Contacts of the helix formed by residues 419 - 425 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103C GLY* 5.5 1.1 - - - -
104C ALA* 4.8 9.0 - - - +
105C HIS* 4.7 19.1 - - + +
292C VAL* 4.3 24.5 - - + -
295C GLU* 3.6 20.1 - - + +
299C SER* 3.1 29.6 - - - +
338C MET* 4.9 3.6 - - - +
340C SER* 3.8 13.7 + - - +
341C SER 6.0 1.3 - - - +
342C ASP* 6.6 0.4 - - + -
417C GLY 5.7 0.2 - - - +
418C THR* 1.3 71.7 - - - +
420C ALA* 1.3 62.4 + - - +
421C TYR* 3.4 1.3 - - - -
422C ILE* 3.5 36.3 + - + +
423C LEU* 4.1 3.8 + - - +
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Residues in contact with ALA 420 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338C MET* 4.0 2.0 - - - +
340C SER* 3.7 19.0 + - - +
382C ASN* 4.0 12.1 - - + +
418C THR* 2.9 19.6 + - - +
419C ILE* 1.3 77.4 - - - +
421C TYR* 1.3 63.7 + - - +
422C ILE 3.4 0.5 + - - -
423C LEU 3.6 2.4 + - - -
424C ALA* 3.4 18.4 + - - +
430C VAL* 3.8 25.3 - - + +
431C ILE 5.3 0.2 - - - -
432C ASP* 3.7 15.5 - - - +
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Residues in contact with TYR 421 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300B ILE* 4.1 31.4 - - + -
301B GLY* 4.1 11.4 - - - +
305B MET* 6.3 3.8 - - - -
298C GLY 5.5 2.4 + - - -
305C MET* 3.9 18.7 - - + +
380C GLY 5.5 3.4 - - - -
381C CYS* 4.8 9.0 - - - -
382C ASN* 3.6 26.1 - - + +
417C GLY* 5.6 2.9 - - - -
418C THR 3.3 28.4 + - - -
420C ALA* 1.3 77.3 - - - +
422C ILE* 1.3 86.2 + - + +
423C LEU 3.2 0.2 - - - -
424C ALA* 3.7 6.3 - - - +
425C GLU* 3.2 27.4 + - - +
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Residues in contact with ILE 422 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299C SER* 3.9 14.4 - - - +
304C GLY 5.2 3.6 - - - +
305C MET* 3.7 50.0 - - + +
419C ILE* 3.5 41.5 - - + +
420C ALA 3.2 0.6 - - - -
421C TYR* 1.3 107.3 - - + +
423C LEU* 1.3 67.3 + - + +
425C GLU* 3.6 20.4 - - - +
426C TYR* 4.9 3.3 - - - -
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Residues in contact with LEU 423 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101C ILE* 5.0 0.7 - - + -
290C ILE* 3.8 23.8 - - + -
309C PHE* 3.9 23.3 - - + -
338C MET* 3.2 43.1 - - + -
419C ILE 4.1 3.5 + - - +
420C ALA 3.6 2.6 + - - -
421C TYR 3.2 0.2 - - - -
422C ILE* 1.3 83.2 - - + +
424C ALA* 1.3 62.3 + - - +
425C GLU 2.9 6.6 + - - -
426C TYR* 3.1 50.3 + - + +
428C MET* 3.5 16.0 - - - +
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Residues in contact with ALA 424 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302B ALA* 3.1 25.1 + - + +
382C ASN* 3.3 29.4 - - - +
420C ALA 3.4 10.6 + - - +
421C TYR* 3.2 6.6 + - - +
423C LEU* 1.3 73.3 - - - +
425C GLU* 1.3 53.3 + - - +
426C TYR 2.9 6.3 - - - -
427C GLY* 2.7 25.3 + - - -
428C MET 4.3 9.2 - - - +
430C VAL* 3.8 17.0 - - + +
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Residues in contact with GLU 425 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301B GLY* 4.1 11.7 - - - -
305B MET* 3.5 42.4 - - + +
306B GLN* 3.2 4.3 - - - +
307B SER* 2.8 38.1 + - - +
305C MET* 6.1 1.4 - - - +
421C TYR* 3.2 15.9 + - - +
422C ILE* 3.6 22.3 - - - +
423C LEU 2.9 0.4 - - - -
424C ALA* 1.3 77.0 - - - +
426C TYR* 1.3 60.7 + - + +
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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