Contacts of the helix formed by residues 272 - 281 (chain D) in PDB entry 3VBB
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 SER 272 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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225D THR* 3.5 29.2 - - - -
271D THR* 1.3 70.0 - - - +
273D GLU* 1.3 64.2 + - - +
274D GLN 3.2 1.3 - - - -
275D PRO* 3.0 14.9 - - - +
276D ILE* 3.0 18.0 + - - +
296D GLY* 3.8 17.0 + - - -
298D SER* 2.9 22.1 + - - -
323D LYS 4.3 0.5 + - - -
325D GLU* 2.8 15.2 + - - +
327D PHE* 3.5 14.8 - - - -
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Residues in contact with GLU 273 (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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237D VAL* 4.9 5.5 - - - +
238D ALA* 5.0 6.4 - - - -
271D THR* 3.5 18.1 + - + +
272D SER* 1.3 75.8 - - - +
274D GLN* 1.3 74.5 + - - +
276D ILE* 4.1 0.6 - - - +
277D ALA* 3.1 31.1 + - - +
325D GLU* 4.0 1.8 - - - +
327D PHE* 3.0 35.1 - - + -
402D GLN* 3.3 28.7 + - - +
425D MET* 5.5 1.0 - - - +
427D ASN* 3.8 27.5 + - + +
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Residues in contact with GLN 274 (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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229D MET* 3.9 13.0 - - + -
234D MET* 3.6 34.4 - - - +
237D VAL* 3.8 23.7 - - + +
238D ALA* 3.8 18.5 - - + +
247D LEU* 4.3 3.8 - - - +
269D ILE* 3.9 2.0 - - + +
270D ALA* 3.3 34.4 - - - +
271D THR* 3.5 18.8 + - - +
273D GLU* 1.3 88.5 - - - +
275D PRO* 1.3 70.8 - - + +
276D ILE 3.3 0.2 + - - -
277D ALA* 3.3 3.3 + - - +
278D ALA* 3.3 18.0 + - - +
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Residues in contact with PRO 275 (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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188C VAL* 4.5 5.2 - - + -
195C PHE* 3.4 28.8 - - + -
225D THR* 3.9 11.4 - - - +
226D PRO* 3.6 14.8 - - + +
229D MET* 4.1 12.8 - - + -
269D ILE* 3.5 29.2 - - + -
271D THR 3.3 10.5 - - - +
272D SER 3.0 15.0 - - - +
274D GLN* 1.3 91.4 - - + +
276D ILE* 1.3 60.3 + - - +
278D ALA* 3.3 6.2 + - - +
279D LEU 3.2 14.6 + - - -
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Residues in contact with ILE 276 (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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195C PHE* 4.4 6.3 - - + -
223D ILE* 3.8 28.7 - - + -
225D THR* 3.9 8.7 - - + -
272D SER* 3.0 25.9 + - - +
273D GLU 4.4 1.8 - - - +
275D PRO* 1.3 73.8 - - - +
277D ALA* 1.3 61.7 + - - +
279D LEU* 2.6 37.0 + - + +
294D TYR* 3.8 27.4 - - + -
296D GLY* 4.1 0.7 - - - -
327D PHE* 3.1 47.8 - - + -
329D TYR* 3.1 16.3 + - + +
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Residues in contact with ALA 277 (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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237D VAL* 3.4 20.9 - - + -
273D GLU* 3.1 24.7 + - - +
274D GLN 3.4 5.4 - - - +
276D ILE* 1.3 73.5 - - - +
278D ALA* 1.3 58.1 + - - +
279D LEU 2.9 9.2 + - - -
280D HIS* 3.3 9.4 + - - -
281D ARG* 3.6 10.0 + - - +
329D TYR* 3.7 12.2 + - - -
402D GLN* 6.4 0.7 - - - -
406D LEU* 4.1 20.5 - - + +
408D ILE* 4.6 1.9 - - - +
425D MET* 5.0 9.2 - - + -
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Residues in contact with ALA 278 (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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184C LYS* 5.2 2.9 - - - +
187C VAL* 5.7 2.6 - - - +
188C VAL* 3.9 18.3 - - + +
229D MET* 4.2 4.0 - - + -
233D VAL* 3.8 29.6 - - + -
237D VAL* 4.4 4.6 - - + +
274D GLN 3.3 7.7 + - - +
275D PRO 3.3 10.7 + - - +
276D ILE 3.3 0.6 - - - -
277D ALA* 1.3 78.2 - - - +
279D LEU* 1.3 63.6 + - - +
280D HIS 3.5 0.2 - - - -
281D ARG* 3.8 28.4 + - - +
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Residues in contact with LEU 279 (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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181C GLU* 4.4 5.4 - - + -
184C LYS* 3.4 55.4 - - + +
195C PHE* 4.1 28.0 - - + -
197C LYS* 5.9 2.7 - - - +
223D ILE* 3.9 25.1 - - + -
275D PRO 3.2 4.9 + - - +
276D ILE* 2.6 30.4 + - + +
277D ALA 2.9 0.2 + - - -
278D ALA* 1.3 81.4 - - - +
280D HIS* 1.3 68.4 + - + +
281D ARG 3.6 1.4 + - - +
283D GLU* 4.1 1.0 - - - +
294D TYR* 3.9 30.7 - - + +
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Residues in contact with HIS 280 (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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184C LYS* 4.2 6.9 + - - -
276D ILE 3.7 0.2 + - - -
277D ALA 3.3 4.6 + - - -
279D LEU* 1.3 95.0 - - + +
281D ARG* 1.3 69.0 + - - +
282D ASP 3.3 0.2 + - - -
283D GLU* 2.6 37.6 + - + +
285D LEU* 3.6 20.4 - - + +
292D ILE* 4.4 13.7 - - + +
294D TYR* 2.9 36.3 + + - -
329D TYR* 4.0 26.2 - + + +
408D ILE* 3.2 26.5 - - + +
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Residues in contact with ARG 281 (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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187C VAL* 4.2 19.7 - - - +
233D VAL* 3.2 33.2 - - - +
236D GLU* 3.0 30.9 + - - +
237D VAL* 5.3 2.2 - - - -
277D ALA 3.6 3.9 + - - +
278D ALA* 3.8 30.2 + - - +
279D LEU 3.4 3.6 - - - +
280D HIS* 1.3 79.9 - - - +
282D ASP* 1.3 73.4 + - + +
283D GLU* 3.1 7.8 + - - +
406D LEU* 3.6 33.4 - - + +
408D ILE* 4.1 2.9 - - - -
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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