Contacts of the helix formed by residues 241 - 252 (chain A) in PDB entry 3I0W
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 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A GLN* 3.5 14.5 - - - +
239A PRO 3.6 0.6 + - - -
240A VAL* 1.3 76.2 - - - +
242A THR* 1.3 66.9 + - - +
243A TRP* 3.4 12.1 + - - -
244A VAL* 2.9 32.4 + - - +
245A LYS* 3.0 22.8 + - - +
259A LEU* 5.8 2.0 - - - -
282A PHE* 3.0 15.0 - - - -
19B 8OG 2.9 44.2 - - - +
20B G 3.6 15.3 - - - +
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Residues in contact with THR 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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241A ASP* 1.3 78.0 - - - +
243A TRP* 1.3 81.2 + - + +
245A LYS* 2.9 34.5 + - - +
246A LYS* 3.1 23.8 + - - +
18B A 2.9 50.4 + - + +
19B 8OG 4.7 0.9 - - - -
20B G 3.2 18.6 + - - +
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Residues in contact with TRP 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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241A ASP* 3.3 21.6 + - - +
242A THR* 1.3 88.1 - - + +
244A VAL* 1.3 61.3 + - - +
246A LYS* 3.2 30.9 + - + +
247A ALA* 3.0 27.2 + - - +
282A PHE* 3.8 22.9 - + + +
285A ALA* 3.5 42.2 - - + +
286A ARG* 3.6 27.5 - - + +
289A ASN* 3.5 26.7 - - - -
290A ILE* 3.7 11.9 - - + -
18B A 4.1 16.1 - - - -
19B 8OG 2.8 31.8 + - - -
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Residues in contact with VAL 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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238A PHE* 3.9 31.9 - - + -
239A PRO 3.4 23.8 - - - +
240A VAL* 4.1 6.7 - - + -
241A ASP* 2.9 23.8 + - - +
243A TRP* 1.3 72.3 - - - +
245A LYS* 1.3 65.8 + - - +
247A ALA* 3.2 6.4 + - - +
248A MET* 2.9 28.6 + - + +
278A GLN* 3.8 20.4 - - + +
281A LEU* 5.1 4.9 - - + -
282A PHE* 4.0 17.5 - - + +
19B 8OG 3.8 4.9 - - - +
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Residues in contact with LYS 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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240A VAL* 4.0 13.2 - - + +
241A ASP 3.0 15.5 + - - +
242A THR* 2.9 46.2 + - - +
244A VAL* 1.3 78.8 - - - +
246A LYS* 1.3 71.8 + - - +
248A MET* 3.2 2.5 + - - +
249A MET* 2.9 58.6 + - + +
257A VAL 5.8 0.4 - - - +
259A LEU* 3.7 18.8 - - + -
262A ILE* 3.9 13.6 - - + +
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Residues in contact with LYS 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 THR* 3.1 23.1 + - - +
243A TRP* 3.2 33.0 + - + +
245A LYS* 1.3 89.0 - - - +
247A ALA* 1.3 62.5 + - - +
249A MET* 3.3 8.7 + - - +
250A SER* 3.1 23.4 + - - -
289A ASN* 4.8 2.6 - - - +
290A ILE* 3.7 37.8 + - + +
18B A 2.7 30.1 + - - -
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Residues in contact with ALA 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 TRP 3.0 13.7 + - - +
244A VAL* 3.6 7.6 - - - +
246A LYS* 1.3 76.5 - - - +
248A MET* 1.3 62.5 + - - +
250A SER* 3.3 4.2 + - - -
251A LEU* 3.2 31.7 + - + +
281A LEU* 4.1 42.0 - - + +
285A ALA* 4.2 4.7 - - + -
290A ILE* 3.7 10.2 - - + +
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Residues in contact with MET 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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238A PHE* 3.8 27.6 - - + -
244A VAL* 2.9 29.5 + - + +
245A LYS 3.8 3.6 - - - +
247A ALA* 1.3 76.8 - - - +
249A MET* 1.3 58.4 + - - +
252A TYR* 2.8 54.2 + - + +
253A VAL* 2.9 17.8 + - + -
262A ILE* 3.7 27.6 - - + +
265A PHE* 3.6 31.0 - - + -
266A GLY* 4.2 6.5 - - - +
270A PHE* 4.4 2.9 - - + -
281A LEU* 3.9 16.6 - - + -
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Residues in contact with MET 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 LYS* 2.9 53.1 + - + +
246A LYS* 3.3 7.4 + - - +
248A MET* 1.3 76.5 - - - +
250A SER* 1.3 60.3 + - - +
251A LEU 3.4 0.4 - - - -
252A TYR 5.0 0.2 + - - -
253A VAL* 3.2 31.8 + - + +
254A ALA 3.8 7.0 - - - +
255A PRO* 3.2 44.7 - - + +
257A VAL 3.9 17.0 - - - +
262A ILE* 4.3 3.6 - - + -
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Residues in contact with SER 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 LYS 3.1 16.1 + - - -
247A ALA* 3.6 8.3 - - - -
248A MET 3.2 0.2 - - - -
249A MET* 1.3 80.6 - - - +
251A LEU* 1.3 69.4 + - - +
290A ILE* 5.0 7.6 - - - -
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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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97A LEU* 3.4 60.8 - - + +
101A SER* 5.3 2.2 - - - +
247A ALA* 3.2 17.1 + - + +
249A MET 5.1 0.2 - - - -
250A SER* 1.3 91.9 - - - +
252A TYR* 1.3 79.0 + - + +
281A LEU* 3.9 24.5 - - + -
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Residues in contact with TYR 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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95A ASP* 2.7 22.4 + - - -
97A LEU* 3.5 30.4 - - + +
98A LEU* 3.4 22.2 - - + +
248A MET* 2.8 39.4 + - + +
251A LEU* 1.3 94.3 - - + +
253A VAL* 1.3 63.6 + - + +
265A PHE* 3.4 38.5 - + + -
269A LYS* 3.5 22.4 - - + -
270A PHE* 3.6 18.8 - + - -
281A LEU* 5.2 0.2 - - + -
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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