Contacts of the helix formed by residues 240 - 252 (chain A) in PDB entry 2I91
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 ASP 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 THR* 3.1 14.2 + - - +
239A LYS* 1.3 76.0 - - - +
241A GLU* 1.3 64.5 + - - +
242A LEU* 2.8 37.5 + - - +
243A GLU* 3.4 20.7 + - + +
244A ILE* 3.3 23.4 + - - +
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Residues in contact with GLU 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 LYS 3.3 6.5 + - - +
240A ASP* 1.3 72.4 + - - +
242A LEU* 1.3 73.8 + - + +
244A ILE* 3.0 14.0 + - + +
245A ILE* 3.0 30.5 + - + +
262A HIS* 5.4 5.6 - - + -
265A SER* 2.3 38.5 + - - -
267A GLU* 4.3 7.9 - - - +
268A ILE* 3.4 22.8 + - + +
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Residues in contact with LEU 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 ASP* 2.8 20.0 + - - +
241A GLU* 1.3 86.6 - - + +
243A GLU* 1.3 54.4 + - - +
245A ILE* 3.6 20.2 + - + +
246A HIS* 3.0 28.9 + - - +
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Residues in contact with GLU 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 ARG* 3.3 36.6 + - - +
238A THR* 2.7 28.7 + - - +
240A ASP* 3.4 22.5 + - - +
241A GLU 3.1 0.4 - - - -
242A LEU* 1.3 76.6 - - - +
244A ILE* 1.3 66.9 + - - +
246A HIS* 3.1 11.1 - - + +
247A LEU* 2.9 35.3 + - + +
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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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235A VAL* 4.4 12.5 - - + +
238A THR* 3.7 19.9 - - + +
239A LYS 5.3 0.7 - - - +
240A ASP 3.4 15.3 - - - +
241A GLU* 3.0 15.0 + - - +
243A GLU* 1.3 76.9 - - - +
245A ILE* 1.3 62.6 + - - +
247A LEU* 3.0 9.8 + - - +
248A ILE* 2.9 40.7 + - + +
258A LEU* 4.3 12.8 - - + -
262A HIS* 3.4 46.9 - - + +
268A ILE* 3.7 19.7 - - + -
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Residues in contact with ILE 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 GLU* 3.0 18.8 + - + +
242A LEU* 3.7 22.2 - - + +
244A ILE* 1.3 78.7 - - - +
246A HIS* 1.3 64.5 + - + +
248A ILE* 3.3 4.3 + - - +
249A ASP* 3.1 30.9 + - - +
267A GLU* 3.9 35.7 - - + +
268A ILE* 4.4 12.3 - - + +
271A SER* 4.0 28.0 - - - +
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Residues in contact with HIS 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 LEU 3.0 17.0 + - - +
243A GLU* 3.1 16.6 - - + +
244A ILE 3.1 0.2 - - - -
245A ILE* 1.3 79.1 - - + +
247A LEU* 1.3 60.1 + - + +
249A ASP* 3.1 11.8 + - + +
250A GLU* 2.9 33.0 + - - +
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Residues in contact with LEU 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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231A ALA* 4.0 10.8 - - + +
234A ARG* 3.8 35.4 - - + -
235A VAL* 3.9 17.7 - - + +
238A THR* 5.5 0.4 - - + -
243A GLU* 2.9 33.0 + - + +
244A ILE* 3.6 6.3 - - - +
246A HIS* 1.3 71.9 - - + +
248A ILE* 1.3 58.9 + - - +
250A GLU* 4.4 6.1 - - - +
251A TYR* 2.8 62.3 + - + +
253A LEU* 4.0 14.4 - - + +
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Residues in contact with ILE 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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235A VAL* 5.9 0.7 - - + -
244A ILE* 2.9 39.0 + - + +
245A ILE* 3.4 8.1 - - - +
247A LEU* 1.3 74.9 - - - +
249A ASP* 1.3 59.5 + - - +
252A ARG* 2.9 31.4 + - - -
253A LEU* 3.5 32.8 - - + +
258A LEU* 3.9 18.4 - - + -
268A ILE* 4.5 5.8 - - + -
271A SER* 3.5 32.3 - - - +
272A LEU* 3.7 23.6 - - + -
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Residues in contact with ASP 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 ILE* 3.1 22.1 + - - +
246A HIS* 3.1 14.7 + - + +
248A ILE* 1.3 82.3 - - - +
250A GLU* 1.3 62.4 + - - +
252A ARG* 4.0 7.1 + - - +
271A SER* 4.1 10.6 + - - +
274A GLN* 4.1 16.5 + - - -
220B PRO* 3.9 39.8 - - + +
224B LYS* 5.8 2.3 + - - +
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Residues in contact with GLU 250 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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227A LYS* 5.4 1.9 + - - -
246A HIS* 2.9 21.7 + - - +
247A LEU* 3.3 5.8 + - - +
249A ASP* 1.3 78.9 - - - +
251A TYR* 1.3 102.6 + - + +
252A ARG* 3.7 0.6 + - - +
224B LYS* 4.1 21.3 + - - +
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Residues in contact with TYR 251 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A MET* 5.5 1.7 - - - +
224A LYS* 5.5 1.6 - - + -
227A LYS* 3.6 47.0 + - + +
228A TYR* 3.5 44.9 - + + -
230A GLU* 5.4 0.3 + - - -
231A ALA* 3.3 26.5 - - + -
247A LEU* 2.8 39.2 + - + +
250A GLU* 1.3 107.2 + - + +
252A ARG* 1.3 73.1 + - - +
253A LEU* 3.0 12.3 + - + -
224B LYS* 5.8 1.1 - - - +
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Residues in contact with ARG 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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166A MET* 5.8 6.1 - - - +
228A TYR* 5.1 1.9 + - - -
248A ILE* 2.9 14.1 + - - -
249A ASP 4.0 5.1 + - - +
250A GLU 3.7 2.0 - - - +
251A TYR* 1.3 80.4 - - - +
253A LEU* 1.3 64.2 + - - +
254A VAL* 3.7 11.0 + - - +
257A HIS* 4.8 2.1 + - - -
275A ASP* 3.5 21.6 + - - +
221B GLU* 3.0 54.5 + - + +
224B LYS* 5.6 6.1 - - - +
14D A 2.5 81.6 + - + +
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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