Contacts of the helix formed by residues 346 - 360 (chain D) in PDB entry 3VI4
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 ASN 346 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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339D THR 3.1 25.7 + - - -
340D LEU* 3.6 7.9 - - - +
341D SER* 2.6 34.5 + - - +
345D SER* 1.3 76.6 + - - +
347D VAL* 1.3 64.4 + - - +
348D ILE 3.2 3.9 + - - -
349D GLN* 3.4 12.2 + - + +
350D LEU* 3.1 26.9 + - - +
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Residues in contact with VAL 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D TYR* 3.4 26.0 - - + +
141D ASN 5.9 1.1 - - - +
142D VAL* 5.1 2.7 - - + -
145D LEU* 4.4 21.5 - - + -
316D ALA* 5.1 6.7 - - + -
340D LEU* 3.4 28.0 - - + -
344D SER* 3.1 20.9 - - - +
345D SER 3.2 5.1 - - - +
346D ASN* 1.3 75.8 + - - +
348D ILE* 1.3 67.3 + - + +
350D LEU* 3.5 7.6 - - - +
351D ILE* 3.0 42.1 + - + +
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Residues in contact with ILE 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D LEU* 3.8 22.7 - - + -
148D ASP* 3.2 37.9 - - + +
149D LEU* 3.5 27.1 - - + +
152D GLU* 3.6 34.1 - - + +
345D SER 4.7 3.1 + - - +
346D ASN 3.2 1.0 - - - -
347D VAL* 1.3 78.3 - - + +
349D GLN* 1.3 67.1 + - - +
351D ILE* 3.0 4.7 + - - +
352D ILE* 2.9 26.3 + - + +
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Residues in contact with GLN 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D GLU* 5.9 4.4 + - - +
346D ASN* 3.4 15.2 + - + +
348D ILE* 1.3 78.4 - - - +
350D LEU* 1.3 54.3 + - - +
352D ILE* 3.0 18.5 + - - +
353D ASP* 2.7 67.0 + - - +
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Residues in contact with LEU 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D ILE* 4.0 17.7 - - + -
316D ALA* 3.7 26.5 - - + -
338D GLY* 3.4 41.6 - - - +
339D THR 3.5 19.1 - - - +
340D LEU* 3.6 18.4 - - + +
346D ASN* 3.1 22.5 + - - +
347D VAL* 3.5 6.1 - - - +
349D GLN* 1.3 76.1 - - - +
351D ILE* 1.3 54.9 + - + +
353D ASP* 3.4 9.1 + - - +
354D ALA* 2.7 36.7 + - + +
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Residues in contact with ILE 351 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125D LEU* 4.3 17.3 - - + -
127D TYR* 4.3 13.0 - - + -
145D LEU* 5.8 1.3 - - + -
149D LEU* 4.4 28.3 - - + -
153D MET* 4.5 12.6 - - - -
253D LEU* 5.4 0.9 - - + -
255D VAL* 3.9 38.4 - - + -
314D ILE* 4.3 10.1 - - + +
316D ALA* 5.9 0.2 - - + -
347D VAL* 3.0 28.4 + - + +
348D ILE* 3.0 6.0 + - - +
350D LEU* 1.3 80.8 - - + +
352D ILE* 1.3 54.0 + - + +
354D ALA* 3.6 6.5 - - - +
355D TYR* 2.7 33.6 + - + +
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Residues in contact with ILE 352 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D LEU* 5.3 0.2 - - + -
152D GLU* 3.9 35.9 - - + +
153D MET* 3.8 29.8 - - - -
156D ILE* 3.8 20.0 - - + -
348D ILE* 2.9 19.9 + - + +
349D GLN* 3.4 20.2 - - - +
351D ILE* 1.3 73.9 - - + +
353D ASP* 1.3 69.4 + - - +
354D ALA 3.1 0.8 + - - -
355D TYR* 3.1 3.1 + - - +
356D ASN* 2.9 46.0 + - - +
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Residues in contact with ASP 353 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D GLN* 2.7 54.0 + - - +
350D LEU* 3.8 7.0 + - - +
352D ILE* 1.3 73.8 - - - +
354D ALA* 1.3 61.4 + - - +
356D ASN* 3.5 6.8 + - - +
357D SER* 3.3 23.0 + - - -
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Residues in contact with ALA 354 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314D ILE* 3.7 32.8 - - + -
336D ALA* 4.1 13.6 - - + +
337D VAL 5.5 4.5 - - - +
338D GLY* 5.9 0.7 - - - -
350D LEU* 2.7 24.7 + - + +
351D ILE 3.6 4.3 - - - +
353D ASP* 1.3 70.7 - - - +
355D TYR* 1.3 64.9 + - - +
357D SER* 3.4 7.8 + - - -
358D LEU* 3.1 28.3 + - - +
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Residues in contact with TYR 355 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ARG* 4.9 4.7 + - - -
121D TYR* 6.0 1.6 - - - +
123D ILE* 4.2 18.1 - - + +
153D MET* 5.0 5.4 - - + -
156D ILE* 3.2 49.4 - - + +
251D THR* 5.2 6.5 + - + +
253D LEU* 4.1 37.0 - - + -
312D GLN* 5.9 3.4 - - - -
314D ILE* 4.5 1.9 - - + +
351D ILE* 2.7 23.9 + - + +
352D ILE* 3.9 3.6 - - - +
354D ALA* 1.3 69.1 - - - +
356D ASN* 1.3 73.9 + - - +
358D LEU* 3.3 12.4 + - + +
359D SER* 2.9 52.5 + - - -
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Residues in contact with ASN 356 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ARG* 4.9 7.1 + - - -
156D ILE* 4.9 5.5 - - - +
352D ILE* 2.9 40.2 + - - +
353D ASP* 3.8 7.1 + - - +
355D TYR* 1.3 85.6 - - - +
357D SER* 1.3 53.1 + - - +
359D SER* 3.1 7.8 + - - -
360D SER* 2.7 39.1 + - - -
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Residues in contact with SER 357 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D ALA* 4.8 6.8 - - - +
353D ASP 3.3 11.2 + - - -
354D ALA* 3.4 11.3 + - - -
356D ASN* 1.3 78.1 - - - +
358D LEU* 1.3 62.7 + - - +
360D SER* 3.3 20.2 + - - -
361D GLU* 3.6 15.6 - - - +
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Residues in contact with LEU 358 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253D LEU* 4.4 10.1 - - + -
312D GLN* 3.9 30.6 + - + +
313D THR 4.7 1.8 - - - +
314D ILE* 4.2 23.6 - - + -
334D LYS* 2.5 50.5 + - + +
335D SER 3.7 37.2 - - - +
336D ALA* 4.2 6.9 - - + +
354D ALA 3.1 18.1 + - - +
355D TYR* 3.4 13.7 - - + +
357D SER* 1.3 77.3 + - - +
359D SER* 1.3 56.7 + - - +
361D GLU* 3.0 7.7 - - - +
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Residues in contact with SER 359 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ARG* 2.9 48.8 + - - +
312D GLN* 5.7 1.8 - - - +
355D TYR* 2.9 46.6 + - - -
356D ASN* 3.6 3.8 + - - -
358D LEU* 1.3 74.0 - - - +
360D SER* 1.3 60.4 + - - +
361D GLU 3.0 8.9 + - - +
362D VAL* 5.5 2.9 - - - +
398D ILE* 3.8 1.6 - - - +
430D PHE* 5.9 9.0 - - - -
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Residues in contact with SER 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117D ARG* 3.9 4.3 - - - +
356D ASN* 2.7 20.4 + - - -
357D SER* 3.3 17.4 + - - -
358D LEU 3.4 0.4 - - - -
359D SER* 1.3 72.2 - - - +
361D GLU* 1.3 57.7 + - - +
396D SER* 3.7 0.5 + - - -
397D ASN* 3.1 15.4 + - - -
398D ILE* 2.7 46.5 + - - +
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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