Contacts of the helix formed by residues 377 - 390 (chain A) in PDB entry 1QI9
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 377 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375A GLU 2.9 12.0 + - - +
376A ASN* 1.3 71.8 - - - +
378A GLU* 1.3 58.7 + - - +
380A LEU* 4.5 3.4 - - - +
381A LYS* 2.9 60.0 + - - +
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Residues in contact with GLU 378 (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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143A TRP* 4.4 3.1 - - + -
163A THR* 3.5 24.0 - - + +
167A ASN* 3.6 20.9 - - + +
376A ASN* 3.4 0.8 + - - -
377A ALA* 1.3 79.5 - - - +
379A LEU* 1.3 60.8 + - - +
381A LYS* 4.4 4.1 - - - +
382A ARG* 2.8 60.3 + - - +
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Residues in contact with LEU 379 (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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139A ALA* 3.9 31.2 - - + -
142A TYR* 3.8 26.2 - - + -
143A TRP* 3.7 35.6 - - + +
146A LEU* 3.8 15.9 - - + -
373A LEU* 4.1 19.3 - - + -
376A ASN* 3.1 26.3 + - + +
378A GLU* 1.3 75.4 - - - +
380A LEU* 1.3 70.7 + - + +
382A ARG* 3.2 5.6 + - - +
383A VAL* 3.1 26.3 + - + +
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Residues in contact with LEU 380 (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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142A TYR* 5.4 2.5 - - + -
357A LEU* 4.2 17.3 - - + -
361A ILE* 3.7 32.5 - - + -
373A LEU* 3.4 24.7 - - + +
374A LEU* 3.8 15.5 - - - +
376A ASN* 2.9 18.7 + - + +
377A ALA* 4.4 2.9 - - - +
379A LEU* 1.3 84.7 - - + +
381A LYS* 1.3 61.3 + - + +
383A VAL* 3.3 7.5 + - + +
384A ALA 2.9 25.3 + - - -
398A IYR 3.4 34.1 - - + +
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Residues in contact with LYS 381 (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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377A ALA* 2.9 40.1 + - - +
378A GLU* 4.4 4.3 - - - +
380A LEU* 1.3 76.5 - - + +
382A ARG* 1.3 59.5 + - + +
384A ALA* 3.6 7.7 - - - +
385A ALA* 3.0 28.4 + - - +
398A IYR 5.3 0.2 - - - -
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Residues in contact with ARG 382 (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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143A TRP* 3.7 23.2 - - - -
146A LEU* 3.6 20.9 - - + +
159A ASP* 2.7 40.2 + - - -
160A ILE* 3.7 27.0 - - - +
163A THR* 3.5 13.6 + - - -
378A GLU* 2.8 38.0 + - - +
379A LEU 3.2 4.9 + - - +
381A LYS* 1.3 74.3 - - + +
383A VAL* 1.3 64.8 + - - +
385A ALA* 3.4 6.3 + - - +
386A ILE* 3.0 25.6 + - - +
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Residues in contact with VAL 383 (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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142A TYR* 3.5 27.4 - - + -
146A LEU* 4.3 12.1 - - + -
379A LEU* 3.1 26.8 + - + +
380A LEU* 3.7 10.1 - - + +
381A LYS 3.3 0.2 - - - -
382A ARG* 1.3 72.9 - - - +
384A ALA* 1.3 67.6 + - - +
386A ILE* 3.2 8.7 + - - +
387A ASN* 3.0 28.0 + - - +
398A IYR 3.7 30.7 - - + +
399A LEU 3.7 17.0 - - - +
401A PRO* 4.8 4.7 - - + -
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Residues in contact with ALA 384 (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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380A LEU 2.9 16.8 + - - +
381A LYS* 3.6 8.5 - - - +
383A VAL* 1.3 77.5 - - - +
385A ALA* 1.3 58.2 + - - +
387A ASN* 4.0 1.0 - - - +
388A ALA* 2.9 32.3 + - - +
396A VAL* 3.7 27.3 - - + +
397A THR 3.7 13.0 - - - -
398A IYR 3.8 13.1 - - + +
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Residues in contact with ALA 385 (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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381A LYS 3.0 14.2 + - - +
382A ARG* 3.7 7.4 - - - +
384A ALA* 1.3 78.8 - - - +
386A ILE* 1.3 64.1 + - - +
388A ALA* 4.1 4.2 - - - +
389A ALA* 3.2 23.4 + - - +
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Residues in contact with ILE 386 (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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145A ALA 5.4 0.9 - - - +
146A LEU* 3.9 33.9 - - + +
233A ASP* 5.4 8.5 - - - +
235A ASN* 3.9 23.8 - - - +
269A ARG* 6.2 0.2 - - - +
382A ARG 3.0 16.8 + - - +
383A VAL* 3.3 12.1 - - - +
385A ALA* 1.3 75.7 - - - +
387A ASN* 1.3 75.9 + - - +
389A ALA* 3.5 6.9 + - + +
390A GLN* 3.4 24.0 + - - +
401A PRO* 4.5 7.2 - - + -
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Residues in contact with ASN 387 (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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235A ASN* 5.5 0.7 + - - -
238A VAL* 3.3 28.0 - - + +
383A VAL* 3.0 18.2 + - - +
384A ALA 4.0 0.7 - - - +
386A ILE* 1.3 87.7 - - - +
388A ALA* 1.3 62.4 + - - +
390A GLN* 3.0 10.3 + - - +
391A ASN* 2.8 34.6 + - - +
397A THR* 3.0 43.7 + - - +
399A LEU 3.1 24.9 + - - +
401A PRO* 3.6 5.0 - - - +
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Residues in contact with ALA 388 (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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384A ALA 2.9 20.0 + - - +
385A ALA* 4.1 5.2 - - - +
387A ASN* 1.3 77.0 - - - +
389A ALA* 1.3 60.9 + - - +
390A GLN 3.3 0.5 + - - -
391A ASN 3.5 3.6 + - - +
394A ASN* 3.0 47.2 + - + +
395A GLU 3.4 14.0 + - - -
396A VAL* 3.8 15.0 - - + -
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Residues in contact with ALA 389 (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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385A ALA 3.2 19.4 + - - +
386A ILE* 3.7 8.1 - - + +
387A ASN 3.2 0.2 - - - -
388A ALA* 1.3 76.2 - - - +
390A GLN* 1.3 58.7 + - - +
391A ASN 4.8 0.7 - - - +
394A ASN* 4.1 10.7 + - - +
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Residues in contact with GLN 390 (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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233A ASP 4.2 4.8 + - - +
234A VAL* 3.4 35.3 - - - +
235A ASN* 2.9 40.6 + - - +
238A VAL* 3.5 24.8 - - + +
386A ILE* 3.4 14.4 + - - +
387A ASN* 3.2 9.8 - - - +
389A ALA* 1.3 78.4 - - - +
391A ASN* 1.3 62.3 + - - +
392A PRO* 4.0 2.3 - - - +
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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