Contacts of the helix formed by residues 385 - 394 (chain C) in PDB entry 3QNQ
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 PRO 385 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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329C ILE* 3.5 21.5 - - + +
330C PHE* 4.0 26.7 - - + -
383C THR* 3.6 7.1 - - + +
384C THR* 1.3 92.0 - - + +
386C ILE* 1.3 67.4 + - - +
387C LEU 3.2 2.8 + - - -
388C PHE* 3.5 24.5 + - + +
389C SER 2.9 18.9 + - - -
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Residues in contact with ILE 386 (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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291C LEU 5.0 0.4 - - - +
295C MET* 3.1 50.5 - - + +
302C LEU* 4.0 28.2 - - + +
329C ILE 4.2 4.9 + - - -
331C ASN* 4.6 3.6 - - - +
384C THR 3.5 4.6 + - - -
385C PRO* 1.3 70.1 - - - +
387C LEU* 1.3 81.2 + - + +
389C SER* 3.1 7.3 - - - -
404C GLN* 2.4 46.8 + - + +
408C PHE* 4.0 23.6 - - + -
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Residues in contact with LEU 387 (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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385C PRO 3.2 1.2 + - - -
386C ILE* 1.3 92.1 - - + +
388C PHE* 1.3 76.9 + - + +
390C GLY* 2.9 11.4 + - - -
391C TYR 3.4 7.1 + - - -
401C VAL* 4.0 25.6 - - + +
404C GLN* 3.3 18.2 - - + +
405C LEU* 3.9 39.0 - - + +
408C PHE* 6.3 1.1 - - + -
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Residues in contact with PHE 388 (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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384C THR* 4.9 6.3 - - + -
385C PRO* 3.9 27.1 - - + +
387C LEU* 1.3 80.2 - - + +
389C SER* 1.3 65.1 + - - +
391C TYR* 3.0 18.3 + - - +
392C LEU* 3.1 28.8 + - + +
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Residues in contact with SER 389 (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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291C LEU* 3.0 40.7 - - - +
380C VAL* 5.0 2.3 - - - +
384C THR* 3.3 25.9 + - - +
385C PRO 2.9 14.3 + - - -
386C ILE* 3.1 17.7 - - - -
388C PHE* 1.3 76.8 - - - +
390C GLY* 1.3 54.3 + - - +
392C LEU* 4.2 3.3 - - - +
393C GLY* 2.8 31.9 + - - -
404C GLN* 3.6 3.4 + - - -
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Residues in contact with GLY 390 (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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292C TRP* 3.5 9.8 - - - -
387C LEU 2.9 6.4 + - - -
389C SER* 1.3 79.4 - - - +
391C TYR* 1.3 65.0 + - - +
394C SER* 3.3 22.9 + - - -
400C GLY* 3.8 9.3 - - - -
401C VAL 4.0 7.2 - - - -
404C GLN* 3.1 30.3 + - - +
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Residues in contact with TYR 391 (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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48C LEU* 4.4 13.4 - - + +
49C PRO* 4.6 3.6 - - - +
50C ILE* 3.1 30.8 - - + +
387C LEU 4.3 0.7 - - - +
388C PHE* 3.0 12.9 + - - +
390C GLY* 1.3 74.0 - - - +
392C LEU* 1.3 90.9 + - + +
394C SER* 2.9 15.2 + - - -
396C GLY* 2.7 55.3 + - - -
397C LYS 3.8 4.2 + - - -
398C ILE* 4.3 14.8 - - + -
401C VAL* 3.4 27.5 - - + +
445C CIT 3.7 10.4 + - - -
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Residues in contact with LEU 392 (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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44C ILE* 4.4 32.9 - - + +
48C LEU* 4.8 15.9 - - + -
376C SER* 3.3 12.8 + - - -
378C ALA* 4.9 2.4 - - - +
380C VAL* 4.3 21.3 - - + +
384C THR* 4.9 11.2 - - + -
388C PHE* 3.1 26.3 + - + +
389C SER* 4.2 1.8 - - - +
391C TYR* 1.3 101.0 - - + +
393C GLY* 1.3 63.9 + - - +
394C SER 3.2 0.5 + - - -
395C GLY* 3.3 4.3 + - - -
396C GLY 4.4 3.1 - - - +
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Residues in contact with GLY 393 (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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287C GLN* 5.5 0.2 - - - +
291C LEU* 4.1 15.7 - - - -
292C TRP* 3.7 15.5 - - - -
375C PRO* 3.2 11.3 - - - +
376C SER* 2.9 23.3 + - - -
377C GLY 4.8 0.2 + - - -
378C ALA 5.2 5.0 - - - +
380C VAL* 4.5 6.4 - - - +
389C SER 2.8 23.5 + - - -
392C LEU* 1.3 73.3 - - - +
394C SER* 1.3 56.2 + - - +
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Residues in contact with SER 394 (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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274C PHE* 4.6 3.6 - - - -
292C TRP* 3.2 24.2 - - - -
373C ALA* 3.7 16.2 + - - +
374C ARG 3.5 17.1 - - - +
376C SER* 3.3 9.7 + - - -
390C GLY 3.3 5.7 + - - -
391C TYR 2.9 10.3 + - - -
393C GLY* 1.3 74.0 - - - +
395C GLY* 1.3 59.6 + - - +
397C LYS* 3.6 36.6 - - - +
400C GLY* 3.5 9.7 + - - -
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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