Contacts of the helix formed by residues 153 - 164 (chain D) in PDB entry 5TJ4
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 GLU 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44D GLU* 5.2 5.0 - - - +
150D ASN* 3.4 18.7 + - - +
151D LEU 3.4 1.1 - - - -
152D GLN* 1.3 80.7 - - + +
154D PRO* 1.3 68.4 - - - +
155D TYR 3.2 0.9 + - - -
156D PHE* 3.4 31.0 + - + -
157D THR* 3.6 12.2 + - - -
344D ARG* 3.1 28.9 + - - -
1N GLC 3.7 18.9 + - - +
2N GLC 2.9 24.1 + - - +
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Residues in contact with PRO 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D GLN 3.8 6.7 - - - +
153D GLU* 1.3 85.8 - - - +
155D TYR* 1.3 55.0 + - - -
156D PHE 3.1 2.9 + - - -
157D THR* 3.7 9.2 - - - +
158D TRP* 2.7 35.7 + - - +
340D TRP* 3.6 28.7 - - + +
343D VAL* 3.7 26.9 - - + -
344D ARG* 3.8 31.6 - - + +
347D VAL* 5.0 5.2 - - + -
2N GLC 3.3 12.3 - - - +
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Residues in contact with TYR 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111D GLU* 3.9 20.8 + - - +
112D ALA* 4.1 7.6 - - - -
113D LEU* 3.3 44.8 + - + +
153D GLU 3.2 0.2 - - - -
154D PRO* 1.3 76.9 - - - +
156D PHE* 1.3 67.6 + + + +
158D TRP* 4.0 2.6 + - - +
159D PRO* 3.5 10.4 - - - +
230D TRP* 4.1 15.0 - + - -
258D PHE* 3.5 34.5 + - + +
260D GLY 4.3 2.9 + - - -
330D MET* 4.4 7.6 - - + -
340D TRP* 3.8 17.8 - + - -
1N GLC 3.5 41.4 + - - -
2N GLC 2.9 35.9 + - - +
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Residues in contact with PHE 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14D ASP* 6.2 0.2 - - - -
113D LEU* 3.7 30.9 - - + +
129D TRP* 6.1 0.5 - - - -
149D PHE* 3.7 18.6 - + + -
150D ASN* 3.3 47.8 - - + +
153D GLU* 3.7 18.2 - - + +
154D PRO 3.1 0.2 - - - -
155D TYR* 1.3 83.3 - + + +
157D THR* 1.3 60.8 - - - +
158D TRP 3.4 0.2 - - - -
159D PRO* 3.2 15.4 - - - +
160D LEU* 5.8 0.3 - - - +
210D TYR* 4.2 20.9 - + - -
226D ILE* 3.7 30.7 - - + +
227D ASN* 4.0 12.8 - - - -
230D TRP* 4.8 4.0 - + - -
1N GLC 3.8 28.7 - - - -
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Residues in contact with THR 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149D PHE* 4.3 8.3 - - - -
150D ASN 4.3 0.5 + - - -
151D LEU* 3.9 20.6 + - - +
153D GLU 3.6 11.3 + - - -
154D PRO* 3.1 10.2 + - - -
156D PHE* 1.3 78.5 - - - +
158D TRP* 1.3 63.4 + - - +
159D PRO 3.3 1.0 - - - -
160D LEU* 3.3 17.1 + - + +
161D ILE* 3.5 22.7 + - + -
195D LEU* 3.3 36.8 - - + +
347D VAL* 3.9 16.9 - - + +
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Residues in contact with TRP 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D PRO* 2.7 23.2 + - - +
155D TYR 4.0 4.5 - - - +
157D THR* 1.3 71.9 - - - +
159D PRO* 1.4 58.4 - - + +
161D ILE* 2.8 31.9 + - + +
162D ALA* 2.7 49.0 + - + +
166D GLY 4.1 5.6 - - - -
167D TYR* 3.7 39.9 - - - -
168D ALA 3.9 1.3 - - - -
182D GLY 4.7 0.9 - - - -
183D VAL* 4.1 13.9 - - + -
256D LYS 4.0 9.5 + - - -
258D PHE* 3.1 43.9 - + - +
339D PHE* 3.6 33.0 - + - -
340D TRP* 4.7 6.3 - + + -
343D VAL* 4.4 17.9 - - + -
361D LEU* 6.2 0.4 - - + -
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Residues in contact with PRO 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113D LEU* 4.2 8.3 - - + -
129D TRP* 6.0 2.5 - - + -
155D TYR 3.5 13.5 - - - +
156D PHE 3.2 19.3 - - - +
157D THR 3.3 1.6 - - - +
158D TRP* 1.4 90.4 - - + +
160D LEU* 1.3 55.4 + - - +
162D ALA 3.5 0.2 + - - -
163D ALA* 3.1 24.3 + - - +
226D ILE* 5.7 2.7 - - + -
247D LEU* 4.2 9.9 - - + -
255D SER* 3.6 16.7 - - - -
256D LYS 3.3 25.5 + - - +
257D PRO* 3.7 32.1 - - + -
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Residues in contact with LEU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129D TRP* 3.8 49.7 - - + +
149D PHE* 5.9 0.9 - - + -
156D PHE 5.8 0.4 - - - +
157D THR* 3.3 10.6 + - - +
158D TRP 3.1 0.2 - - - -
159D PRO* 1.3 77.9 - - - +
161D ILE* 1.3 66.4 + - + +
163D ALA* 3.3 17.6 + - - +
164D ASP 4.4 0.3 + - - -
191D GLY* 3.6 28.8 - - - +
194D PHE* 4.3 9.2 - - + -
195D LEU* 3.9 29.6 - - + +
250D PHE* 3.7 33.7 - - + -
255D SER* 4.6 3.5 - - - -
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Residues in contact with ILE 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D THR* 3.6 33.0 - - + +
158D TRP* 2.8 36.6 + - + +
160D LEU* 1.3 77.7 - - + +
162D ALA* 1.3 62.3 + - - +
163D ALA 3.4 0.3 + - - -
164D ASP 4.3 0.2 + - - -
166D GLY* 3.5 11.7 + - - -
187D GLY 3.5 14.2 - - - +
188D ALA* 3.6 28.0 - - + +
191D GLY* 4.3 7.4 - - - +
192D LEU* 4.1 27.4 - - + +
343D VAL* 4.9 2.7 - - + -
347D VAL* 4.0 19.3 - - + -
361D LEU* 5.3 7.4 - - + -
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D TRP* 2.7 42.2 + - + +
159D PRO 3.9 0.9 - - - +
161D ILE* 1.3 71.5 - - - +
163D ALA* 1.3 67.3 + - - +
165D GLY* 3.3 9.0 + - - -
166D GLY* 3.5 25.8 + - - +
256D LYS* 3.6 35.5 - - + +
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Residues in contact with ALA 163 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159D PRO 3.1 13.8 + - - +
160D LEU* 3.4 14.6 - - - +
161D ILE 3.2 1.4 - - - -
162D ALA* 1.3 79.2 - - - +
164D ASP* 1.3 64.1 + - - +
165D GLY* 3.2 1.0 + - - -
250D PHE* 4.0 23.8 - - + +
253D GLN* 4.0 18.2 + - - +
254D PRO* 3.6 23.7 - - - +
255D SER* 4.2 4.7 - - - +
256D LYS* 4.5 7.0 - - - +
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Residues in contact with ASP 164 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322A GLU* 4.6 7.6 - - - +
160D LEU 4.4 1.4 + - - -
161D ILE 4.3 2.8 + - - -
163D ALA* 1.3 78.3 - - - +
165D GLY* 1.3 56.2 + - - +
186D ALA* 4.8 1.4 - - - +
187D GLY* 3.5 32.5 + - - +
190D ALA* 4.0 2.8 - - + +
250D PHE* 4.3 17.5 - - + -
251D LYS* 3.6 32.7 - - + +
253D GLN* 3.3 26.7 + - - +
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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