Contacts of the helix formed by residues 251 - 270 (chain A) in PDB entry 3IEU
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 GLY 251 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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247A ILE* 3.3 28.1 - - - +
248A GLY 3.0 6.2 + - - -
249A ASN 3.0 1.2 + - - -
250A LYS* 1.3 76.8 - - - +
252A ALA* 1.3 58.7 + - - +
253A LYS 3.4 2.7 - - - -
254A ILE* 3.4 6.4 - - - +
255A LYS* 3.1 27.5 + - - +
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Residues in contact with ALA 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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249A ASN 3.2 13.4 + - - +
250A LYS* 3.2 15.7 - - + -
251A GLY* 1.3 77.1 - - - +
253A LYS* 1.3 59.8 + - - +
255A LYS* 3.5 11.0 - - + +
256A THR* 2.9 37.0 + - - +
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Residues in contact with LYS 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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205A PHE* 3.7 35.6 + - + +
206A LEU* 4.2 12.6 - - + -
209A GLU* 4.2 14.1 + - - -
245A MET 3.9 10.1 - - - +
246A VAL 3.3 15.5 - - - +
247A ILE 3.2 7.6 + - - +
248A GLY* 3.5 13.5 - - - -
249A ASN 4.6 1.3 + - - +
252A ALA* 1.3 78.9 - - - +
254A ILE* 1.3 57.6 - - - +
255A LYS 3.3 0.2 + - - -
256A THR* 3.3 4.8 + - - -
257A ILE* 3.0 35.9 + - + +
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Residues in contact with ILE 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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235A ILE* 4.0 18.8 - - + -
246A VAL* 3.3 16.5 + - + +
247A ILE* 3.2 24.1 + - + +
251A GLY* 3.4 14.1 - - - +
253A LYS* 1.3 76.2 - - - +
255A LYS* 1.3 67.6 + - - +
257A ILE* 4.0 8.1 - - + -
258A GLY* 3.2 17.3 + - - -
277A LEU* 3.8 37.4 - - + +
279A VAL* 4.1 19.1 - - + -
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Residues in contact with LYS 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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251A GLY 3.1 17.7 + - - +
252A ALA* 3.5 11.9 - - - +
253A LYS 3.1 0.6 - - - -
254A ILE* 1.3 85.8 - - + +
256A THR* 1.3 57.1 + - - +
258A GLY* 3.4 1.2 + - - -
259A ILE* 3.0 47.4 + - + +
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Residues in contact with THR 256 (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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205A PHE* 3.6 37.7 - - + -
252A ALA* 2.9 19.2 + - - +
253A LYS* 3.7 4.9 - - - -
255A LYS* 1.3 76.1 - - - +
257A ILE* 1.3 60.6 + - - +
259A ILE* 3.1 10.1 + - + +
260A GLU* 2.8 36.9 + - + +
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Residues in contact with ILE 257 (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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198A ILE* 4.9 4.3 - - + +
201A LYS* 4.1 21.1 - - + +
202A LEU* 3.5 35.7 - - + +
205A PHE* 4.1 28.5 - - + -
206A LEU* 4.7 5.6 - - + -
235A ILE* 5.0 0.9 - - + -
246A VAL* 4.6 5.2 - - + +
253A LYS* 3.0 34.0 + - + +
254A ILE* 4.1 12.8 - - + +
256A THR* 1.3 75.4 - - - +
258A GLY* 1.3 58.8 + - - +
260A GLU* 3.4 2.6 + - - +
261A ALA* 2.9 30.5 + - + +
277A LEU* 3.9 17.0 - - + -
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Residues in contact with GLY 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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254A ILE 3.2 11.6 + - - -
255A LYS 3.7 3.4 - - - -
257A ILE* 1.3 79.5 - - - +
259A ILE* 1.3 62.0 + - - +
262A ARG* 2.9 28.6 + - - +
275A LEU* 3.7 10.0 - - - +
277A LEU* 3.6 20.1 - - - +
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Residues in contact with ILE 259 (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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255A LYS* 3.0 42.6 + - + +
256A THR* 3.1 10.5 + - + +
258A GLY* 1.3 74.9 - - - +
260A GLU* 1.3 78.5 + - - +
262A ARG* 3.5 17.0 + - - +
263A LYS* 3.0 24.1 + - + +
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Residues in contact with GLU 260 (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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201A LYS* 3.7 27.3 - - + -
205A PHE* 3.7 26.2 - - + -
256A THR* 2.8 25.7 + - + +
259A ILE* 1.3 88.3 - - - +
261A ALA* 1.3 57.4 + - - +
263A LYS* 3.3 31.8 + - - +
264A ASP* 2.9 33.8 + - - +
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Residues in contact with ALA 261 (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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197A ILE* 3.8 18.0 - - + +
198A ILE* 4.4 11.4 - - + -
201A LYS* 4.0 10.7 - - + +
257A ILE* 2.9 20.7 + - + +
258A GLY* 4.6 0.2 - - - -
260A GLU* 1.3 75.3 - - - +
262A ARG* 1.3 59.2 + - - +
265A MET* 2.9 53.4 + - + +
275A LEU* 3.8 7.9 - - + -
277A LEU* 5.4 0.7 - - + -
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Residues in contact with ARG 262 (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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258A GLY 2.9 19.3 + - - +
259A ILE* 3.9 23.1 + - - +
261A ALA* 1.3 75.8 - - - +
263A LYS* 1.3 68.6 - - - +
265A MET* 3.5 6.3 - - - +
266A GLN* 3.0 45.6 + - - +
273A VAL* 3.3 31.2 + - + +
274A HIS* 4.9 0.2 - - - +
275A LEU* 3.5 29.5 - - + +
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Residues in contact with LYS 263 (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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259A ILE* 3.0 15.9 + - + +
260A GLU* 3.3 32.7 + - - +
261A ALA 3.1 0.2 - - - -
262A ARG* 1.3 77.9 - - - +
264A ASP* 1.3 77.7 + - - +
265A MET 2.9 5.4 + - - -
266A GLN* 2.9 22.7 + - - +
267A GLU* 3.2 22.5 + - + +
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Residues in contact with ASP 264 (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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197A ILE* 3.9 24.1 - - + +
200A GLU* 3.9 4.7 - - - +
201A LYS* 2.7 35.7 + - - -
260A GLU* 2.9 17.7 + - - +
263A LYS* 1.3 87.2 - - - +
265A MET* 1.3 56.9 + - - +
267A GLU* 3.7 13.3 + - - +
268A MET* 3.1 28.9 + - - +
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Residues in contact with MET 265 (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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194A ALA* 4.2 13.2 - - - +
197A ILE* 3.8 23.5 - - + +
198A ILE* 4.3 12.3 - - + -
231A ILE* 3.7 25.4 - - - -
261A ALA* 2.9 47.0 + - + +
262A ARG* 3.5 6.5 - - - +
263A LYS 2.9 1.0 + - - -
264A ASP* 1.3 76.0 - - - +
266A GLN* 1.3 59.5 + - - +
268A MET* 3.4 1.1 + - - -
269A PHE* 2.9 50.4 + - + -
273A VAL* 4.1 12.3 - - + -
275A LEU* 3.3 29.8 - - + -
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Residues in contact with GLN 266 (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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262A ARG* 3.0 39.7 + - - +
263A LYS* 2.9 11.6 + - - +
265A MET* 1.3 74.6 - - - +
267A GLU* 1.3 53.3 + - - +
269A PHE* 4.9 0.2 - - - -
270A GLU* 2.7 35.5 + - - -
271A ALA 2.9 25.8 + - - +
272A PRO* 3.8 4.3 - - - +
273A VAL* 2.9 41.7 + - + +
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Residues in contact with GLU 267 (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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263A LYS* 3.2 18.8 + - + +
264A ASP* 3.8 20.6 - - - +
266A GLN* 1.3 80.7 - - - +
268A MET* 1.3 59.5 + - - +
270A GLU* 3.5 18.9 + - - +
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Residues in contact with MET 268 (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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193A MET* 3.6 47.3 - - + -
197A ILE* 4.6 11.2 - - + -
264A ASP 3.1 18.5 + - - +
265A MET 4.1 2.0 - - - +
266A GLN 3.4 0.2 - - - -
267A GLU* 1.3 77.5 - - - +
269A PHE* 1.3 76.1 + - + +
270A GLU* 4.4 6.4 - - - +
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Residues in contact with PHE 269 (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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190A GLN* 3.5 53.4 - - + +
193A MET* 4.2 7.4 - - + -
194A ALA* 4.3 7.0 - - + -
197A ILE* 5.5 0.7 - - + -
221A PHE* 3.8 23.6 - + - -
229A TYR* 4.1 30.7 - + + -
231A ILE* 4.2 4.0 - - + -
265A MET* 2.9 37.9 + - + +
266A GLN* 4.3 1.8 - - - +
268A MET* 1.3 103.3 - - + +
270A GLU* 1.3 72.0 + - - +
271A ALA* 3.1 7.8 + - + +
273A VAL* 4.5 7.4 - - + -
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Residues in contact with GLU 270 (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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266A GLN 2.7 12.2 + - - -
267A GLU* 3.8 13.0 - - - +
268A MET 3.3 7.8 - - - +
269A PHE* 1.3 79.0 - - - +
271A ALA* 1.3 59.1 + - - +
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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