Contacts of the helix formed by residues 238 - 252 (chain A) in PDB entry 1VXO
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 VAL 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A ALA* 4.7 2.0 - - - +
159A HIS* 3.7 45.3 - - + +
237A SER* 1.4 72.7 - - - +
239A ALA* 1.3 61.8 + - + +
241A GLY* 3.4 0.5 + - - -
242A ARG* 2.9 31.4 + - - +
295A VAL* 3.6 17.3 - - + -
296A ILE 3.3 23.1 + - - +
297A ASP* 4.0 9.9 - - + -
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Residues in contact with ALA 239 (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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237A SER* 3.2 8.4 + - - +
238A VAL* 1.3 84.3 - - + +
240A GLU* 1.4 57.1 + - - +
242A ARG* 3.4 8.0 + - - +
243A ARG* 2.9 29.7 + - - +
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Residues in contact with GLU 240 (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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236A VAL* 4.0 13.0 - - + -
237A SER* 3.1 20.1 + - - +
239A ALA* 1.4 73.1 - - - +
241A GLY* 1.3 67.6 + - - +
243A ARG* 2.6 47.3 + - - +
244A ARG* 2.7 61.9 + - - +
283A PRO* 3.5 10.4 - - - +
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Residues in contact with GLY 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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157A ALA* 3.3 25.6 + - - +
236A VAL* 3.9 15.0 - - - +
237A SER 2.9 16.7 + - - -
238A VAL* 3.8 1.8 - - - -
240A GLU* 1.3 75.2 - - - +
242A ARG* 1.3 54.6 + - - +
244A ARG* 3.3 8.5 + - - +
245A ALA* 3.0 25.3 + - - +
292A PHE* 5.3 2.3 - - - -
295A VAL* 5.2 0.4 - - - -
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Residues in contact with ARG 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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157A ALA 3.4 12.0 + - - +
158A LEU* 3.5 23.0 - - + +
159A HIS* 2.9 31.7 + - - +
238A VAL 2.9 17.1 + - - +
239A ALA* 3.6 7.4 - - - +
241A GLY* 1.3 74.5 - - - +
243A ARG* 1.3 67.7 + - - +
245A ALA* 3.0 3.3 + - - +
246A VAL* 2.9 34.8 + - + +
259A ASP* 2.9 40.2 + - - -
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Residues in contact with ARG 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 ALA 2.9 18.7 + - - +
240A GLU* 2.6 46.9 + - - +
242A ARG* 1.3 79.6 - - - +
244A ARG* 1.3 62.5 + - - +
246A VAL* 3.6 6.3 + - - +
247A GLU* 3.0 46.6 + - - +
250A ARG* 5.6 0.2 + - - -
281A VAL 3.0 28.4 + - - -
282A LEU 4.4 1.0 + - - -
283A PRO* 3.4 23.4 - - - +
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Residues in contact with ARG 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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236A VAL* 3.8 29.6 - - - +
240A GLU* 2.7 51.9 + - - +
241A GLY* 3.8 6.3 - - - +
242A ARG 3.1 0.2 - - - -
243A ARG* 1.3 82.7 - - - +
245A ALA* 1.3 61.2 + - - +
247A GLU* 3.4 5.5 + - - -
248A LEU* 2.9 27.4 + - - +
281A VAL* 3.7 27.5 - - + +
282A LEU* 4.0 5.2 - - - +
283A PRO* 3.5 22.1 - - - +
289A ARG* 6.0 4.9 - - - +
290A PHE 2.9 19.0 + - - -
291A SER* 2.8 38.8 + - - +
292A PHE* 4.3 9.8 - - + -
293A VAL* 4.8 0.2 - - - +
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Residues in contact with ALA 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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156A LEU* 3.8 31.0 - - + -
157A ALA 4.1 3.4 - - - +
158A LEU* 3.6 29.8 - - + -
241A GLY 3.0 13.1 + - - +
242A ARG 3.0 8.0 + - - +
244A ARG* 1.3 74.3 - - - +
246A VAL* 1.3 65.2 + - - +
248A LEU* 3.1 5.3 + - - +
249A GLY* 3.0 18.9 + - - -
262A LEU* 4.0 7.7 - - + +
266A LEU* 4.7 2.8 - - + +
292A PHE* 4.4 1.9 - - + -
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 4.6 4.0 - - + -
242A ARG* 2.9 33.1 + - + +
243A ARG* 3.9 6.3 - - - +
245A ALA* 1.3 72.7 - - - +
247A GLU* 1.3 54.0 + - - +
249A GLY* 3.0 2.6 + - - -
250A ARG* 2.7 55.7 + - - +
256A LEU* 4.1 21.3 - - + +
262A LEU* 3.9 20.6 - - + -
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Residues in contact with GLU 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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243A ARG* 3.0 31.7 + - - +
244A ARG* 3.7 5.8 - - - +
246A VAL* 1.3 77.9 - - - +
248A LEU* 1.3 62.6 + - - +
250A ARG* 2.8 41.7 + - - +
251A ASN* 2.8 41.9 + - - +
280A ASN 4.5 4.7 - - - +
281A VAL* 3.8 24.9 - - + -
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Residues in contact with LEU 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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45A PHE* 5.9 0.2 - - + -
152A ALA* 4.1 12.8 - - + -
156A LEU* 4.0 15.0 - - + -
244A ARG 2.9 14.6 + - - +
245A ALA 3.4 8.1 - - - +
246A VAL 3.1 0.2 - - - -
247A GLU* 1.3 75.0 - - - +
249A GLY* 1.3 66.3 + - - +
251A ASN* 2.9 19.9 + - - +
252A LEU* 3.3 11.4 + - + +
266A LEU* 3.9 21.5 - - + -
274A LEU* 4.3 14.8 - - + +
277A VAL* 3.8 26.7 - - + -
278A GLU* 4.3 15.0 - - - -
281A VAL* 3.7 9.6 - - + +
292A PHE* 3.9 26.2 - - + -
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Residues in contact with GLY 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 ALA 3.0 10.7 + - - -
246A VAL 3.0 4.0 + - - -
248A LEU* 1.3 76.8 - - - +
250A ARG* 1.3 62.3 + - - +
252A LEU 3.0 12.1 + - - -
254A CYS* 3.1 31.5 + - - +
256A LEU* 4.0 2.2 - - - -
262A LEU* 3.7 26.2 - - - -
266A LEU* 4.3 4.7 - - - +
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Residues in contact with ARG 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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243A ARG 5.6 0.2 + - - -
246A VAL* 2.7 39.6 + - - +
247A GLU* 2.8 38.2 + - - +
248A LEU 3.2 0.2 - - - -
249A GLY* 1.3 72.9 - - - +
251A ASN* 1.3 61.2 + - - +
253A ASN* 3.4 17.2 + - - +
254A CYS 4.8 2.7 - - - +
256A LEU* 3.6 28.5 - - + +
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Residues in contact with ASN 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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247A GLU* 2.8 45.2 + - - +
248A LEU* 2.9 13.4 + - - +
250A ARG* 1.3 77.2 - - - +
252A LEU* 1.3 60.9 + - - +
253A ASN* 3.4 9.2 + - - +
277A VAL* 3.9 25.9 - - + +
280A ASN* 2.9 40.9 + - - +
281A VAL* 4.6 1.2 - - - +
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Residues in contact with LEU 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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248A LEU* 3.8 16.4 - - + +
249A GLY 3.0 7.1 + - - +
251A ASN* 1.3 81.3 - - - +
253A ASN* 1.3 76.0 + - - +
254A CYS* 3.3 7.4 + - - -
266A LEU* 3.8 26.2 - - + -
269A LYS* 3.4 38.2 + - + +
273A GLU* 3.7 33.0 - - + +
274A LEU* 3.9 18.8 - - + -
277A VAL* 4.1 15.3 - - + -
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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