Contacts of the helix formed by residues 170 - 187 (chain D) in PDB entry 5T0H
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 MET 170 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167D ILE* 4.0 29.8 - - + +
168D GLY* 3.1 2.0 - - - +
169D GLY* 1.3 77.8 - - - +
171D ASP* 1.3 51.2 + - - +
172D ILE* 3.2 3.1 - - - -
173D GLN* 2.7 30.7 + - + +
174D LYS* 2.6 46.7 + - + +
211D GLY* 4.2 20.0 - - - +
215D LEU* 3.5 37.7 - - + -
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Residues in contact with ASP 171 (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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168D GLY* 2.9 30.4 - - - +
169D GLY 3.3 2.2 - - - -
170D MET* 1.3 75.4 - - - +
172D ILE* 1.3 62.3 + - + +
174D LYS* 3.0 34.4 + - - +
175D GLN* 2.9 28.6 + - - +
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Residues in contact with ILE 172 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169D GLY 4.9 7.0 - - - +
170D MET* 4.9 2.5 - - - -
171D ASP* 1.3 79.5 - - + +
173D GLN* 1.3 65.4 + - + +
175D GLN* 3.3 22.3 - - - +
176D GLU* 4.4 1.7 + - - +
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Residues in contact with GLN 173 (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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170D MET* 2.7 38.7 + - + +
172D ILE* 1.3 79.3 - - + +
174D LYS* 1.3 59.1 + - - -
175D GLN 3.6 0.2 + - - -
176D GLU* 4.0 13.2 + - - +
177D VAL* 4.3 8.0 + - - +
204D MET* 5.2 13.3 - - - +
205D TYR 5.2 8.7 + - - +
210D CYS 5.8 2.0 + - - -
212D LYS* 5.9 1.8 - - - +
215D LEU* 4.8 16.5 - - + +
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Residues in contact with LYS 174 (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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164D TYR* 3.9 34.9 - - + -
167D ILE 4.8 9.4 + - - +
168D GLY* 5.4 0.4 - - - -
170D MET* 2.6 28.3 + - + +
171D ASP* 3.0 36.4 + - - +
173D GLN* 1.3 72.0 - - - +
175D GLN* 1.3 54.0 + - - +
176D GLU 3.2 1.3 - - - -
177D VAL* 3.1 13.6 + - + -
178D ARG* 2.5 60.4 + - - +
215D LEU* 5.8 9.2 - - + -
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Residues in contact with GLN 175 (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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369C TYR* 4.9 15.0 + - - +
372C ARG* 5.3 8.3 - - - +
389C LYS* 6.4 0.2 - - - +
171D ASP 2.9 11.9 + - - +
172D ILE* 3.3 19.5 - - - +
173D GLN 3.2 1.0 - - - -
174D LYS* 1.3 76.5 - - - +
176D GLU* 1.3 63.7 + - - +
178D ARG* 3.3 18.2 - - - +
179D GLU* 3.3 33.7 + - - +
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Residues in contact with GLU 176 (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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172D ILE 4.4 1.8 + - - +
173D GLN 4.0 9.5 + - - +
174D LYS 3.2 0.2 - - - -
175D GLN* 1.3 75.9 - - - +
177D VAL* 1.3 59.4 + - + +
179D GLU* 3.0 6.7 + - - +
180D ALA* 2.6 55.5 + - + +
199D PRO* 5.9 2.9 - - - +
201D GLY 4.4 11.4 - - - +
202D VAL* 4.7 11.3 - - + +
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Residues in contact with VAL 177 (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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173D GLN 4.3 11.0 - - - +
174D LYS* 3.1 14.8 + - + +
176D GLU* 1.3 79.6 - - + +
178D ARG* 1.3 64.5 + - - +
180D ALA* 3.8 3.6 - - - -
181D VAL* 3.2 40.2 + - + +
202D VAL* 5.4 11.9 - - + -
204D MET* 6.5 0.7 - - - -
219D VAL* 4.3 20.6 - - + -
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Residues in contact with ARG 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372C ARG* 5.6 6.5 - - - +
164D TYR* 5.2 8.7 + - - -
174D LYS* 2.5 51.9 + - - +
175D GLN* 3.3 23.6 - - - +
176D GLU 3.0 0.2 + - - -
177D VAL* 1.3 76.3 - - - +
179D GLU* 1.3 63.4 + - + +
181D VAL 3.9 0.3 + - - -
182D GLU* 3.1 55.7 - - - +
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Residues in contact with GLU 179 (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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365C GLU* 4.7 3.6 - - - +
368C MET* 3.5 44.1 - - - +
369C TYR* 3.9 20.9 - - - -
371C LEU* 4.8 13.6 - - + +
372C ARG* 3.4 33.4 - - + -
175D GLN* 3.3 20.1 + - - +
176D GLU* 3.0 7.9 + - - +
178D ARG* 1.3 81.3 - - + +
180D ALA* 1.3 56.5 + - - +
181D VAL 3.4 0.4 - - - -
182D GLU* 5.2 0.7 - - - -
183D LEU* 4.8 2.1 - - - +
184D PRO* 3.3 19.9 - - - +
191D TYR* 4.4 3.1 + - - -
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Residues in contact with ALA 180 (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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176D GLU* 2.6 49.6 + - + +
177D VAL* 4.3 3.1 - - - -
178D ARG 3.3 0.2 - - - -
179D GLU* 1.3 70.9 - - - +
181D VAL* 1.3 64.2 + - + +
184D PRO* 3.3 18.6 - - - +
199D PRO* 5.8 2.2 - - + +
201D GLY 5.6 0.4 - - - +
202D VAL* 4.7 16.0 - - + +
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Residues in contact with VAL 181 (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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177D VAL* 3.2 38.6 + - + +
179D GLU 3.4 1.4 - - - -
180D ALA* 1.3 85.3 - - + +
182D GLU* 1.3 75.0 + - + +
184D PRO* 3.3 4.9 - - - +
185D LEU* 3.1 25.1 + - + +
202D VAL* 6.0 3.8 - - + -
219D VAL* 4.0 27.6 - - + -
223D THR* 4.7 6.7 - - + +
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Residues in contact with GLU 182 (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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177D VAL 4.4 0.2 + - - -
178D ARG* 3.1 47.8 - - - +
179D GLU* 5.2 0.6 - - - -
181D VAL* 1.3 82.6 - - + +
183D LEU* 1.3 81.4 + - + +
185D LEU* 3.7 3.3 - - - +
186D THR* 2.9 32.7 + - + +
223D THR* 4.9 14.4 - - + -
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Residues in contact with LEU 183 (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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371C LEU* 3.6 39.5 - - + +
372C ARG* 4.2 9.2 - - + +
374C ARG* 3.5 35.2 - - - +
179D GLU* 4.8 2.2 - - - +
182D GLU* 1.3 96.7 - - + +
184D PRO* 1.3 68.3 - - + +
186D THR* 3.6 9.2 - - + -
187D HIS* 2.7 47.4 + - + +
190D LEU* 4.0 5.8 - - + -
191D TYR* 4.2 3.1 - - + +
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Residues in contact with PRO 184 (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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179D GLU 3.3 19.7 - - - +
180D ALA* 3.3 26.9 - - - +
181D VAL* 3.3 13.5 - - - +
183D LEU* 1.3 88.6 - - + +
185D LEU* 1.3 57.3 + - - +
187D HIS 3.4 2.6 - - - +
188D PHE* 3.0 28.8 - - - -
191D TYR* 3.1 30.4 - - + +
198D PRO* 5.2 7.0 - - + +
199D PRO* 6.0 2.5 - - + +
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Residues in contact with LEU 185 (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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181D VAL* 3.1 20.3 + - + +
182D GLU 3.7 2.2 - - - +
184D PRO* 1.3 79.6 - - - +
186D THR* 1.3 63.8 + - - +
187D HIS 3.4 0.5 + - - -
188D PHE* 3.7 25.3 - - + -
223D THR* 4.6 24.2 - - + -
224D THR 5.2 4.3 - - - +
225D ALA* 4.8 17.3 - - + -
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Residues in contact with THR 186 (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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374C ARG* 5.2 0.9 - - - +
182D GLU* 2.9 22.8 + - + +
183D LEU* 3.6 11.4 - - + -
185D LEU* 1.3 79.2 - - - +
187D HIS* 1.3 93.3 + - + +
188D PHE 4.2 0.8 + - - -
189D GLU* 4.3 2.8 - - - +
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Residues in contact with HIS 187 (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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374C ARG* 3.1 46.6 + - - -
183D LEU* 2.7 36.3 + - + +
184D PRO 3.4 2.9 - - - +
185D LEU 3.3 0.2 - - - -
186D THR* 1.3 102.9 + - + +
188D PHE* 1.3 62.6 + - - +
189D GLU* 3.5 15.0 + - - +
190D LEU* 4.1 22.2 + - + +
191D TYR* 3.2 18.8 - - + -
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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