Contacts of the helix formed by residues 224 - 237 (chain D) in PDB entry 2VUU
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 224 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183D PRO 3.3 8.1 + - - -
184D ASP* 3.1 38.1 + - - -
185D ILE 3.3 7.9 - - - -
186D PRO* 3.7 2.2 - - - +
223D LEU* 1.3 74.0 - - - +
225D PRO* 1.3 59.5 - - - +
226D VAL* 3.7 3.8 + - - +
227D GLN* 2.6 59.4 + - - +
228D VAL* 3.0 9.3 + - - -
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Residues in contact with PRO 225 (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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177D TRP* 3.7 14.0 - - + -
181D PHE* 3.8 21.8 - - + -
182D ASP 3.1 28.3 - - - +
183D PRO* 3.3 6.3 - - + +
185D ILE 3.2 8.7 - - - +
187D LEU* 4.5 10.5 - - + -
223D LEU 4.0 1.5 - - - +
224D SER* 1.3 80.7 - - - +
226D VAL* 1.3 61.2 + - - +
228D VAL* 3.2 6.9 + - + +
229D CYS* 3.0 26.9 + - - -
242D TYR* 3.5 36.6 - - + -
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Residues in contact with VAL 226 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183D PRO* 2.8 40.8 - - + +
184D ASP* 3.5 13.2 - - - +
224D SER* 2.8 6.3 + - - +
225D PRO* 1.3 74.5 - - - +
227D GLN* 1.3 60.7 + - + +
229D CYS* 3.3 4.9 + - - +
230D ALA* 2.8 28.5 + - + +
242D TYR* 4.4 12.3 - - + -
239H ARG* 6.2 2.9 - - - +
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Residues in contact with GLN 227 (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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186D PRO* 4.9 5.5 - - - +
222D THR 4.3 2.7 + - - +
223D LEU* 3.2 24.2 - - + +
224D SER* 2.6 50.1 + - - +
226D VAL* 1.3 74.1 - - + +
228D VAL* 1.3 56.0 + - - +
230D ALA* 3.0 10.2 + - - +
231D ALA* 2.7 36.3 + - - +
234D ARG* 4.4 2.5 + - - +
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Residues in contact with VAL 228 (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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157D PHE* 3.4 39.0 - - + -
167D MET* 5.0 0.4 - - + -
177D TRP* 3.7 5.4 - - + -
189D TRP* 3.5 36.1 - - + +
223D LEU* 3.8 17.5 - - + -
224D SER 3.0 19.3 + - - +
225D PRO* 3.2 10.1 + - + +
227D GLN* 1.3 75.6 - - - +
229D CYS* 1.3 58.5 + - - +
231D ALA* 3.4 3.1 + - - +
232D PHE* 2.9 42.5 + - + -
331D MET* 4.3 6.1 - - + -
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Residues in contact with CYS 229 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D MET* 4.5 1.8 - - - -
177D TRP* 3.7 26.9 - - - -
225D PRO 3.0 15.7 + - - +
226D VAL* 3.5 8.7 - - - +
228D VAL* 1.3 76.0 - - - +
230D ALA* 1.3 54.5 + - - +
232D PHE* 3.2 2.6 + - - -
233D SER* 2.7 36.8 + - - -
240D VAL* 3.2 39.3 - - + +
241D THR* 3.8 4.3 - - - -
242D TYR* 3.8 25.8 - - - +
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Residues in contact with ALA 230 (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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226D VAL* 2.8 17.4 + - + +
227D GLN* 3.0 14.8 + - - +
229D CYS* 1.3 76.1 - - - +
231D ALA* 1.3 56.9 + - - +
233D SER* 3.3 8.7 + - - -
234D ARG* 2.9 48.1 + - - +
240D VAL 5.6 0.4 - - - -
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Residues in contact with ALA 231 (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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223D LEU* 5.0 2.9 - - + -
227D GLN 2.7 15.5 + - - +
228D VAL* 3.4 10.1 - - - +
230D ALA* 1.3 70.0 - - - +
232D PHE* 1.3 60.3 + - - +
234D ARG* 3.2 23.7 + - - +
235D ALA* 2.8 30.6 + - - +
331D MET* 4.1 25.4 - - + -
332D GLU* 4.2 13.2 - - + +
335D ALA* 4.9 0.2 - - - -
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Residues in contact with PHE 232 (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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157D PHE* 3.5 26.5 - + + -
167D MET* 4.0 20.2 - - + -
228D VAL* 2.9 36.2 + - + +
229D CYS 3.6 6.3 - - - +
231D ALA* 1.3 78.4 - - - +
233D SER* 1.3 57.4 + - - +
235D ALA 3.1 0.2 + - - -
236D LEU* 2.7 53.0 + - + +
240D VAL* 3.9 16.4 - - + -
331D MET* 3.5 31.6 - - + -
334D TYR* 4.3 6.5 - + - -
335D ALA* 3.8 22.2 - - + -
339D PHE* 3.5 30.5 - + - -
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Residues in contact with SER 233 (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 CYS 2.7 21.3 + - - -
230D ALA* 3.4 9.9 - - - -
232D PHE* 1.3 72.6 - - - +
234D ARG* 1.3 58.8 + - - +
237D ASN* 3.0 26.5 + - - -
238D ARG 2.5 24.4 + - - +
239D ARG* 4.1 1.6 - - - -
240D VAL* 3.4 26.5 + - - +
234H ARG* 3.5 15.3 + - - +
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Residues in contact with ARG 234 (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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227D GLN* 4.4 2.8 + - - +
230D ALA* 2.9 24.6 + - - +
231D ALA* 3.4 36.7 - - - +
233D SER* 1.3 77.4 - - - +
235D ALA* 1.3 65.2 + - - +
237D ASN* 3.6 18.6 + - - +
332D GLU* 2.8 33.7 + - - +
233H SER* 4.4 3.4 - - - +
234H ARG* 4.3 19.5 - - + +
237H ASN* 2.8 56.5 + - - +
336H ARG* 5.3 2.8 + - - -
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Residues in contact with ALA 235 (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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231D ALA 2.8 17.4 + - - +
232D PHE 3.7 0.9 - - - +
234D ARG* 1.3 79.5 - - - +
236D LEU* 1.3 61.0 + - - +
237D ASN* 3.8 7.6 + - - -
332D GLU* 3.6 19.9 - - + +
335D ALA* 3.6 10.3 - - + -
336D ARG* 3.6 46.9 + - + +
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Residues in contact with LEU 236 (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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175D PHE* 4.3 24.9 - - + -
232D PHE* 2.7 49.0 + - + +
235D ALA* 1.3 76.2 - - + +
237D ASN* 1.3 72.6 + - - +
238D ARG* 3.5 19.7 + - + +
240D VAL* 4.8 2.9 - - + -
335D ALA 3.6 23.3 - - - +
336D ARG* 4.9 1.1 - - - +
339D PHE* 4.2 10.3 - - + -
340D PRO* 4.2 7.9 - - + -
350D TRP* 4.0 24.0 - - + -
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Residues in contact with ASN 237 (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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233D SER 3.0 13.1 + - - -
234D ARG 3.6 11.3 + - - +
235D ALA 3.4 9.1 + - - -
236D LEU* 1.3 83.5 + - - +
238D ARG* 1.3 67.0 + - - +
234H ARG* 4.1 13.9 - - - +
332H GLU* 3.4 23.7 - - - +
336H ARG* 4.1 12.1 + - - -
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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