Contacts of the helix formed by residues 294 - 306 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A TYR* 3.6 1.9 + - - -
211A PHE 5.5 0.2 - - - -
237A THR* 5.3 0.4 - - - -
239A ARG* 3.4 30.5 - - - +
241A GLU* 4.2 7.2 - - - +
292A PHE 3.4 2.2 + - - +
293A LYS* 1.3 74.8 - - - +
295A VAL* 1.3 59.3 + - - +
296A ALA* 3.5 9.6 + - - +
297A GLU* 2.7 40.4 + - - +
298A GLY* 2.8 27.2 + - - -
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Residues in contact with VAL 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 3.8 8.3 - - - +
211A PHE* 3.6 44.5 + - + +
237A THR* 5.9 0.2 - - - +
241A GLU* 3.1 33.6 + - + +
245A ALA* 4.0 9.9 - - + +
246A VAL* 3.8 35.0 - - + +
249A ALA* 4.5 2.2 - - + -
294A THR* 1.3 73.5 - - - +
296A ALA* 1.3 66.7 + - - +
299A VAL* 2.9 32.9 + - + +
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Residues in contact with ALA 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
241A GLU* 5.1 1.2 + - - -
249A ALA* 4.3 13.4 - - + +
294A THR* 3.3 9.6 + - - +
295A VAL* 1.3 81.9 - - - +
297A GLU* 1.3 55.1 + - + +
300A THR* 2.5 36.6 + - - +
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Residues in contact with GLU 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
292A PHE 4.2 1.6 - - - +
293A LYS* 3.3 21.6 - - + -
294A THR* 2.7 46.2 + - - +
296A ALA* 1.3 79.9 - - + +
298A GLY* 1.3 62.9 + - - +
300A THR* 3.3 6.1 + - - -
301A GLU* 3.0 24.6 + - - +
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Residues in contact with GLY 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 3.2 21.5 - - - -
213A TYR* 3.7 18.4 - - - -
293A LYS* 4.2 8.8 - - - +
294A THR 2.8 14.8 + - - -
297A GLU* 1.3 74.1 - - - +
299A VAL* 1.3 55.9 + - - +
301A GLU* 3.3 5.0 + - - +
302A TYR* 2.9 30.0 + - - +
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Residues in contact with VAL 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171A TYR* 3.6 23.8 + - + -
185A ALA* 4.7 3.4 - - + -
246A VAL* 4.2 17.0 - - + +
249A ALA* 3.7 17.9 - - + -
250A THR* 3.4 28.0 - - - +
295A VAL* 2.9 39.0 + - + +
298A GLY* 1.3 71.6 - - - -
300A THR* 1.3 58.5 + - - +
302A TYR* 3.3 4.8 + - - +
303A MET* 2.8 46.7 + - + +
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Residues in contact with THR 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A ALA* 3.8 24.9 - - + +
252A ALA* 5.6 2.5 - - + -
253A TYR* 4.3 21.8 - - + +
296A ALA 2.5 25.6 + - - +
297A GLU* 3.3 8.1 + - - -
298A GLY 3.3 0.2 - - - -
299A VAL* 1.3 77.4 - - - +
301A GLU* 1.3 61.2 + - - +
303A MET* 3.1 6.6 + - - +
304A ALA* 3.0 23.2 + - - +
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Residues in contact with GLU 301 (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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213A TYR* 3.3 24.0 + - - +
293A LYS* 2.9 38.7 + - - +
297A GLU 3.0 17.2 + - - +
298A GLY* 3.3 5.3 + - - +
300A THR* 1.3 76.5 - - - +
302A TYR* 1.3 62.1 + - - +
304A ALA* 3.4 8.0 + - + +
305A TRP* 3.1 21.8 + - + +
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Residues in contact with TYR 302 (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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171A TYR* 4.0 11.2 - + + -
172A GLY* 3.0 35.4 + - - -
173A PRO* 3.3 21.5 - - + -
174A ARG 5.2 0.2 + - - -
175A GLU* 2.6 35.0 + - - +
183A SER* 3.9 9.4 - - - -
185A ALA* 4.0 13.9 - - + -
186A PHE* 3.3 19.6 - - - -
213A TYR* 4.1 11.6 - - + -
298A GLY 2.9 14.1 + - - +
299A VAL* 3.4 8.7 - - - +
301A GLU* 1.3 75.2 - - - +
303A MET* 1.3 63.8 + - + +
305A TRP* 3.1 6.5 + + - -
306A LEU* 2.9 56.8 + - + +
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Residues in contact with MET 303 (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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185A ALA* 3.6 31.2 - - + +
189A ASN* 3.6 29.2 - - + +
250A THR* 3.6 29.6 - - + +
253A TYR* 3.5 38.2 + - + -
254A HIS* 3.9 9.6 - - - -
299A VAL* 2.8 36.3 + - + +
300A THR* 3.1 4.4 + - - +
302A TYR* 1.3 75.5 - - + +
304A ALA* 1.3 62.3 - - - +
306A LEU* 3.3 11.3 + - + -
307A ASN* 2.6 28.8 + - - +
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Residues in contact with ALA 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A TYR* 3.4 21.0 - - + +
300A THR 3.0 11.7 + - - +
301A GLU* 3.5 11.9 - - + +
303A MET* 1.3 77.3 - - - +
305A TRP* 1.3 61.3 + - - +
307A ASN 3.1 21.7 + - - -
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Residues in contact with TRP 305 (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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173A PRO* 3.6 47.4 - - + +
174A ARG* 4.0 30.9 - - + +
213A TYR* 5.7 0.9 - - - +
301A GLU* 3.1 10.5 + - + +
302A TYR* 3.1 9.0 + + - +
304A ALA* 1.3 79.6 - - - +
306A LEU* 1.3 88.1 + - + +
307A ASN 3.1 3.4 + - - +
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Residues in contact with LEU 306 (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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186A PHE* 4.1 25.4 - - + -
189A ASN* 3.6 37.7 + - + +
193A ASN* 5.2 1.4 + - - -
302A TYR* 2.9 52.2 + - + +
303A MET* 3.7 12.6 - - + +
304A ALA 3.2 0.6 - - - -
305A TRP* 1.3 91.7 - - + +
307A ASN* 1.3 74.0 + - - +
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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