Contacts of the helix formed by residues 242 - 258 (chain A) in PDB entry 3I5Y
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 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A VAL* 4.7 1.3 - - - -
187A ALA 3.5 9.4 - - - +
189A THR* 3.4 38.6 - - - +
190A ARG* 3.5 12.6 - - + +
193A ALA* 4.4 3.1 - - + -
218A LEU 3.3 2.8 + - - -
219A VAL* 3.4 18.1 - - - +
220A GLY 3.7 0.9 + - - -
241A ALA* 1.3 76.5 - - - +
243A PRO* 1.3 74.6 - - + +
244A GLY 3.4 0.8 + - - -
245A ARG 3.4 0.2 + - - -
246A LEU* 3.1 22.6 + - - +
6B U 3.5 12.5 + - - -
7B U 2.9 18.2 + - - -
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Residues in contact with PRO 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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186A VAL* 4.0 8.3 - - + -
187A ALA 3.4 13.5 - - - +
242A THR* 1.3 87.4 - - - +
244A GLY* 1.3 64.0 + - - +
246A LEU* 3.2 2.3 + - - +
247A ILE* 3.0 30.7 + - - +
272A LEU* 4.0 13.7 - - + -
277A PHE* 3.7 25.8 - - + -
280A ASP* 4.0 24.7 - - + +
281A LEU* 4.2 3.4 - - + -
284A ILE* 3.8 16.4 - - + -
6B U 3.7 11.2 - - - +
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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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242A THR 3.4 0.8 - - - -
243A PRO* 1.3 80.7 - - - +
245A ARG* 1.3 61.6 + - - +
247A ILE* 3.4 7.6 + - - +
248A ASP 3.2 15.2 + - - -
280A ASP* 4.7 4.7 + - - -
6B U 3.0 13.9 + - - -
7B U 3.0 38.0 - - - +
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Residues in contact with ARG 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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218A LEU* 3.8 11.9 - - + +
219A VAL* 3.3 27.4 + - - +
220A GLY 3.7 6.7 - - - +
221A GLY 3.7 4.9 - - - +
222A THR* 3.0 41.0 + - - -
223A ASP 4.2 0.6 + - - -
224A PHE* 3.6 42.1 - - - +
227A ALA* 5.1 4.9 - - - +
242A THR 3.4 1.0 + - - +
243A PRO 3.4 0.2 - - - -
244A GLY* 1.3 70.6 - - - +
246A LEU* 1.3 65.5 + - - +
248A ASP* 3.3 2.4 - - - +
249A VAL* 3.0 24.7 + - + +
7B U 2.9 50.6 + - - +
8B U 2.7 34.9 + - - -
9B U 4.8 2.0 + - - -
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Residues in contact with LEU 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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184A VAL* 3.8 25.8 - - + -
186A VAL* 3.9 18.4 - - + -
218A LEU* 4.4 11.6 + - + -
239A VAL* 4.7 2.2 - - + -
241A ALA* 3.8 17.7 - - + -
242A THR 3.1 18.2 + - - +
243A PRO 3.6 3.8 - - - +
245A ARG* 1.3 75.9 - - - +
247A ILE* 1.3 55.4 + - - +
249A VAL* 3.3 3.7 + - + -
250A LEU* 2.8 63.9 + - + +
258A PHE* 4.4 19.3 - - + -
284A ILE* 4.0 20.2 - - + -
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Residues in contact with ILE 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 PRO 3.0 17.7 + - - +
244A GLY* 3.7 6.5 - - - +
246A LEU* 1.3 72.3 - - - +
248A ASP* 1.3 68.8 + - - +
250A LEU* 3.1 6.8 + - + -
251A GLU* 2.9 48.8 + - + +
280A ASP* 3.6 48.0 - - + +
283A THR* 4.2 20.2 - - + -
284A ILE* 3.6 18.2 - - + +
287A ILE* 5.5 1.6 - - + -
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Residues in contact with ASP 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 PHE* 3.2 13.1 - - + -
244A GLY 3.2 6.0 + - - +
245A ARG 3.3 11.0 - - - +
247A ILE* 1.3 80.4 - - - +
249A VAL* 1.3 60.3 + - - +
251A GLU* 3.8 5.2 + - - -
252A LYS* 2.6 53.9 + - - +
7B U 2.6 47.0 + - - +
10B U 2.6 40.6 + - - +
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Residues in contact with VAL 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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218A LEU* 4.1 29.8 - - + -
224A PHE* 3.6 26.2 - - + -
228A MET* 3.6 30.5 - - + -
231A MET* 5.6 1.8 - - + -
245A ARG* 3.0 21.7 + - + +
246A LEU* 3.8 3.1 - - + +
247A ILE 3.2 0.2 - - - -
248A ASP* 1.3 73.1 - - - +
250A LEU* 1.3 61.6 + - - +
252A LYS* 3.1 2.6 + - - -
253A TYR* 2.8 36.0 + - + -
257A PHE* 5.8 0.4 - - + -
258A PHE* 4.4 16.6 - - + -
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Residues in contact with LEU 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 LEU* 2.8 43.2 + - + +
247A ILE* 3.7 4.9 - - - +
249A VAL* 1.3 74.2 - - - +
251A GLU* 1.3 62.4 + - - +
252A LYS 3.0 1.6 + - - -
254A SER* 3.1 38.9 + - - +
258A PHE* 3.6 46.0 - - + -
284A ILE* 4.2 35.0 - - + +
287A ILE* 4.1 22.2 - - + +
288A LEU* 4.1 12.8 - - + -
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Residues in contact with GLU 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 ILE* 2.9 37.1 + - + +
248A ASP* 4.2 5.6 - - - +
249A VAL 3.3 0.4 - - - -
250A LEU* 1.3 76.2 - - - +
252A LYS* 1.3 73.5 + - + +
254A SER* 5.4 0.4 - - - -
283A THR* 5.3 4.3 - - - +
287A ILE* 4.3 18.3 - - + +
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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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224A PHE* 4.6 2.0 - - + -
248A ASP* 2.6 41.0 + - - +
249A VAL 3.1 2.1 + - - +
250A LEU 3.1 0.4 - - - -
251A GLU* 1.3 95.8 + - + +
253A TYR* 1.3 87.8 + - + +
254A SER 3.8 0.9 - - - -
10B U 3.2 43.3 - - - +
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Residues in contact with TYR 253 (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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224A PHE* 4.1 14.8 - + - -
228A MET* 4.0 30.1 - - + +
249A VAL* 2.8 25.0 + - + +
252A LYS* 1.3 97.2 - - + +
254A SER* 1.3 66.2 + - - +
255A ASN* 3.2 3.6 - - - +
256A LYS* 3.2 26.5 + - + +
257A PHE* 3.3 38.3 + + + -
258A PHE* 3.7 5.2 - - - -
10B U 3.3 26.9 + - - -
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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 LEU* 3.1 29.7 + - - -
251A GLU 5.4 0.3 - - - -
252A LYS 3.8 0.6 - - - -
253A TYR* 1.3 77.2 - - - +
255A ASN* 1.3 58.7 + - - +
258A PHE* 2.9 44.9 + - - +
259A ARG* 3.6 2.7 + - - +
287A ILE* 3.9 19.4 - - - +
288A LEU* 6.0 0.2 - - - -
291A LYS* 3.2 33.0 - - - +
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Residues in contact with ASN 255 (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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180A MET* 5.7 1.4 - - - +
253A TYR* 3.2 1.4 - - - -
254A SER* 1.3 82.7 + - - +
256A LYS* 1.3 61.4 + - - +
258A PHE 4.6 0.2 + - - -
259A ARG* 3.0 39.6 + - - +
260A PHE* 6.0 0.2 - - - -
291A LYS* 3.2 29.4 - - - +
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Residues in contact with LYS 256 (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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180A MET* 3.6 10.8 - - - +
232A ASN* 3.1 30.7 + - - +
235A ARG* 3.3 29.3 + - - +
253A TYR* 3.2 22.4 + - + +
255A ASN* 1.3 82.1 - - - +
257A PHE* 1.3 85.0 + - + +
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Residues in contact with PHE 257 (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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179A TYR 5.0 2.0 - - - -
180A MET* 4.1 11.1 - - - +
181A VAL* 3.1 34.5 + - + +
228A MET* 4.8 7.4 - - + -
231A MET* 3.5 59.0 - - + -
232A ASN* 3.4 24.7 - - - -
235A ARG* 3.8 30.1 - - - -
236A PRO* 5.3 2.5 - - + -
249A VAL* 5.8 0.2 - - + -
253A TYR* 3.3 30.5 + + + -
256A LYS* 1.3 99.4 - - + +
258A PHE* 1.3 75.2 + + + +
259A ARG 3.7 3.2 + - - -
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Residues in contact with PHE 258 (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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181A VAL* 4.0 26.7 - - + -
184A VAL* 4.0 12.3 - - + -
218A LEU* 4.4 5.4 - - + -
231A MET* 4.0 21.1 - - + -
239A VAL* 4.2 9.2 - - + -
246A LEU* 4.4 15.9 - - + -
249A VAL* 4.4 13.5 - - + -
250A LEU* 3.6 27.6 - - + -
253A TYR 3.7 12.6 - - - -
254A SER* 2.9 20.3 + - - +
257A PHE* 1.3 94.9 - + + +
259A ARG* 1.3 62.2 + - - +
260A PHE 3.3 4.0 + - - -
261A VAL* 3.7 16.3 + - + +
288A LEU* 4.0 30.4 - - + +
291A LYS* 4.8 5.0 - - + +
292A ASN* 5.1 0.5 + - - -
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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