Contacts of the helix formed by residues 385 - 394 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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329B ILE* 3.3 21.9 - - + +
330B PHE* 3.7 30.7 - - + -
383B THR 3.9 5.2 - - - +
384B THR* 1.3 90.6 - - + +
386B ILE* 1.3 66.5 + - - +
387B LEU 3.0 2.8 + - - -
388B PHE* 3.3 26.7 + - + -
389B SER 2.9 20.3 + - - -
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Residues in contact with ILE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B LEU 5.2 0.2 - - - +
295B MET* 3.1 49.1 - - + +
302B LEU* 4.0 30.7 - - + -
329B ILE 4.1 5.3 + - - -
331B ASN* 4.6 5.0 - - - +
384B THR 3.3 5.0 + - - -
385B PRO* 1.3 70.8 - - - +
387B LEU* 1.3 75.7 + - + +
389B SER* 3.6 2.4 + - - -
390B GLY 3.5 1.7 + - - -
404B GLN* 2.5 47.5 + - + +
408B PHE* 4.5 22.0 - - + -
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Residues in contact with LEU 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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385B PRO* 3.0 1.0 + - - +
386B ILE* 1.3 92.6 - - + +
388B PHE* 1.3 74.0 + - + +
389B SER 3.1 2.1 + - - -
390B GLY 3.5 8.1 + - - -
391B TYR* 3.6 9.7 + - - +
401B VAL* 3.6 44.1 - - + +
404B GLN* 3.9 8.6 - - + +
405B LEU* 3.8 30.7 - - + -
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Residues in contact with PHE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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384B THR* 4.5 7.0 - - + -
385B PRO* 3.3 28.2 + - + +
387B LEU* 1.3 83.4 - - + +
389B SER* 1.3 62.6 + - - +
391B TYR* 3.7 4.9 + - - +
392B LEU* 3.1 41.7 + - + +
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Residues in contact with SER 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291B LEU* 3.3 29.1 + - - +
380B VAL* 4.7 2.0 - - - +
384B THR* 3.4 33.1 - - - +
385B PRO 2.9 16.8 + - - -
386B ILE* 3.6 4.0 + - - -
387B LEU 3.1 0.2 - - - -
388B PHE* 1.3 78.8 - - - +
390B GLY* 1.3 56.2 + - - +
392B LEU* 3.9 1.8 - - - +
393B GLY* 2.9 28.1 + - - -
404B GLN* 2.8 19.6 + - - -
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Residues in contact with GLY 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B TRP* 3.4 14.1 - - - -
387B LEU 3.5 0.4 + - - -
389B SER* 1.3 77.0 + - - +
391B TYR* 1.3 67.4 + - - +
393B GLY 3.4 0.3 + - - -
394B SER* 3.3 24.3 + - - -
400B GLY* 4.1 10.6 - - - -
404B GLN* 3.1 34.5 + - - +
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Residues in contact with TYR 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 4.2 22.8 - - + +
49B PRO* 4.6 6.1 - - - +
50B ILE* 4.5 15.6 + - - +
387B LEU 3.6 8.6 + - - +
388B PHE* 3.9 8.5 - - - +
389B SER 3.4 0.2 - - - -
390B GLY* 1.3 77.7 - - - +
392B LEU* 1.3 75.1 + - + +
394B SER* 3.2 4.5 + - - -
396B GLY* 3.1 55.0 + - - -
397B LYS 3.4 10.3 + - - -
398B ILE* 3.9 32.3 - - + -
401B VAL* 3.6 20.2 - - + +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ILE* 3.6 36.0 - - + +
48B LEU* 4.3 14.6 - - + -
376B SER* 4.2 3.6 + - - -
378B ALA* 4.9 7.8 - - - +
380B VAL* 5.0 14.9 - - + +
384B THR* 5.3 6.7 - - + -
388B PHE* 3.1 31.5 + - + +
389B SER* 4.2 2.5 - - - +
391B TYR* 1.3 99.6 - - + +
393B GLY* 1.3 60.6 + - - +
394B SER 3.3 0.2 - - - -
395B GLY* 3.4 12.5 + - - -
396B GLY 4.3 3.6 - - - +
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Residues in contact with GLY 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B GLN* 5.8 0.8 - - - +
291B LEU* 4.1 12.3 - - - -
292B TRP* 3.8 14.8 - - - -
375B PRO* 3.1 10.7 - - - +
376B SER* 2.8 24.6 + - - -
377B GLY 4.5 0.7 + - - -
378B ALA 5.3 3.1 - - - +
380B VAL* 4.3 5.8 - - - +
389B SER 2.9 18.5 + - - -
390B GLY 3.4 1.8 + - - -
391B TYR 3.2 0.4 - - - -
392B LEU* 1.3 73.1 - - - +
394B SER* 1.3 55.7 + - - +
395B GLY 3.1 5.4 - - - -
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Residues in contact with SER 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292B TRP* 3.6 13.0 - - - -
373B ALA* 3.8 15.5 + - - +
374B ARG 3.4 12.5 + - - +
376B SER* 3.8 5.6 - - - -
390B GLY 3.3 10.1 + - - -
391B TYR 3.2 3.7 + - - -
393B GLY* 1.3 75.0 - - - +
395B GLY* 1.3 64.4 + - - +
396B GLY 3.1 0.2 - - - -
397B LYS* 3.1 53.0 + - - +
400B GLY* 3.7 11.1 - - - -
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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