Contacts of the helix formed by residues 419 - 425 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103B GLY* 5.5 1.3 - - - -
104B ALA* 4.8 9.4 - - - +
105B HIS* 4.7 19.5 - - + +
292B VAL* 4.3 23.1 - - + -
295B GLU* 3.6 20.4 - - + +
299B SER* 3.1 29.4 - - - +
338B MET* 4.9 3.6 - - - +
340B SER* 3.8 15.4 + - - +
341B SER 6.0 1.3 - - - +
342B ASP* 6.6 0.4 - - + -
417B GLY 5.7 0.2 - - - +
418B THR* 1.3 73.0 - - - +
420B ALA* 1.3 62.4 + - - +
421B TYR 3.4 1.6 - - - -
422B ILE* 3.5 35.3 + - + +
423B LEU* 4.2 4.7 + - - +
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Residues in contact with ALA 420 (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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338B MET* 4.0 2.5 - - - +
340B SER* 3.7 19.0 + - - +
382B ASN* 4.0 12.6 - - + +
418B THR* 3.0 19.5 - - - +
419B ILE* 1.3 77.7 - - - +
421B TYR* 1.3 64.7 + - - +
422B ILE 3.4 0.3 + - - -
423B LEU 3.6 2.3 + - - -
424B ALA* 3.4 18.7 + - - +
430B VAL* 3.9 25.4 - - + +
431B ILE 5.3 0.2 - - - -
432B ASP* 3.7 14.1 - - - +
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Residues in contact with TYR 421 (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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305B MET* 4.0 18.6 - - + +
380B GLY 5.6 3.1 - - - -
381B CYS* 4.8 9.6 - - - -
382B ASN* 3.6 27.4 - - + +
417B GLY* 5.7 3.4 - - - -
418B THR 3.3 27.6 - - - -
420B ALA* 1.3 77.5 - - - +
422B ILE* 1.3 88.5 + - + +
423B LEU 3.2 0.4 - - - -
424B ALA* 3.7 6.0 - - - +
425B GLU* 3.2 27.2 + - - +
300D ILE* 4.3 30.1 - - + -
301D GLY* 4.3 10.8 - - - +
305D MET* 6.5 0.9 - - - -
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Residues in contact with ILE 422 (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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299B SER* 3.9 14.1 - - - -
304B GLY 5.1 3.6 - - - +
305B MET* 3.7 49.8 - - + +
419B ILE* 3.5 41.1 - - + +
420B ALA 3.2 0.8 - - - -
421B TYR* 1.3 109.0 - - + +
423B LEU* 1.3 66.2 + - + +
425B GLU* 3.6 20.3 - - - +
426B TYR* 4.9 3.5 - - - -
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Residues in contact with LEU 423 (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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101B ILE* 5.0 0.2 - - + -
290B ILE* 3.7 23.6 - - + -
309B PHE* 3.9 23.6 - - + -
338B MET* 3.2 42.6 - - + -
419B ILE 4.2 2.4 + - - +
420B ALA 3.6 2.2 + - - -
421B TYR 3.2 0.2 - - - -
422B ILE* 1.3 82.4 - - + +
424B ALA* 1.3 62.9 + - - +
425B GLU 2.9 6.7 + - - -
426B TYR* 3.1 47.7 + - + +
428B MET* 3.5 17.2 - - - +
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Residues in contact with ALA 424 (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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382B ASN* 3.3 29.8 - - - +
420B ALA 3.4 11.5 + - - +
421B TYR* 3.2 5.6 + - - +
423B LEU* 1.3 73.9 - - - +
425B GLU* 1.3 53.3 + - - +
426B TYR 2.9 6.1 - - - -
427B GLY* 2.7 25.5 + - - -
428B MET 3.9 9.1 + - - +
430B VAL* 3.9 17.4 - - + +
301D GLY 4.7 0.2 - - - -
302D ALA* 3.3 24.2 + - + +
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Residues in contact with GLU 425 (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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305B MET* 6.1 1.4 - - - +
421B TYR* 3.2 15.1 + - - +
422B ILE* 3.6 21.3 - - - +
423B LEU 2.9 0.4 - - - -
424B ALA* 1.3 76.8 - - - +
426B TYR* 1.3 60.8 + - + +
427B GLY 3.4 0.2 - - - -
301D GLY* 4.2 5.2 - - - -
302D ALA 4.2 8.3 - - - +
305D MET* 3.8 39.4 - - + +
306D GLN* 3.4 4.0 - - - +
307D SER* 3.0 36.4 + - - +
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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