Contacts of the helix formed by residues 242 - 255 (chain A) in PDB entry 2OB2
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 ARG 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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240A ASN* 3.4 24.2 + - - +
241A ASP* 1.3 77.4 + - - +
243A PHE* 1.3 55.8 + - - +
244A GLY 3.1 3.2 + - - -
245A ALA* 3.1 16.9 + - + +
246A ILE* 2.7 70.2 + - + +
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Residues in contact with PHE 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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234A ILE 3.7 7.4 - - - -
235A GLY 4.1 0.2 - - - +
241A ASP* 3.2 17.6 + - - +
242A ARG* 1.3 73.9 - - - +
244A GLY* 1.3 57.9 + - - +
246A ILE* 3.5 9.1 + - - +
247A MET* 2.8 64.9 + - + +
316A VAL* 4.8 5.6 - - + -
317A MET* 4.3 19.5 - - + -
320A HIS* 3.4 54.7 - + + +
321A TYR* 4.0 21.5 - + - -
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Residues in contact with GLY 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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235A GLY* 3.3 22.0 + - - -
242A ARG 3.2 1.0 - - - -
243A PHE* 1.3 75.2 - - - +
245A ALA* 1.3 56.8 + - - +
247A MET* 3.1 1.4 + - - +
248A GLN* 2.8 39.2 + - - +
262A LEU* 3.9 8.7 - - - -
263A MET* 3.5 24.7 - - - +
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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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241A ASP 5.5 0.8 + - - +
242A ARG* 3.4 22.6 - - + +
244A GLY* 1.3 73.2 - - - +
246A ILE* 1.3 57.3 + - + +
248A GLN* 4.1 6.2 - - - +
249A SER* 2.9 35.1 + - - +
263A MET* 3.7 10.8 - - + +
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Residues in contact with ILE 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 ARG* 2.7 64.9 + - + +
243A PHE* 3.8 7.4 - - - +
245A ALA* 1.3 73.3 - - + +
247A MET* 1.3 58.0 + - - +
249A SER* 3.8 3.3 - - - -
250A ASN* 2.9 56.4 + - - +
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Residues in contact with MET 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 PRO* 3.7 10.1 - - + -
243A PHE* 2.8 54.5 + - + +
244A GLY 3.6 2.2 - - - +
246A ILE* 1.3 79.3 - - - +
248A GLN* 1.3 62.2 + - - +
250A ASN* 3.4 5.8 + - - +
251A LEU* 3.0 44.6 + - + +
259A MET* 3.9 20.6 - - - +
262A LEU* 3.3 36.3 - - + -
321A TYR* 4.7 8.7 - - - -
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Residues in contact with GLN 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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244A GLY 2.8 20.4 + - - +
245A ALA* 4.1 5.3 - - - +
247A MET* 1.3 73.0 - - - +
249A SER* 1.3 62.4 + - - +
251A LEU* 3.4 7.0 + - - +
252A LYS* 3.0 25.6 + - - +
257A LEU 4.5 1.8 - - - +
259A MET* 2.7 35.4 + - + +
260A PRO* 4.4 6.7 + - - +
262A LEU* 3.7 23.6 - - + +
263A MET* 3.5 28.9 - - - +
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Residues in contact with SER 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* 2.9 23.9 + - - +
246A ILE* 3.8 5.2 - - - -
248A GLN* 1.3 75.9 - - - +
250A ASN* 1.3 61.7 + - - +
252A LYS* 3.3 4.7 + - - +
253A GLU* 2.9 33.2 + - - +
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Residues in contact with ASN 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 ILE* 2.9 42.0 + - - +
247A MET* 3.8 5.9 - - - +
249A SER* 1.3 80.1 - - - +
251A LEU* 1.3 53.2 + - + +
253A GLU* 4.9 4.9 - - - +
254A SER* 2.5 42.0 + - - +
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Residues in contact with LEU 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 MET* 3.0 31.1 + - + +
248A GLN* 3.9 3.4 - - - +
249A SER 3.3 0.2 - - - -
250A ASN* 1.3 77.5 - - + +
252A LYS* 1.3 57.1 + - - +
254A SER* 3.3 7.0 - - - +
255A ARG* 3.0 28.3 + - + +
257A LEU* 2.8 58.3 + - + +
259A MET* 3.6 47.3 - - + -
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Residues in contact with LYS 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 GLN 3.0 18.4 + - - +
249A SER* 3.7 5.6 - - - +
251A LEU* 1.3 74.4 - - - +
253A GLU* 1.3 64.9 + - - +
256A ASN* 3.3 45.9 + - - +
257A LEU 3.6 10.7 + - - +
258A GLU* 5.5 12.6 - - + +
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Residues in contact with GLU 253 (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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249A SER 2.9 17.8 + - - +
250A ASN* 4.4 5.2 - - - +
252A LYS* 1.3 79.5 - - - +
254A SER* 1.3 63.2 + - - +
256A ASN 4.7 0.2 + - - -
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Residues in contact with SER 254 (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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250A ASN 2.5 29.3 + - - -
251A LEU* 3.3 10.9 - - - +
253A GLU* 1.3 77.6 - - - +
255A ARG* 1.3 86.5 + - - +
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Residues in contact with ARG 255 (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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4A ILE* 3.5 25.8 + - + +
7A GLN* 3.8 17.4 + - - +
8A THR* 4.1 12.3 - - - +
11A ASP* 2.4 37.4 + - - -
251A LEU* 3.0 20.4 + - - +
254A SER* 1.3 97.8 + - - +
256A ASN* 1.3 71.3 + - - +
257A LEU* 3.2 15.9 - - + +
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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