Contacts of the helix formed by residues 247 - 260 (chain A) in PDB entry 5EML
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 SER 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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235A ILE 5.4 0.2 + - - -
237A LEU* 4.2 28.6 - - - +
246A LEU* 1.3 74.8 - - - +
248A LYS* 1.3 66.4 + - - +
249A MET* 3.3 9.1 + - - +
250A HIS* 2.8 36.2 + - - +
251A GLN* 3.0 17.7 + - - +
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Residues in contact with LYS 248 (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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246A LEU 3.7 1.0 + - - -
247A SER* 1.3 70.2 - - - +
249A MET* 1.3 75.5 + - + +
251A GLN* 3.0 30.2 + - - +
252A ARG* 3.0 22.5 + - - +
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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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212A LEU* 4.0 20.7 - - + +
215A ASN* 5.5 5.2 - - - +
247A SER* 3.2 8.6 + - - +
248A LYS* 1.3 87.8 - - + +
250A HIS* 1.3 63.9 + - - +
252A ARG* 3.0 56.4 + - - +
253A LEU* 3.1 12.0 + - - +
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Residues in contact with HIS 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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208A ILE* 4.1 4.3 - - + -
209A GLY 3.0 20.6 + - - -
210A ALA* 3.1 23.2 + - - -
212A LEU* 3.5 32.6 - - + +
235A ILE* 3.5 33.5 - - + +
237A LEU* 6.3 0.9 - - + -
246A LEU* 3.9 22.0 - - + -
247A SER* 2.8 32.7 + - - +
249A MET* 1.3 78.5 - - + +
251A GLN* 1.3 56.8 + - - +
253A LEU* 3.4 5.7 + - + +
254A ILE* 2.9 35.4 + - + +
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Residues in contact with GLN 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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246A LEU* 3.6 18.2 + - + +
247A SER 3.0 9.3 + - - +
248A LYS* 3.0 50.5 + - - +
250A HIS* 1.3 73.5 - - - +
252A ARG* 1.3 67.3 + - - +
254A ILE* 2.9 9.5 + - - +
255A PHE* 2.8 45.3 + - + -
283A TYR* 3.3 22.0 + - - +
286A TYR* 5.7 0.5 - - - -
287A LEU* 3.7 17.9 - - + +
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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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215A ASN* 3.4 29.7 + - - +
248A LYS 3.0 10.5 + - - +
249A MET* 3.0 47.6 + - + +
251A GLN* 1.3 75.7 - - - +
253A LEU* 1.3 62.6 + - - +
255A PHE* 3.2 11.6 + - + +
256A ARG* 3.0 34.9 + - + +
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Residues in contact with LEU 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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157A LEU* 4.1 16.6 - - + -
206A LEU* 5.6 5.6 - - + -
208A ILE* 3.9 35.2 - - + -
212A LEU* 4.2 16.8 - - + -
218A ILE* 4.1 27.6 - - + -
249A MET 3.1 11.2 + - - +
250A HIS* 3.7 9.2 - - - +
252A ARG* 1.3 72.8 - - - +
254A ILE* 1.3 68.0 + - + +
256A ARG* 3.2 15.0 + - + +
257A LEU* 2.9 46.5 + - + +
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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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208A ILE* 4.9 3.1 - - + -
231A LEU* 4.0 27.8 - - + -
246A LEU* 4.0 19.1 - - + -
250A HIS* 2.9 28.5 + - + +
251A GLN* 2.9 9.2 + - - +
253A LEU* 1.3 75.0 - - + +
255A PHE* 1.3 54.2 + - - +
257A LEU* 2.9 12.7 + - + +
258A LEU* 2.7 51.4 + - + +
264A PHE* 3.8 29.4 - - + -
284A LEU* 4.5 9.4 - - + +
287A LEU* 4.3 16.8 - - + -
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Residues in contact with PHE 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 GLN* 2.8 46.6 + - + -
252A ARG* 3.4 11.2 - - + +
254A ILE* 1.3 76.3 - - + +
256A ARG* 1.3 62.0 + - - +
258A LEU* 3.3 12.4 + - + +
259A LYS* 3.2 24.6 + - - +
287A LEU* 3.2 44.9 - - + -
290A ASN* 4.2 9.2 - - + -
291A ARG* 3.7 29.0 - - + -
292A PRO* 5.5 2.7 - - + -
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Residues in contact with ARG 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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215A ASN* 6.0 2.0 - - - +
218A ILE* 4.1 18.2 - - - +
219A ASP* 4.5 10.5 + - - -
222A LEU* 3.4 37.0 - - - +
252A ARG* 3.0 26.7 + - + +
253A LEU* 3.4 16.6 - - + +
255A PHE* 1.3 74.5 - - - +
257A LEU* 1.3 63.5 + - + +
259A LYS* 3.3 18.1 + - - +
260A LEU* 3.3 12.2 + - - +
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Residues in contact with LEU 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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206A LEU* 4.7 12.1 - - + -
208A ILE* 3.9 20.6 - - + -
226A ILE* 4.6 15.7 - - + -
229A ALA* 4.1 14.4 - - + -
253A LEU* 2.9 44.6 + - + +
254A ILE* 3.4 10.3 - - + +
256A ARG* 1.3 73.6 - - + +
258A LEU* 1.3 66.1 + - - +
260A LEU* 3.1 12.1 + - + +
261A GLU 3.0 15.6 + - - -
262A VAL* 3.5 38.9 + - + +
264A PHE* 3.8 8.5 - - + -
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Residues in contact with LEU 258 (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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13A ARG 5.5 1.3 - - - +
14A VAL* 3.8 24.7 - - + -
254A ILE* 2.7 43.3 + - + +
255A PHE* 3.7 20.9 - - + +
256A ARG 3.3 0.2 - - - -
257A LEU* 1.3 71.4 - - - +
259A LYS* 1.3 56.4 + - - +
261A GLU* 2.7 31.5 + - - +
264A PHE* 3.8 21.3 - - + -
284A LEU 5.4 0.7 - - - +
287A LEU 4.6 0.9 - - - -
288A SER* 3.9 29.6 - - - +
291A ARG* 4.2 26.3 + - - +
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Residues in contact with LYS 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 PHE 3.2 12.8 + - - +
256A ARG* 3.3 13.9 - - - +
258A LEU* 1.3 75.8 - - - +
260A LEU* 1.3 57.6 + - - +
261A GLU* 3.6 6.6 + - - +
291A ARG* 5.4 13.0 - - - +
292A PRO* 5.8 2.2 + - - +
294A PRO* 5.9 1.2 - - - +
298A GLU* 3.9 32.3 + - - -
305A GLU* 5.1 2.2 - - - +
507A HIS* 2.9 38.2 + - + -
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Residues in contact with LEU 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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222A LEU 4.5 9.4 - - - +
224A GLU 4.6 1.8 - - - +
226A ILE* 4.4 32.1 - - + +
256A ARG 3.3 8.4 + - - +
257A LEU* 3.1 14.3 + - + +
258A LEU 3.1 0.8 - - - -
259A LYS* 1.3 76.6 - - - +
261A GLU* 1.3 74.7 + - - +
262A VAL* 3.2 9.4 + - + +
507A HIS* 4.1 18.6 - - + +
508A ASN* 3.8 47.6 - - + +
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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