5 + - + +
424T ALA* 3.7 6.6 - - - +
425T GLU* 3.2 26.4 + - - +
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Residues in contact with ILE 422 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299T SER* 3.9 13.9 - - - -
304T GLY 5.2 3.4 - - - +
305T MET* 3.7 50.3 - - + +
419T ILE* 3.5 40.6 - - + +
420T ALA 3.2 0.8 - - - -
421T TYR* 1.3 109.8 - - + +
423T LEU* 1.3 67.2 + - + +
425T GLU* 3.5 20.3 - - - +
426T TYR* 4.9 3.5 - - - -
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Residues in contact with LEU 423 (chain T).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101T ILE* 5.0 0.2 - - + -
103T GLY* 6.3 0.2 - - - -
290T ILE* 3.8 23.1 - - + -
309T PHE* 3.9 23.6 - - + -
338T MET* 3.2 42.2 - - + -
419T ILE 4.2 2.6 + - - +
420T ALA 3.6 2.0 + - - -
421T TYR 3.2 0.2 - - - -
422T ILE* 1.3 83.6 - - + +
424T ALA* 1.3 63.1 + - - +
425T GLU 2.8 6.9 + - - -
426T TYR* 3.1 47.5 + - + +
428T MET* 3.5 17.0 - - - +
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Residues in contact with ALA 424 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302S ALA* 3.2 25.5 + - + +
382T ASN* 3.3 30.3 - - - +
420T ALA 3.4 10.4 + - - +
421T TYR* 3.3 5.5 + - - +
423T LEU* 1.3 73.0 - - - +
425T GLU* 1.3 54.1 + - - +
426T TYR 2.9 6.3 - - - -
427T GLY* 2.7 24.8 + - - -
428T MET 4.3 9.9 - - - +
430T VAL* 3.8 16.7 - - + +
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Residues in contact with GLU 425 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301S GLY* 4.1 12.6 - - - -
302S ALA 4.1 0.4 - - - +
305S MET* 3.6 41.7 - - + +
306S GLN* 3.2 3.7 - - - +
307S SER* 2.9 35.1 + - - +
305T MET* 6.1 1.4 - - - +
421T TYR* 3.2 15.1 + - - +
422T ILE* 3.5 22.2 - - - +
423T LEU 2.8 0.4 - - - -
424T ALA* 1.3 77.9 - - - +
426T TYR* 1.3 61.3 + - + +
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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