Contacts of the helix formed by residues 368 - 377 (chain A) in PDB entry 3QN3
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 ALA 368 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119A ARG* 4.0 7.0 - - - +
366A GLU 3.3 5.3 + - - +
367A ASP* 1.3 70.9 + - - +
369A PHE* 1.3 64.6 + - - +
370A ILE 3.2 2.9 - - - -
371A ALA* 3.0 17.3 + - - +
372A ASP* 3.7 6.8 + - - +
394A ALA* 3.7 19.1 - - + +
395A LYS* 4.1 11.2 - - - -
398A ARG* 3.7 29.6 - - + -
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Residues in contact with PHE 369 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A MET* 3.5 52.3 - - + -
118A ALA* 4.6 3.6 - - + -
119A ARG* 3.3 19.5 - - + +
129A LEU* 3.4 32.1 - - + -
133A LEU* 3.9 15.5 - - + -
333A PRO* 6.0 1.3 - - + -
339A ILE* 3.5 35.9 - - + -
367A ASP* 2.8 23.2 + - - +
368A ALA* 1.3 71.4 - - - +
370A ILE* 1.3 63.3 + - + +
372A ASP* 3.1 6.6 + - - +
373A PHE* 2.9 47.5 + + - -
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Residues in contact with ILE 370 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A MET* 6.5 0.2 - - - -
333A PRO* 4.2 23.8 - - + -
358A MET* 3.5 14.6 - - + +
359A SER* 3.8 15.9 - - - +
360A HIS* 3.7 30.7 - - + +
364A GLU* 4.8 3.4 - - - +
369A PHE* 1.3 80.1 - - + +
371A ALA* 1.3 62.2 + - - +
373A PHE* 3.7 8.5 - - + -
374A ALA* 2.9 30.3 + - - +
382A ILE* 3.9 8.1 - - + +
383A LYS 4.5 0.4 - - - +
384A THR* 3.7 25.4 - - - +
395A LYS* 3.9 22.4 - - + -
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Residues in contact with ALA 371 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368A ALA 3.0 12.6 + - - +
370A ILE* 1.3 83.9 - - - +
372A ASP* 1.3 63.5 + - - +
374A ALA* 3.3 2.8 + - - +
375A VAL* 3.2 24.3 + - - +
382A ILE* 4.1 11.4 - - - -
395A LYS* 3.7 30.5 - - + +
398A ARG* 3.8 15.7 - - + -
399A LEU* 3.7 14.1 - - + +
402A ILE* 4.5 0.4 - - - -
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Residues in contact with ASP 372 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119A ARG* 5.4 1.4 + - - -
129A LEU* 3.3 25.9 - - + +
130A TYR* 3.0 34.6 + - - +
133A LEU* 5.0 0.7 - - + -
368A ALA 3.7 6.6 + - - +
369A PHE 3.1 7.4 + - - +
371A ALA* 1.3 80.4 - - - +
373A PHE* 1.3 52.6 + - - +
375A VAL 3.3 0.9 + - - -
376A ALA* 2.8 34.5 + - - +
398A ARG* 2.8 48.9 + - - +
402A ILE* 4.0 10.5 - - - -
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Residues in contact with PHE 373 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 3.8 18.6 - - + +
333A PRO* 4.1 10.3 - - + -
339A ILE* 3.6 45.8 - - + -
342A THR* 3.8 24.9 - - + -
343A MET* 3.8 20.4 - - + -
358A MET* 3.8 19.7 - - + -
369A PHE* 2.9 32.1 + + + +
370A ILE* 3.7 7.9 - - - +
371A ALA 3.2 0.2 - - - -
372A ASP* 1.3 73.7 - - - +
374A ALA* 1.3 66.5 + - - +
376A ALA* 4.2 3.4 - - + -
377A LEU* 3.1 45.8 + - + +
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Residues in contact with ALA 374 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A ILE 4.4 2.6 - - - +
142A PRO* 4.1 20.6 - - + -
358A MET* 3.8 15.0 - - + +
370A ILE 2.9 18.2 + - - +
371A ALA 3.3 5.1 + - - +
373A PHE* 1.3 77.0 - - - +
375A VAL* 1.3 58.9 + - - +
377A LEU 3.8 0.2 - - - -
378A ASN* 3.2 3.3 + - - -
379A THR* 3.1 49.0 + - - +
380A GLY 4.7 0.2 + - - -
381A GLN 4.5 0.9 - - - +
382A ILE* 4.2 6.1 - - + -
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Residues in contact with VAL 375 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TYR* 3.9 28.5 - - + -
138A ALA* 3.7 4.1 - - - -
139A SER* 4.0 18.4 - - - +
140A ILE 3.7 22.2 - - - +
141A LEU* 4.1 10.8 - - + -
142A PRO* 4.1 3.1 - - + -
371A ALA 3.2 13.5 + - - +
372A ASP 3.8 4.7 - - - +
374A ALA* 1.3 73.9 - - - +
376A ALA* 1.3 65.9 + - - +
378A ASN* 3.0 20.1 + - - +
399A LEU* 3.7 20.2 - - + -
402A ILE* 4.0 18.2 - - + -
406A SER* 5.4 1.1 - - - -
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Residues in contact with ALA 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A TYR* 3.5 18.3 - - - +
133A LEU* 3.4 32.8 - - + -
134A GLY* 3.5 19.0 - - - +
137A ASN 5.2 0.2 - - - -
138A ALA* 3.9 10.5 - - - -
372A ASP 2.8 20.9 + - - +
373A PHE* 3.2 7.6 + - + +
375A VAL* 1.3 74.3 - - - +
377A LEU* 1.3 65.3 + - + +
378A ASN* 3.6 3.5 + - - -
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Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A LEU* 5.2 4.7 - - + +
134A GLY* 5.9 0.2 - - - -
343A MET* 3.9 30.5 - - + +
346A VAL* 3.8 38.1 - - + -
347A ARG* 6.2 3.1 - - + -
350A GLN* 3.2 19.6 + - - +
358A MET* 4.0 10.5 - - + -
373A PHE* 3.1 39.6 + - + +
376A ALA* 1.3 81.7 - - + +
378A ASN* 1.3 70.9 + - - +
379A THR* 3.1 10.7 + - + -
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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