Contacts of the helix formed by residues 248 - 256 (chain A) in PDB entry 5ETE
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 248 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A GLU* 3.2 22.7 - - - +
236A ASN* 3.7 32.8 - - + +
237A TYR* 3.8 27.5 - - + +
243A GLY 4.3 2.4 + - - -
245A SER* 2.7 31.9 + - - +
247A ASN* 1.3 84.2 - - - +
249A GLY* 1.3 56.1 + - - +
250A HIS 3.4 0.2 + - - -
251A PHE* 3.4 5.5 + - - +
252A THR* 3.1 28.4 + - - +
301A DIO 4.1 5.1 - - - +
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Residues in contact with GLY 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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216A ASN* 4.3 1.4 - - - +
233A GLU* 3.4 0.8 + - - -
244A PHE* 4.0 13.5 - - - -
245A SER 3.3 13.9 + - - -
246A SER 4.6 3.3 + - - -
247A ASN 3.9 0.2 - - - -
248A THR* 1.3 75.0 - - - +
250A HIS* 1.3 64.6 + - - +
252A THR* 3.4 11.7 + - - -
253A GLN* 3.5 7.1 + - - +
286A ASN* 2.9 28.2 + - - -
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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 HIS* 5.9 4.8 + + - -
215A GLU 5.2 0.7 - - - -
216A ASN* 3.2 37.5 + - + +
217A LEU* 4.1 14.6 + - - +
230A TRP* 3.7 35.2 - + + -
233A GLU* 2.8 29.8 + - - +
246A SER 5.3 8.2 + - - -
249A GLY* 1.3 75.7 - - - +
251A PHE* 1.3 65.1 - - - +
253A GLN 3.3 2.1 + - - -
254A VAL* 3.0 26.9 + - - +
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Residues in contact with PHE 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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177A HIS* 3.9 12.3 - + - -
230A TRP 3.4 19.3 + - - +
231A TYR* 3.9 26.5 - + - +
233A GLU* 3.2 15.3 + - + -
234A ILE* 3.6 48.2 - - + +
237A TYR* 3.8 31.4 - + + -
239A PHE* 4.4 4.0 - + - -
248A THR* 3.6 7.9 - - - +
250A HIS* 1.3 78.8 - - - +
252A THR* 1.3 71.3 + - + +
254A VAL* 3.1 14.6 + - - +
255A VAL* 3.2 27.1 + - + +
295A VAL* 4.0 18.2 - - + -
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Residues in contact with THR 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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237A TYR* 3.7 30.7 - - + -
243A GLY 4.9 0.7 - - - +
244A PHE* 6.0 0.2 - - - -
248A THR* 3.1 20.7 + - - +
249A GLY* 3.4 8.3 + - - -
250A HIS 3.3 0.2 - - - -
251A PHE* 1.3 85.0 - - + +
253A GLN* 1.3 56.0 + - - +
255A VAL* 3.9 6.9 - - - +
256A TRP* 3.1 33.5 + - - +
286A ASN* 2.6 27.0 + - - -
291A TYR* 3.9 11.9 - - + -
295A VAL* 3.8 20.1 - - + +
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Residues in contact with GLN 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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174A ARG* 4.5 1.7 + - - -
183A LEU* 6.0 0.2 - - - +
214A GLY* 3.6 20.4 - - - -
215A GLU 4.1 3.5 + - - +
216A ASN* 3.8 10.8 - - - +
249A GLY 3.5 16.6 + - - +
250A HIS 3.3 4.8 + - - +
251A PHE 3.2 0.8 - - - -
252A THR* 1.3 77.1 + - - +
254A VAL* 1.3 64.8 + - - +
255A VAL 3.3 0.2 + - - -
256A TRP* 3.4 8.0 + - - +
259A THR* 3.2 25.3 + - - -
281A TYR* 3.6 45.4 - - + +
285A GLY* 3.0 27.8 + - - +
286A ASN* 3.8 10.3 + - - +
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Residues in contact with VAL 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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170A HIS* 4.3 26.4 - - + +
173A LYS* 4.6 10.8 - - + -
174A ARG* 3.0 25.6 + - + -
183A LEU* 4.7 4.0 - - - +
216A ASN* 3.9 13.0 - - - +
227A VAL* 5.0 6.3 - - + +
230A TRP* 4.1 21.3 - - + -
231A TYR* 4.4 19.1 - - + +
250A HIS 3.0 18.7 + - - +
251A PHE* 3.1 10.5 + - - +
253A GLN* 1.3 77.6 - - - +
255A VAL* 1.3 65.9 + - + +
281A TYR* 4.3 8.3 - - - +
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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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174A ARG* 3.4 18.2 - - + +
177A HIS* 3.8 36.8 - - + +
180A THR* 3.5 18.3 + - + +
231A TYR* 3.9 18.4 - - + -
251A PHE* 3.2 28.9 + - + +
252A THR* 4.1 4.3 - - - +
254A VAL* 1.3 77.9 - - + +
256A TRP* 1.3 65.7 + - - +
257A LYS 3.0 4.0 + - - -
294A ASN 3.5 4.2 - - - +
295A VAL* 4.0 25.7 - - + -
296A GLU 5.3 1.6 + - - +
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Residues in contact with TRP 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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174A ARG* 3.0 18.1 + - - +
252A THR 3.1 28.2 + - - +
253A GLN* 3.4 12.4 + - - +
255A VAL* 1.3 72.5 - - - +
257A LYS* 1.3 66.9 + - - +
258A SER* 3.2 18.6 + - - -
259A THR* 3.2 32.3 + - - +
284A ALA 3.7 8.0 + - - -
285A GLY* 3.5 16.8 - - - -
286A ASN* 3.4 26.9 - - - -
287A TYR* 3.6 29.0 - + + -
290A GLU* 3.8 22.9 - - + -
291A TYR* 3.9 21.5 - + - -
294A ASN* 3.4 38.5 + - + +
295A VAL* 3.9 8.1 - - + -
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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