Contacts of the helix formed by residues 294 - 306 (chain I) in PDB entry 2X86
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 294 (chain I).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171I TYR* 3.6 1.8 + - - -
211I PHE 5.5 0.4 - - - -
237I THR* 5.3 0.4 - - - -
239I ARG* 3.4 31.4 - - - +
241I GLU* 4.2 6.3 - - - -
292I PHE 3.4 1.5 + - - +
293I LYS* 1.3 74.8 - - - +
295I VAL* 1.3 60.1 + - - +
296I ALA* 3.5 9.6 + - - +
297I GLU* 2.7 39.3 + - - +
298I GLY* 2.8 26.9 + - - -
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Residues in contact with VAL 295 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171I TYR* 3.8 8.1 - - - +
211I PHE* 3.6 44.7 + - + +
241I GLU* 3.1 33.1 + - + +
245I ALA* 4.0 10.8 - - + +
246I VAL* 3.8 34.8 - - + +
249I ALA* 4.5 2.0 - - + -
294I THR* 1.3 73.1 - - - +
296I ALA* 1.3 67.3 + - - +
299I VAL* 2.9 37.2 + - + +
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Residues in contact with ALA 296 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241I GLU* 4.8 1.4 + - - -
249I ALA* 4.3 12.2 - - + +
294I THR* 3.3 9.6 + - - +
295I VAL* 1.3 81.6 - - - +
297I GLU* 1.3 54.5 + - + +
300I THR* 2.5 36.5 + - - +
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Residues in contact with GLU 297 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292I PHE 4.2 1.6 - - - +
293I LYS* 3.3 20.3 - - + -
294I THR* 2.7 46.8 + - - +
296I ALA* 1.3 80.5 - - + +
298I GLY* 1.3 65.0 + - - +
300I THR* 3.3 6.2 + - - -
301I GLU* 3.0 24.1 + - - +
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Residues in contact with GLY 298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171I TYR* 3.2 22.2 - - - -
213I TYR* 3.7 18.8 - - - -
293I LYS* 4.3 7.4 - - - +
294I THR 2.8 14.3 + - - -
297I GLU* 1.3 74.3 - - - +
299I VAL* 1.3 56.9 + - - +
301I GLU* 3.3 5.6 + - - +
302I TYR* 2.9 29.6 + - - +
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Residues in contact with VAL 299 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171I TYR* 3.6 23.8 + - + -
185I ALA* 4.7 4.0 - - + -
246I VAL* 4.2 16.4 - - + +
249I ALA* 3.7 18.2 - - + -
250I THR* 3.4 28.5 - - - +
295I VAL* 2.9 39.2 + - + +
298I GLY* 1.3 71.1 - - - -
300I THR* 1.3 58.7 + - - +
302I TYR* 3.3 5.2 + - - +
303I MET* 2.8 47.0 + - + +
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Residues in contact with THR 300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249I ALA* 3.7 25.6 - - + +
252I ALA* 5.6 2.5 - - + -
253I TYR* 4.3 21.2 - - + +
296I ALA 2.5 25.6 + - - +
297I GLU* 3.3 8.1 + - - -
299I VAL* 1.3 77.2 - - - +
301I GLU* 1.3 61.6 + - - +
303I MET* 3.1 5.8 + - - +
304I ALA* 3.0 23.4 + - - +
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Residues in contact with GLU 301 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213I TYR* 3.4 24.0 + - - +
293I LYS* 2.9 38.7 + - - +
297I GLU 3.0 17.4 + - - +
298I GLY* 3.3 4.9 + - - +
300I THR* 1.3 77.7 - - - +
302I TYR* 1.3 62.7 + - - +
304I ALA* 3.4 6.7 + - - +
305I TRP* 3.1 21.6 + - + +
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Residues in contact with TYR 302 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171I TYR* 3.9 11.2 - + + -
172I GLY* 3.0 35.7 + - - -
173I PRO* 3.3 21.3 - - + +
174I ARG 5.1 0.4 + - - -
175I GLU* 2.6 34.3 + - - +
183I SER* 3.9 9.9 - - - -
185I ALA* 4.0 15.0 - - + -
186I PHE* 3.3 19.1 - - - -
213I TYR* 4.1 11.4 - - + -
298I GLY 2.9 16.9 + - - +
299I VAL* 3.4 5.4 - - - +
301I GLU* 1.3 74.2 - - - +
303I MET* 1.3 62.5 + - + +
305I TRP* 3.1 6.5 + + - +
306I LEU* 2.8 58.1 + - + +
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Residues in contact with MET 303 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185I ALA* 3.6 32.3 - - + +
189I ASN* 3.6 28.7 - - + +
249I ALA 5.1 0.2 - - - +
250I THR* 3.6 29.6 - - + +
253I TYR* 3.5 38.1 + - + -
254I HIS* 3.9 9.4 - - - -
299I VAL* 2.8 38.4 + - + +
300I THR* 3.1 3.8 + - - +
302I TYR* 1.3 74.8 - - + +
304I ALA* 1.3 62.4 + - - +
306I LEU* 3.3 12.0 + - + -
307I ASN* 2.6 28.9 + - - +
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Residues in contact with ALA 304 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253I TYR* 3.4 21.3 + - + +
300I THR 3.0 11.2 + - - +
301I GLU* 3.5 11.4 - - + +
302I TYR 3.2 0.2 - - - -
303I MET* 1.3 77.3 - - - +
305I TRP* 1.3 62.4 + - - +
307I ASN 3.1 21.3 + - - -
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Residues in contact with TRP 305 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173I PRO* 3.6 49.9 - - + +
174I ARG* 4.0 29.2 - - + +
213I TYR* 5.7 0.9 - - - +
301I GLU* 3.1 9.9 + - + +
302I TYR* 3.1 8.8 + + - +
304I ALA* 1.3 80.2 - - - +
306I LEU* 1.3 88.3 + - + +
307I ASN* 3.1 3.5 + - - +
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Residues in contact with LEU 306 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186I PHE* 4.1 24.9 - - + -
189I ASN* 3.6 38.8 + - + +
193I ASN* 5.2 0.9 + - - -
302I TYR* 2.8 52.5 + - + +
303I MET* 4.1 12.3 - - + -
304I ALA 3.2 0.6 - - - -
305I TRP* 1.3 91.1 - - + +
307I ASN* 1.3 76.0 + - - +
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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