Contacts of the helix formed by residues 241 - 255 (chain A) in PDB entry 4EY6
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 MET 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A PRO* 3.4 45.6 - - + +
163A GLY* 4.9 2.0 - - - +
240A GLY* 1.3 69.9 - - - -
242A GLY* 1.3 58.3 + - - +
244A ALA* 3.2 2.6 + - - +
245A ARG* 2.9 28.3 + - - +
302A VAL* 3.8 5.1 - - + +
303A VAL 3.5 17.4 + - - +
304A ASP* 3.7 30.7 - - + +
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Residues in contact with GLY 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 GLY 3.3 0.6 - - - -
241A MET* 1.3 79.0 - - - +
243A GLU* 1.3 57.9 + - - +
245A ARG* 3.4 6.9 + - - +
246A ARG* 3.1 25.9 + - - +
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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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239A VAL* 3.5 19.3 - - + -
240A GLY* 3.3 6.8 + - - +
242A GLY* 1.3 73.5 - - - +
244A ALA* 1.3 65.0 + - - +
246A ARG* 2.8 44.7 + - - +
247A ARG* 2.9 54.7 + - - +
290A PRO* 3.6 10.3 - - - +
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Residues in contact with ALA 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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158A PHE 5.9 0.4 - - - +
160A ALA* 3.4 26.5 + - + +
162A PRO* 4.5 1.1 - - + -
239A VAL* 3.9 14.3 - - + +
240A GLY 2.9 17.9 + - - +
241A MET* 3.5 5.4 - - - +
243A GLU* 1.3 77.2 - - - +
245A ARG* 1.3 56.9 + - - +
247A ARG* 3.2 7.5 + - - +
248A ALA* 3.0 25.1 + - - +
299A PHE* 5.3 1.7 - - - -
302A VAL* 3.8 19.7 - - + -
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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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160A ALA 3.8 9.4 + - - -
161A LEU* 3.7 21.0 - - + +
162A PRO* 3.1 31.6 + - + +
241A MET 2.9 16.0 + - - +
242A GLY* 3.7 8.1 - - - +
244A ALA* 1.3 73.4 - - - +
246A ARG* 1.3 64.2 + - - +
248A ALA* 3.4 1.2 + - - +
249A THR* 2.8 37.7 + - - +
266A ASP* 2.8 41.0 + - - -
269A LEU* 6.2 0.2 - - - +
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Residues in contact with ARG 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 GLY 3.1 16.5 + - - +
243A GLU* 2.8 41.4 + - - +
244A ALA 3.3 0.4 - - - -
245A ARG* 1.3 77.3 - - - +
247A ARG* 1.3 63.5 + - - +
249A THR* 3.3 7.0 + - - -
250A GLN* 2.9 45.5 + - + +
288A VAL 3.2 26.6 + - - -
289A LEU 5.4 0.2 - - - -
290A PRO* 3.5 25.3 - - - +
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Residues in contact with ARG 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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239A VAL* 4.0 18.1 - - - +
243A GLU* 2.9 47.9 + - - +
244A ALA* 3.7 5.4 - - - +
246A ARG* 1.3 91.3 - - - +
248A ALA* 1.3 64.7 + - - +
250A GLN* 3.3 5.7 + - - +
251A LEU* 2.9 24.3 + - - +
288A VAL* 3.8 23.8 - - + +
289A LEU* 3.9 17.2 - - - +
290A PRO* 4.2 6.5 - - - +
296A ARG* 6.0 4.4 - - - +
297A PHE 3.0 18.2 + - - -
298A SER* 2.7 39.9 + - - +
299A PHE* 4.1 12.3 - - + -
300A VAL* 4.9 2.2 - - - +
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Residues in contact with ALA 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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159A LEU* 3.7 34.5 - - + +
160A ALA 3.6 16.4 - - - +
161A LEU* 3.8 20.0 - - + -
244A ALA 3.0 17.8 + - - +
245A ARG 3.9 0.2 - - - +
247A ARG* 1.3 76.1 - - - +
249A THR* 1.3 61.8 + - - +
251A LEU* 3.3 3.3 + - - +
252A ALA* 3.1 22.3 + - - +
269A LEU* 4.4 4.7 - - + +
273A LEU* 4.8 0.5 - - - +
299A PHE* 4.2 3.0 - - + -
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Residues in contact with THR 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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161A LEU* 4.3 7.1 - - - +
245A ARG* 2.8 31.2 + - - +
246A ARG* 3.5 6.7 - - - -
248A ALA* 1.3 74.7 - - - +
250A GLN* 1.3 64.4 + - - +
252A ALA* 3.2 7.9 + - + +
253A HIS* 3.1 22.7 + - + +
258A PRO 5.7 4.7 - - - +
269A LEU* 4.4 15.1 - - + +
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Residues in contact with GLN 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 ARG* 2.9 29.6 + - + +
247A ARG* 3.7 7.4 - - - +
249A THR* 1.3 76.2 - - - +
251A LEU* 1.3 64.0 + - - +
253A HIS* 3.5 14.2 + - - +
254A LEU* 3.0 46.2 + - + +
287A HIS 3.6 16.2 + - - -
288A VAL* 3.8 23.7 - - + +
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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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155A ALA* 3.9 15.3 - - + -
159A LEU* 3.9 16.4 - - + -
247A ARG 2.9 16.2 + - - +
248A ALA 3.7 5.6 - - - +
249A THR 3.2 0.4 - - - -
250A GLN* 1.3 73.9 - - - +
252A ALA* 1.3 67.7 + - - +
254A LEU* 3.1 11.6 + - - +
255A VAL* 3.2 23.7 + - + +
273A LEU* 4.8 5.4 - - + -
281A LEU* 4.1 28.0 - - + +
284A HIS* 4.0 35.2 - - + +
285A GLU* 4.6 2.2 - - - +
288A VAL* 4.2 10.1 - - + +
299A PHE* 3.8 23.6 - - + -
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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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248A ALA 3.1 13.6 + - - +
249A THR 3.2 8.7 + - - +
251A LEU* 1.3 76.2 - - - +
253A HIS* 1.3 61.5 + - - +
255A VAL* 3.2 3.3 + - - +
256A GLY 3.1 4.9 + - - -
257A CYS* 2.8 43.4 + - + +
258A PRO 4.8 1.3 - - - -
269A LEU* 3.8 33.0 - - + -
273A LEU* 3.9 14.8 - - + +
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Residues in contact with HIS 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 THR* 3.1 14.1 + - + +
250A GLN* 3.7 22.1 + - - +
252A ALA* 1.3 77.1 - - - +
254A LEU* 1.3 73.9 + - + +
255A VAL 3.2 1.0 + - - -
256A GLY* 3.2 12.0 + - - -
257A CYS 3.7 9.6 + - - +
258A PRO 5.7 0.2 - - - -
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Residues in contact with LEU 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 GLN* 3.0 43.9 + - + +
251A LEU* 3.1 5.1 + - - +
253A HIS* 1.3 87.2 - - + +
255A VAL* 1.3 58.3 + - - +
256A GLY 3.5 0.4 + - - -
284A HIS* 3.8 46.1 + - + +
287A HIS* 3.6 31.4 - - + +
288A VAL* 4.0 13.2 - - + -
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Residues in contact with VAL 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 LEU* 3.2 26.6 + - + +
252A ALA 3.5 10.3 - - - +
253A HIS 3.1 0.4 - - - -
254A LEU* 1.3 79.7 - - - +
256A GLY* 1.3 54.7 + - - +
257A CYS* 4.0 8.1 - - - -
273A LEU* 3.9 22.4 - - + -
276A ARG* 2.7 40.9 + - + +
280A VAL* 4.0 22.3 - - + +
281A LEU* 4.3 5.4 - - + -
284A HIS* 3.6 27.1 - - + -
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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