Contacts of the helix formed by residues 240 - 252 (chain A) in PDB entry 3ZVV
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 THR 240 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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238A ASP 3.5 3.6 + - - -
239A ASP* 1.3 72.5 - - - +
241A PRO* 1.4 77.4 - - - +
242A GLY* 3.4 7.8 + - - +
243A ALA* 3.1 29.6 + - + +
244A ILE* 3.0 23.6 + - - +
283A GLY 3.5 10.9 + - - -
284A GLU* 4.4 17.7 + - - +
285A THR 3.5 14.9 + - - -
286A PRO* 4.4 0.4 - - - -
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Residues in contact with PRO 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ASP 4.0 1.1 - - - +
240A THR* 1.4 90.3 - - - +
242A GLY* 1.3 53.8 + - - +
244A ILE* 3.4 14.3 + - + +
245A LEU* 3.0 37.4 + - + +
272A LEU* 4.3 9.9 - - + +
281A LEU 3.2 28.7 - - - +
282A VAL* 4.0 7.0 - - + +
283A GLY 3.6 8.5 - - - +
285A THR 3.2 15.5 - - - +
287A ILE* 4.5 7.9 - - + -
290A PHE* 3.6 23.3 - - + -
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Residues in contact with GLY 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A THR* 3.1 10.1 + - - -
241A PRO* 1.3 78.5 - - - +
243A ALA* 1.4 55.1 + - - +
245A LEU* 3.3 13.4 + - - +
246A GLN* 3.2 31.0 + - - +
283A GLY 5.2 0.4 + - - -
284A GLU* 5.7 3.6 - - - -
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Residues in contact with ALA 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A ASP* 4.9 12.3 - - + +
240A THR* 3.1 31.7 + - + +
242A GLY* 1.4 71.8 - - - +
244A ILE* 1.3 60.2 + - - +
246A GLN* 3.6 8.3 + - - +
247A SER* 3.0 26.3 + - - -
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Residues in contact with ILE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A ILE* 4.0 15.7 - - + -
224A ILE* 4.7 13.7 - - + -
233A ILE* 4.9 8.4 - - + +
235A VAL* 3.3 29.2 - - + -
239A ASP* 4.0 5.2 - - + +
240A THR 3.0 15.6 + - - +
241A PRO* 3.6 11.9 - - + +
242A GLY 3.3 0.2 - - - -
243A ALA* 1.3 73.9 - - - +
245A LEU* 1.3 59.7 + - - +
247A SER* 3.2 8.5 + - - -
248A PHE* 3.0 26.9 + - - +
272A LEU* 4.4 14.6 - - + -
287A ILE* 3.5 44.4 - - + -
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Residues in contact with LEU 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241A PRO* 3.0 21.7 + - + +
242A GLY* 3.3 12.8 + - - +
244A ILE* 1.3 76.5 - - - +
246A GLN* 1.3 61.8 + - + +
248A PHE* 3.2 18.6 + - + +
249A PHE* 3.2 35.6 + - + -
270A PHE* 4.0 22.0 - - + +
271A VAL* 4.8 4.0 - - + -
272A LEU* 3.9 25.4 - - + +
282A VAL* 6.3 1.1 - - + -
307A LEU* 3.4 32.3 - - + -
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Residues in contact with GLN 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A GLY 3.2 16.6 + - - +
243A ALA* 4.0 7.2 - - - +
244A ILE 3.3 0.2 - - - -
245A LEU* 1.3 74.6 - - + +
247A SER* 1.3 60.8 + - - +
249A PHE* 3.7 24.7 + - - +
250A THR* 3.0 27.7 + - - -
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Residues in contact with SER 247 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A ILE* 4.3 17.6 - - - +
234A LYS 4.8 3.6 + - - -
235A VAL* 5.6 3.7 - - - +
243A ALA 3.0 18.7 + - - -
244A ILE* 3.2 10.7 + - - -
246A GLN* 1.3 76.9 - - - +
248A PHE* 1.3 57.6 + - - +
250A THR* 3.9 5.4 - - - +
251A LYS* 3.3 26.2 + - - +
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Residues in contact with PHE 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224A ILE* 3.6 40.8 - - + -
226A ARG* 5.7 9.0 - - + -
231A GLN* 4.1 19.7 - - + -
233A ILE* 3.3 27.3 - - + +
244A ILE 3.0 11.6 + - - +
245A LEU* 3.2 13.4 + - + +
247A SER* 1.3 75.4 - - - +
249A PHE* 1.3 73.0 + + - +
250A THR 3.2 0.4 + - - -
251A LYS* 3.4 2.8 + - + +
252A MET* 3.0 66.0 + - + +
307A LEU* 3.7 31.4 - - + -
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Residues in contact with PHE 249 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A LEU* 3.2 33.9 + - + +
246A GLN* 3.7 25.1 + - - +
247A SER 3.6 0.2 - - - -
248A PHE* 1.3 91.9 - + - +
250A THR* 1.3 59.5 + - - +
252A MET* 2.8 29.7 - - + +
253A ALA* 3.7 7.1 + - - +
269A ASP* 6.2 1.3 - - + -
270A PHE* 3.9 34.1 - + + -
307A LEU* 4.4 10.8 - - + -
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Residues in contact with THR 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A GLN 3.0 19.6 + - - -
247A SER* 3.9 6.7 - - - +
248A PHE 3.2 0.4 - - - -
249A PHE* 1.3 76.4 - - - +
251A LYS* 1.4 66.2 + - - +
252A MET 3.2 0.7 + - - -
253A ALA* 4.1 11.4 + - - +
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Residues in contact with LYS 251 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A GLN* 4.8 17.0 - - + +
232A THR 4.5 10.9 + - - -
233A ILE* 4.5 25.5 - - + +
234A LYS* 5.8 4.2 - - - +
247A SER 3.3 15.2 + - - +
248A PHE 3.4 3.6 + - - +
250A THR* 1.4 79.7 - - - +
252A MET* 1.4 58.9 + - + +
253A ALA 4.1 1.6 + - - -
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Residues in contact with MET 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226A ARG* 6.5 1.1 - - - -
231A GLN* 5.5 10.8 - - + +
248A PHE* 3.0 58.0 + - + +
249A PHE* 2.8 24.1 - - + +
251A LYS* 1.4 76.2 - - + +
253A ALA* 1.4 58.9 + - - +
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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