Contacts of the helix formed by residues 419 - 425 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103L GLY* 5.5 0.9 - - - -
104L ALA* 4.8 9.0 - - - +
105L HIS* 4.7 19.1 - - + +
292L VAL* 4.3 23.8 - - + -
295L GLU* 3.5 20.3 - - + +
299L SER* 3.1 29.8 - - - +
338L MET* 4.9 3.3 - - - +
340L SER* 3.9 14.8 + - - +
341L SER 6.0 0.7 - - - +
418L THR* 1.3 72.2 - - - +
420L ALA* 1.3 61.1 + - - +
421L TYR 3.4 1.6 - - - -
422L ILE* 3.5 35.9 + - + +
423L LEU* 4.2 4.2 + - - +
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Residues in contact with ALA 420 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338L MET* 4.0 2.1 - - - +
340L SER* 3.7 21.9 + - - +
382L ASN* 4.0 12.6 - - + +
418L THR* 2.9 19.5 + - - +
419L ILE* 1.3 77.2 - - - +
421L TYR* 1.3 64.0 + - - +
422L ILE 3.4 0.7 + - - -
423L LEU 3.6 2.1 + - - -
424L ALA* 3.4 18.7 + - - +
430L VAL* 3.9 23.5 - - + +
431L ILE 5.3 0.9 - - - -
432L ASP* 3.7 13.5 - - - +
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Residues in contact with TYR 421 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300K ILE* 4.1 33.0 - - + -
301K GLY* 4.1 11.2 - - - +
305K MET* 6.3 2.7 - - - -
298L GLY 5.5 2.3 + - - -
305L MET* 4.0 18.3 - - + +
380L GLY 5.5 3.4 - - - -
381L CYS* 4.7 9.2 - - - -
382L ASN* 3.6 25.9 - - + +
417L GLY* 5.6 2.9 - - - -
418L THR 3.2 26.9 - - - -
420L ALA* 1.3 77.5 - - - +
422L ILE* 1.3 87.7 + - + +
423L LEU 3.2 0.7 + - - -
424L ALA* 3.8 6.3 - - - +
425L GLU* 3.2 26.3 + - - +
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Residues in contact with ILE 422 (chain L).
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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299L SER* 3.9 13.7 - - - -
304L GLY 5.1 4.0 - - - +
305L MET* 3.8 48.9 - - + +
419L ILE* 3.5 42.8 - - + +
420L ALA 3.2 0.4 - - - -
421L TYR* 1.3 105.8 - - + +
423L LEU* 1.3 67.8 + - + +
425L GLU* 3.6 19.9 - - - +
426L TYR* 4.9 3.3 - - - -
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Residues in contact with LEU 423 (chain L).
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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101L ILE* 4.9 0.7 - - + -
290L ILE* 3.8 23.3 - - + -
309L PHE* 3.9 23.1 - - + -
338L MET* 3.3 42.4 - - + -
419L ILE 4.2 2.8 + - - +
420L ALA 3.6 2.2 + - - -
421L TYR 3.2 0.2 - - - -
422L ILE* 1.3 84.1 - - + +
424L ALA* 1.3 63.4 + - - +
425L GLU 2.9 6.8 + - - -
426L TYR* 3.1 47.4 + - + +
428L MET* 3.5 17.3 - - - +
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Residues in contact with ALA 424 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302K ALA* 3.0 30.8 + - + +
382L ASN* 3.3 28.7 - - - +
420L ALA 3.4 11.9 + - - +
421L TYR* 3.2 6.0 + - - +
423L LEU* 1.3 73.3 - - - +
425L GLU* 1.3 54.1 + - - +
426L TYR 2.9 5.8 - - - -
427L GLY* 2.8 22.3 + - - -
428L MET 4.3 9.4 - - - +
430L VAL* 3.8 17.2 - - + +
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Residues in contact with GLU 425 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301K GLY* 4.0 5.8 - - - +
302K ALA 4.0 8.5 - - - +
305K MET* 3.5 42.2 - - + +
306K GLN* 3.1 4.8 - - - +
307K SER* 2.8 35.6 + - - +
305L MET* 6.1 1.4 - - - +
421L TYR* 3.2 13.7 + - - +
422L ILE* 3.6 21.4 - - - +
423L LEU 2.9 0.4 - - - -
424L ALA* 1.3 77.6 - - - +
426L TYR* 1.3 60.9 + - + +
427L GLY 3.4 0.2 - - - -
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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