Contacts of the helix formed by residues 168 - 182 (chain W) in PDB entry 5XTE
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 ASN 168 (chain W).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11O PHE* 3.2 33.0 - - - -
29O LEU* 4.1 13.0 - - - +
47O ARG* 6.2 2.7 - - - +
49O PHE* 6.5 0.7 - - + -
164W VAL 4.4 1.5 + - - +
165W ALA 3.5 11.3 + - - +
166W PHE 3.0 5.6 - - - +
167W GLN* 1.3 77.9 - - - +
169W PRO* 1.3 66.5 - - - +
170W GLN* 2.7 29.3 + - - +
171W THR* 2.6 32.2 + - + -
172W HIS 3.8 2.1 + - - -
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Residues in contact with PRO 169 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29O LEU* 5.9 1.1 - - + -
40O GLN* 5.9 6.3 - - + -
41O PRO* 4.6 14.1 - - + -
166W PHE 5.2 1.6 - - - +
167W GLN 3.5 10.0 - - - +
168W ASN* 1.3 91.4 - - - +
170W GLN* 1.3 80.4 + - - +
171W THR 3.5 0.2 + - - -
172W HIS* 3.6 12.3 + - + +
173W VAL 3.7 4.2 + - - -
268W HIS* 3.6 37.6 + - + +
339W TYR* 5.3 0.2 - - - +
341W ILE* 6.2 2.2 - - + -
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Residues in contact with GLN 170 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O PHE* 5.3 1.1 - - + -
27O ARG* 4.2 21.1 - - + -
28O PRO* 2.5 37.1 + - + +
29O LEU* 3.8 10.1 - - - +
168W ASN* 2.7 22.0 - - - +
169W PRO* 1.3 85.8 - - - +
171W THR* 1.3 67.1 + - + +
173W VAL* 3.2 4.0 + - - +
174W ILE* 2.9 29.0 + - + +
339W TYR* 3.2 32.5 - - + +
341W ILE* 4.0 18.0 - - - +
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Residues in contact with THR 171 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11O PHE* 3.6 21.3 - - + -
27O ARG* 3.2 28.5 - - - +
165W ALA 3.2 17.2 + - - +
166W PHE* 4.0 6.3 - - - -
168W ASN* 2.6 30.0 + - + +
170W GLN* 1.3 75.5 - - - +
172W HIS* 1.3 68.3 + - - +
174W ILE 3.0 1.2 + - - -
175W GLU* 2.5 47.0 + - - +
191W TYR* 5.4 5.6 - - - +
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Residues in contact with HIS 172 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166W PHE* 4.3 43.8 - + + +
168W ASN 3.8 3.6 + - - +
169W PRO* 3.6 10.9 + - + +
170W GLN 3.3 0.2 - - - -
171W THR* 1.3 83.9 + - - +
173W VAL* 1.3 56.9 + - - +
175W GLU* 4.4 2.5 - - - +
176W ASN* 2.7 37.2 + - - +
260W GLU* 2.6 44.7 + - - +
262W ASN* 5.3 3.2 + - - -
268W HIS* 5.6 2.2 - - - +
441W SER* 4.0 7.4 - - - -
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Residues in contact with VAL 173 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169W PRO 3.7 1.3 + - - +
170W GLN 3.2 7.7 + - - +
171W THR 3.1 0.4 - - - -
172W HIS* 1.3 79.3 - - - +
174W ILE* 1.3 62.5 + - + +
176W ASN* 3.1 9.2 + - - +
177W LEU* 2.8 23.5 + - + +
260W GLU* 5.2 0.7 - - - -
268W HIS* 3.3 47.3 - - + +
269W ALA* 4.3 0.9 - - - -
270W ALA* 4.3 7.6 - - + +
339W TYR* 4.1 19.7 - - + +
439W ALA* 3.9 29.4 - - + +
440W ALA 4.8 0.7 - - - +
441W SER* 3.8 13.7 - - - +
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Residues in contact with ILE 174 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27O ARG* 3.2 58.8 - - + +
170W GLN* 2.9 21.0 + - + +
173W VAL* 1.3 79.8 - - + +
175W GLU* 1.3 60.5 + - - +
177W LEU* 2.9 31.7 + - + +
178W HIS* 2.9 33.7 + - + +
326W PHE* 3.9 26.9 - - + -
339W TYR* 4.8 15.0 - - + -
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Residues in contact with GLU 175 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27O ARG* 4.4 12.7 + - - +
116W ARG* 3.4 27.8 + - - +
166W PHE* 4.1 11.8 - - + -
171W THR* 2.5 50.4 + - - +
172W HIS* 5.2 1.3 - - - +
174W ILE* 1.3 77.3 - - - +
176W ASN* 1.3 63.3 + - - +
178W HIS 3.6 0.9 + - - -
179W ALA* 3.3 19.2 + - - +
187W ALA 4.9 1.9 - - - +
189W PRO* 5.0 10.2 - - + +
190W LEU* 4.2 26.5 - - + +
191W TYR* 3.7 28.8 + - + -
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Residues in contact with ASN 176 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172W HIS* 2.7 27.0 + - - +
173W VAL* 3.1 11.0 + - - +
175W GLU* 1.3 77.5 - - - +
177W LEU* 1.3 58.6 + - - +
179W ALA* 3.3 5.8 + - - +
180W ALA* 2.9 24.1 + - - +
258W ILE* 3.2 38.3 - - + +
260W GLU* 2.9 19.0 - - + +
439W ALA* 4.2 5.2 - - + -
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Residues in contact with LEU 177 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173W VAL* 2.8 14.3 + - + +
174W ILE* 2.9 23.1 + - + +
176W ASN* 1.3 74.7 - - - +
178W HIS* 1.3 63.1 + - + +
180W ALA* 3.1 4.0 + - + +
181W ALA* 2.9 32.2 + - + +
270W ALA* 4.1 20.9 - - + +
272W VAL* 3.7 37.9 - - + -
326W PHE* 4.3 19.1 - - + -
335W LEU* 5.5 4.5 - - + -
437W SER* 5.0 4.7 - - - -
438W MET* 4.4 7.9 - - - +
439W ALA* 3.7 28.0 - - + +
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Residues in contact with HIS 178 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10O PRO* 4.1 7.8 - - + +
27O ARG* 5.3 1.3 - - - -
116W ARG* 3.2 44.5 + - - +
174W ILE* 2.9 44.7 + - + +
175W GLU 4.0 0.2 - - - +
177W LEU* 1.3 77.2 - - + +
179W ALA* 1.3 62.7 + - - +
181W ALA* 3.1 12.8 + - - +
182W TYR* 3.2 24.0 + - + -
186W LEU 3.8 8.9 + - - +
187W ALA* 3.6 7.6 - - - +
326W PHE* 4.8 3.8 - + - -
328W ALA* 4.2 16.6 - - + -
330W TYR* 3.9 31.2 + + - -
335W LEU* 4.0 15.3 - - + +
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Residues in contact with ALA 179 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175W GLU 3.3 11.8 + - - +
176W ASN* 3.3 15.0 + - - +
177W LEU 3.2 0.6 - - - -
178W HIS* 1.3 78.8 - - - +
180W ALA* 1.3 57.3 + - - +
182W TYR 3.9 8.8 - - - +
187W ALA* 4.0 21.0 + - + +
189W PRO* 6.3 0.2 - - + -
254W ARG* 2.8 16.7 + - - -
258W ILE* 3.8 13.4 - - + +
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Residues in contact with ALA 180 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176W ASN 2.9 15.7 + - - +
177W LEU* 3.1 8.2 + - + +
179W ALA* 1.3 79.3 - - - +
181W ALA* 1.3 56.3 + - - +
254W ARG* 3.1 17.7 + - - +
256W GLY 3.0 36.2 + - - +
257W GLU 4.1 0.2 - - - -
258W ILE* 3.9 17.5 - - + +
437W SER* 3.4 10.4 + - - -
438W MET 3.9 14.8 - - - +
439W ALA* 4.9 0.2 - - + -
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Residues in contact with ALA 181 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177W LEU* 2.9 17.5 + - + +
178W HIS* 3.1 1.3 + - - +
180W ALA* 1.3 80.5 - - - +
182W TYR* 1.3 82.6 + - + +
253W TYR* 3.4 11.6 - - + -
254W ARG* 3.3 20.5 + - - -
272W VAL* 5.7 1.6 - - + -
335W LEU* 4.0 20.6 - - + -
437W SER* 4.0 16.4 - - - +
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Residues in contact with TYR 182 (chain W).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449K PHE* 5.0 0.9 - - - -
178W HIS* 3.2 21.4 + + - +
179W ALA 3.9 8.0 - - - +
180W ALA 3.7 1.2 - - - -
181W ALA* 1.3 86.6 - - + +
183W ARG* 1.3 64.2 + - - +
184W ASN 4.1 4.0 - - - +
186W LEU* 3.5 41.2 - - + +
187W ALA* 3.3 30.2 - - + +
251W ALA* 3.8 21.3 - - + -
252W ASN 3.3 17.3 - - - +
253W TYR* 4.9 3.8 - - + -
254W ARG* 4.1 8.2 - - - +
274W GLU* 5.0 2.0 - - - -
330W TYR* 4.7 2.5 - + - -
333W SER* 3.7 26.4 + - - -
334W GLY 4.3 0.2 - - - -
335W LEU* 3.3 46.9 - - + +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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