Contacts of the helix formed by residues 419 - 425 (chain S) 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 S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103S GLY* 5.5 1.6 - - - -
104S ALA* 4.8 9.2 - - - +
105S HIS* 4.7 19.1 - - + +
292S VAL* 4.3 24.0 - - + -
295S GLU* 3.5 20.1 - - + +
299S SER* 3.2 29.6 - - - +
338S MET* 4.9 3.1 - - - +
340S SER* 3.8 14.2 + - - +
341S SER 6.0 1.6 - - - +
342S ASP* 6.5 0.7 - - + -
418S THR* 1.3 72.8 - - - +
420S ALA* 1.3 62.4 + - - +
421S TYR* 3.4 1.6 - - - -
422S ILE* 3.4 34.4 + - + +
423S LEU* 4.1 4.7 + - - +
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Residues in contact with ALA 420 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338S MET* 4.0 2.3 - - - +
340S SER* 3.7 21.8 + - - +
382S ASN* 4.0 12.6 - - + +
418S THR* 3.0 19.2 + - - +
419S ILE* 1.3 80.2 - - - +
421S TYR* 1.3 62.0 + - - +
422S ILE 3.4 0.3 + - - -
423S LEU 3.6 2.6 + - - -
424S ALA* 3.4 18.0 + - - +
430S VAL* 3.9 24.1 - - + +
431S ILE 5.3 0.2 - - - -
432S ASP* 3.7 14.8 - - - +
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Residues in contact with TYR 421 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300R ILE* 4.1 33.0 - - + -
301R GLY* 4.2 11.8 - - - +
305R MET* 6.5 1.6 - - - -
305S MET* 4.0 18.6 - - + +
380S GLY 5.6 3.1 - - - -
381S CYS* 4.8 9.4 - - - -
382S ASN* 3.6 26.5 - - + +
417S GLY* 5.7 2.9 - - - -
418S THR 3.3 27.3 + - - -
420S ALA* 1.3 76.1 - - - +
422S ILE* 1.3 88.1 + - + +
423S LEU 3.2 0.9 + - - -
424S ALA* 3.8 6.3 - - - +
425S GLU* 3.2 26.2 + - - +
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Residues in contact with ILE 422 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299S SER* 3.9 13.7 - - - -
304S GLY 5.2 4.5 - - - +
305S MET* 3.7 49.8 - - + +
419S ILE* 3.5 41.5 - - + +
420S ALA 3.2 0.4 - - - -
421S TYR* 1.3 109.1 - - + +
423S LEU* 1.3 66.8 + - + +
425S GLU* 3.6 20.5 - - - +
426S TYR* 4.9 3.6 - - - -
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Residues in contact with LEU 423 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101S ILE* 5.0 0.4 - - + -
290S ILE* 3.8 22.7 - - + -
309S PHE* 3.9 22.9 - - + -
338S MET* 3.2 43.3 - - + -
419S ILE 4.1 2.8 + - - +
420S ALA 3.6 2.2 + - - -
421S TYR 3.2 0.4 - - - -
422S ILE* 1.3 83.1 - - + +
424S ALA* 1.3 63.0 + - - +
425S GLU 2.9 6.6 + - - -
426S TYR* 3.1 47.2 + - + +
428S MET* 3.5 17.6 - - - +
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Residues in contact with ALA 424 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302R ALA* 3.0 29.6 + - + +
382S ASN* 3.3 30.7 - - - +
420S ALA 3.4 11.0 + - - +
421S TYR* 3.3 6.6 + - - +
423S LEU* 1.3 73.1 - - - +
425S GLU* 1.3 53.6 + - - +
426S TYR 2.9 6.1 - - - -
427S GLY* 2.8 23.1 + - - -
428S MET 4.3 9.2 - - - +
430S VAL* 3.8 16.1 - - + +
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Residues in contact with GLU 425 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301R GLY* 4.0 5.8 - - - -
302R ALA 3.9 9.6 - - - +
305R MET* 3.7 41.6 - - + +
306R GLN* 3.2 6.2 - - - -
307R SER* 3.0 35.4 + - - +
305S MET* 6.2 1.0 - - - +
421S TYR* 3.2 14.2 + - - +
422S ILE* 3.6 22.4 - - - +
423S LEU 2.9 0.8 - - - -
424S ALA* 1.3 77.7 - - - +
426S TYR* 1.3 60.0 + - + +
427S 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