Contacts of the helix formed by residues 224 - 237 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183H PRO 3.0 20.5 + - - -
184H ASP* 3.5 25.0 - - - -
185H ILE 3.4 7.9 - - - -
186H PRO* 3.7 1.7 - - - +
223H LEU* 1.3 74.4 - - - +
225H PRO* 1.3 69.1 - - - +
226H VAL* 3.6 2.4 + - - +
227H GLN* 2.7 50.0 + - - +
228H VAL* 2.9 9.6 + - - -
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Residues in contact with PRO 225 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177H TRP* 3.4 18.4 - - + -
181H PHE* 3.8 21.3 - - + -
182H ASP 2.9 28.5 - - - +
183H PRO* 3.4 5.2 - - + +
185H ILE 3.3 9.2 - - - +
187H LEU* 4.7 6.5 - - + -
189H TRP* 5.7 0.4 - - + -
223H LEU 4.4 1.3 - - - +
224H SER* 1.3 79.5 - - - +
226H VAL* 1.3 63.6 + - - +
228H VAL* 3.0 6.8 + - + +
229H CYS* 3.0 25.3 + - - -
242H TYR* 3.4 37.2 - - + -
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Residues in contact with VAL 226 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183H PRO* 3.0 39.9 - - + +
184H ASP* 4.3 9.2 - - - +
224H SER* 2.9 3.7 + - - +
225H PRO* 1.3 74.6 - - - +
227H GLN* 1.3 61.8 + - + +
229H CYS* 3.1 6.6 + - - +
230H ALA* 2.8 29.0 + - + +
242H TYR* 4.3 14.1 - - + +
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Residues in contact with GLN 227 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239D ARG* 6.3 0.8 - - - +
186H PRO* 4.5 7.6 - - - +
222H THR 4.6 1.4 + - - +
223H LEU* 3.6 25.3 - - + +
224H SER* 2.7 49.1 + - - +
226H VAL* 1.3 71.9 - - + +
228H VAL* 1.3 55.8 + - - +
230H ALA* 3.7 8.8 - - - +
231H ALA* 2.7 35.3 + - - +
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Residues in contact with VAL 228 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157H PHE* 3.7 35.0 - - + -
167H MET* 5.9 0.7 - - - -
177H TRP* 3.9 6.5 - - + -
189H TRP* 3.5 39.5 - - + +
223H LEU* 3.6 19.3 - - + -
224H SER 2.9 13.4 + - - +
225H PRO* 3.0 8.7 + - + +
227H GLN* 1.3 75.1 - - - +
229H CYS* 1.3 58.6 + - - +
231H ALA* 3.1 9.5 - - - +
232H PHE* 2.9 34.6 + - + -
331H MET* 3.8 9.9 - - + -
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Residues in contact with CYS 229 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H MET* 4.9 1.6 - - - -
177H TRP* 3.7 22.0 - - - -
225H PRO 3.0 16.4 + - - -
226H VAL* 3.3 8.5 - - - +
228H VAL* 1.3 74.3 - - - +
230H ALA* 1.3 60.3 + - - +
232H PHE* 3.2 3.6 + - - -
233H SER* 2.8 24.6 + - - -
240H VAL* 3.4 42.4 - - + +
241H THR* 3.9 4.7 - - - -
242H TYR* 3.6 33.0 - - - +
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Residues in contact with ALA 230 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239D ARG* 6.2 2.7 - - + +
226H VAL* 2.8 22.6 + - + +
227H GLN* 3.2 9.8 + - - +
229H CYS* 1.3 73.1 - - - +
231H ALA* 1.3 63.1 + - - +
233H SER* 3.1 16.6 + - - -
234H ARG* 3.1 31.3 + - - +
240H VAL 5.3 1.1 - - - -
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Residues in contact with ALA 231 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223H LEU* 4.9 4.5 - - + -
227H GLN 2.7 14.1 + - - +
228H VAL* 3.1 11.4 - - - +
230H ALA* 1.3 78.6 - - - +
232H PHE* 1.3 63.3 + - - +
234H ARG* 3.3 18.3 + - - +
235H ALA* 3.1 22.5 + - - +
331H MET* 3.8 26.2 - - + -
332H GLU* 4.4 15.1 - - + +
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Residues in contact with PHE 232 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157H PHE* 3.9 28.0 - + + -
167H MET* 3.2 38.4 - - + -
228H VAL* 2.9 26.0 + - + +
229H CYS 3.2 7.4 + - - +
231H ALA* 1.3 76.7 - - - +
233H SER* 1.3 56.6 + - - +
235H ALA* 3.6 0.2 - - - +
236H LEU* 3.0 47.7 + - + +
240H VAL* 4.0 2.9 - - + -
331H MET* 3.6 27.6 - - + -
334H TYR* 3.9 22.2 - + - -
335H ALA* 3.7 20.9 - - + -
339H PHE* 3.6 29.6 - + - -
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Residues in contact with SER 233 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234D ARG* 4.4 4.2 - - - +
229H CYS 2.8 13.5 + - - -
230H ALA* 3.1 14.1 + - - -
232H PHE* 1.3 74.3 - - - +
234H ARG* 1.3 58.3 + - - +
237H ASN* 2.6 35.7 + - - -
238H ARG 2.7 27.2 + - - -
239H ARG* 4.1 2.4 - - - -
240H VAL* 3.8 12.7 + - - -
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Residues in contact with ARG 234 (chain H).
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* 3.5 33.3 + - - +
234D ARG* 4.3 11.9 - - + +
237D ASN* 4.1 12.7 - - - +
238D ARG 3.7 22.6 + - - +
239D ARG* 4.7 14.3 - - - +
230H ALA* 3.1 30.1 + - - +
231H ALA* 3.8 17.1 - - - +
233H SER* 1.3 78.0 - - - +
235H ALA* 1.3 58.8 + - - +
237H ASN* 3.4 14.4 - - - +
332H GLU* 3.4 34.1 + - - +
336H ARG* 2.6 22.4 + - - +
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Residues in contact with ALA 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231H ALA 3.1 8.0 + - - +
232H PHE 3.6 4.5 - - - +
234H ARG* 1.3 79.2 - - - +
236H LEU* 1.3 60.9 + - + +
237H ASN* 3.7 2.3 + - - -
332H GLU* 3.6 11.8 - - + +
335H ALA* 3.4 19.7 - - + -
336H ARG* 3.0 67.1 + - + +
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Residues in contact with LEU 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167H MET* 5.1 0.2 - - + -
175H PHE* 4.0 30.5 - - + -
232H PHE* 3.0 38.8 + - + +
235H ALA* 1.3 78.8 - - + +
237H ASN* 1.3 73.5 + - - +
238H ARG* 3.1 21.0 + - + +
240H VAL* 4.8 3.1 - - + -
335H ALA 3.9 19.1 - - - +
336H ARG* 5.1 0.4 - - - -
339H PHE* 4.4 9.0 - - + -
340H PRO* 4.0 10.3 - - + -
350H TRP* 4.0 23.8 - - + -
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Residues in contact with ASN 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D ARG* 2.8 57.9 + - - +
332D GLU* 4.2 10.8 + - - +
233H SER 2.6 19.2 + - - -
234H ARG 3.4 7.0 - - - +
235H ALA 3.4 8.1 + - - -
236H LEU* 1.3 77.3 + - - +
238H ARG* 1.3 57.9 + - - +
336H ARG* 4.2 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
------------------------------------------------------------
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