Contacts of the helix formed by residues 419 - 425 (chain Q) 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 Q).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103Q GLY* 5.5 1.1 - - - -
104Q ALA* 4.8 9.0 - - - +
105Q HIS* 4.7 19.5 - - + +
292Q VAL* 4.3 22.9 - - + -
295Q GLU* 3.5 20.3 - - + +
299Q SER* 3.2 29.2 - - - +
338Q MET* 4.9 3.5 - - - +
340Q SER* 3.8 14.6 + - - +
341Q SER 6.0 1.6 - - - +
342Q ASP* 6.6 0.4 - - + -
418Q THR* 1.3 71.3 - - - +
420Q ALA* 1.3 62.8 + - - +
421Q TYR* 3.4 2.0 - - - -
422Q ILE* 3.5 36.2 + - + +
423Q LEU* 4.2 3.6 + - - +
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Residues in contact with ALA 420 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338Q MET* 4.0 2.4 - - - +
340Q SER* 3.7 19.2 + - - +
382Q ASN* 4.0 12.6 - - + +
418Q THR* 2.9 19.0 - - - +
419Q ILE* 1.3 79.4 - - - +
421Q TYR* 1.3 61.7 + - - +
422Q ILE 3.4 0.5 + - - -
423Q LEU 3.6 2.3 + - - -
424Q ALA* 3.5 18.7 + - - +
430Q VAL* 3.9 25.4 - - + +
431Q ILE 5.3 0.2 - - - -
432Q ASP* 3.7 14.4 - - - +
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Residues in contact with TYR 421 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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300M ILE* 4.0 33.0 - - + -
301M GLY* 4.1 11.8 - - - +
305M MET* 6.3 2.9 - - - -
298Q GLY 5.5 2.6 + - - -
305Q MET* 3.9 18.8 - - + +
380Q GLY 5.5 3.4 - - - -
381Q CYS* 4.7 9.2 - - - -
382Q ASN* 3.6 26.5 - - + +
417Q GLY* 5.6 2.7 - - - -
418Q THR 3.3 27.6 + - - -
420Q ALA* 1.3 76.7 - - - +
422Q ILE* 1.3 86.1 + - + +
423Q LEU 3.2 1.2 + - - -
424Q ALA* 3.8 6.6 - - - +
425Q GLU* 3.2 26.7 + - - +
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Residues in contact with ILE 422 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299Q SER* 3.9 13.7 - - - -
304Q GLY 5.2 4.0 - - - +
305Q MET* 3.8 49.1 - - + +
419Q ILE* 3.5 40.4 - - + +
420Q ALA 3.2 0.8 - - - -
421Q TYR* 1.3 107.5 - - + +
423Q LEU* 1.3 67.2 + - + +
425Q GLU* 3.6 19.6 - - - +
426Q TYR* 4.9 3.3 - - - -
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Residues in contact with LEU 423 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101Q ILE* 5.0 0.4 - - + -
103Q GLY* 6.3 0.2 - - - -
290Q ILE* 3.8 23.8 - - + -
309Q PHE* 3.9 23.6 - - + -
338Q MET* 3.2 42.8 - - + -
419Q ILE 4.2 3.3 + - - +
420Q ALA 3.6 2.4 + - - -
421Q TYR 3.2 0.2 - - - -
422Q ILE* 1.3 82.3 - - + +
424Q ALA* 1.3 62.8 + - - +
425Q GLU 2.9 6.6 + - - -
426Q TYR* 3.1 48.4 + - + +
428Q MET* 3.5 17.9 - - - +
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Residues in contact with ALA 424 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302M ALA* 3.0 30.9 + - + +
382Q ASN* 3.3 30.1 - - - +
420Q ALA 3.5 10.8 + - - +
421Q TYR* 3.3 6.0 + - - +
423Q LEU* 1.3 74.6 - - - +
425Q GLU* 1.3 53.0 + - - +
426Q TYR 2.9 6.3 - - - -
427Q GLY* 2.7 21.7 + - - -
428Q MET 4.3 9.6 - - - +
430Q VAL* 3.8 17.2 - - + +
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Residues in contact with GLU 425 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301M GLY* 4.0 6.0 + - - -
302M ALA 4.0 8.1 - - - +
305M MET* 3.5 42.8 - - + +
306M GLN* 3.1 4.2 - - - +
307M SER* 2.8 36.1 + - - +
305Q MET* 6.1 0.5 - - - +
421Q TYR* 3.2 14.6 + - - +
422Q ILE* 3.6 21.5 - - - +
423Q LEU 2.9 0.4 - - - -
424Q ALA* 1.3 77.7 - - - +
426Q TYR* 1.3 61.1 + - + +
427Q 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