Contacts of the helix formed by residues 171 - 185 (chain D) in PDB entry 1H4L
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 PRO 171 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153D ARG* 4.0 12.6 - - + +
156D GLY* 3.5 15.6 - - - +
157D GLU* 3.3 50.5 - - - +
160D CYS* 3.8 9.4 - - + -
169D LEU 4.6 1.1 - - - +
170D SER* 1.3 89.2 - - - +
172D THR* 1.3 60.3 + - - +
173D ASP 3.4 0.2 - - - -
174D PRO* 3.4 7.6 - - + +
175D VAL* 3.3 21.2 - - - +
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Residues in contact with THR 172 (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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153D ARG* 6.6 0.2 - - - -
170D SER* 2.9 16.9 + - - -
171D PRO* 1.3 77.2 - - - +
173D ASP* 1.3 60.8 + - - +
175D VAL* 3.3 9.5 + - + +
176D LEU* 2.9 30.6 + - + +
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Residues in contact with ASP 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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168D HIS* 4.8 5.9 - - - +
169D LEU* 3.9 10.9 - - + +
170D SER* 3.0 27.9 + - - +
172D THR* 1.3 76.5 - - - +
174D PRO* 1.3 63.1 - - + +
176D LEU* 2.6 37.1 + - - +
177D TRP* 2.9 35.1 + - + +
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Residues in contact with PRO 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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155D LEU* 6.2 0.4 - - + -
156D GLY* 4.3 13.0 - - - +
159D LEU* 3.6 36.3 - - + -
169D LEU* 3.6 16.2 - - + -
170D SER 3.1 15.0 - - - +
171D PRO 3.4 7.6 - - - +
173D ASP* 1.3 92.9 - - + +
175D VAL* 1.3 57.1 + - + +
177D TRP* 3.3 28.6 + - + +
178D LEU* 3.0 34.4 + - + +
222D LEU* 5.2 1.1 - - + -
226D LEU* 4.1 2.4 - - + +
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Residues in contact with VAL 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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152D LEU* 3.5 54.7 - - + +
153D ARG* 4.1 6.3 - - + +
155D LEU* 5.5 0.9 - - + -
156D GLY 4.6 2.2 - - - +
171D PRO 3.3 18.6 - - - +
172D THR* 3.3 11.6 + - + +
173D ASP 3.0 0.6 - - - -
174D PRO* 1.3 73.2 - - - +
176D LEU* 1.3 62.0 + - - +
178D LEU* 3.3 8.1 + - + +
179D ARG* 2.7 43.0 + - + +
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Residues in contact with LEU 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 THR* 2.9 15.6 + - + +
173D ASP* 2.6 26.2 + - - +
175D VAL* 1.3 74.4 - - - +
177D TRP* 1.3 57.4 + - + +
179D ARG* 3.5 8.7 + - + +
180D SER* 2.6 44.6 + - - +
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Residues in contact with TRP 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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169D LEU* 4.6 8.3 - - + -
173D ASP* 2.9 36.3 + - + +
174D PRO* 3.4 30.3 - - + +
176D LEU* 1.3 84.3 - - + +
178D LEU* 1.3 65.4 + - - +
180D SER* 3.4 11.6 + - - -
181D VAL* 3.3 22.2 - - - +
219D ASP* 3.9 35.2 - - + -
222D LEU* 4.5 10.5 - - + -
223D GLN* 3.9 61.6 - - + +
226D LEU* 4.1 8.3 - - + -
227D LEU* 4.7 9.4 - - + +
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Residues in contact with LEU 178 (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 LEU* 4.3 15.0 - - + -
155D LEU* 3.2 35.2 - - + -
174D PRO 3.0 23.4 + - - +
175D VAL* 3.8 6.5 - - + +
177D TRP* 1.3 76.6 - - - +
179D ARG* 1.3 63.9 + - - +
180D SER 3.3 0.7 + - - -
181D VAL* 3.8 2.8 + - - +
182D ASP* 3.4 14.0 + - - +
196D ILE* 3.3 25.5 - - + +
204D LEU* 3.7 20.4 - - + -
226D LEU* 3.8 25.1 - - + -
227D LEU* 4.5 4.3 - - + -
230D LEU* 4.1 26.3 - - + +
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Residues in contact with ARG 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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148D THR* 3.2 31.7 - - - +
149D SER* 3.8 11.5 - - - +
152D LEU* 3.3 20.7 - - + +
175D VAL* 2.7 38.6 + - + +
176D LEU* 3.8 11.4 - - + +
178D LEU* 1.3 73.2 - - + +
180D SER* 1.3 61.8 + - - +
182D ASP* 3.7 6.1 + - - +
183D ARG* 3.0 25.3 + - - +
196D ILE* 4.3 19.9 + - + +
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Residues in contact with SER 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 LEU* 2.6 31.6 + - - +
177D TRP* 3.5 9.1 - - - -
178D LEU 3.2 0.6 - - - -
179D ARG* 1.3 73.8 - - - +
181D VAL* 1.3 64.5 + - - +
183D ARG* 2.8 24.8 + - - +
184D SER* 2.9 16.1 + - - -
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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 TRP 3.3 17.5 + - - +
178D LEU 4.4 0.7 - - - +
180D SER* 1.3 74.0 - - - +
182D ASP* 1.3 59.8 + - - +
183D ARG 2.8 1.2 + - - -
184D SER* 3.1 9.4 + - - -
185D LEU* 2.7 39.7 + - + +
227D LEU* 4.7 11.4 - - + -
230D LEU* 3.6 30.7 - - + -
234D TYR* 3.8 9.4 - - + +
247D PRO* 3.7 32.3 - - + +
248D PHE* 4.0 17.3 - - + -
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Residues in contact with ASP 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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178D LEU 3.4 15.6 + - - +
179D ARG* 4.2 7.7 + - - +
180D SER 3.3 0.4 - - - -
181D VAL* 1.3 80.9 - - - +
183D ARG* 1.3 60.4 + - - +
185D LEU* 4.1 3.0 - - - +
186D LEU* 3.8 8.5 - - - +
191D GLN* 2.7 39.8 + - - -
194D GLY* 4.0 5.9 - - - -
195D PHE 3.1 13.5 + - - -
196D ILE* 3.2 36.4 + - + +
234D TYR* 2.9 21.3 + - - +
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Residues in contact with ARG 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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179D ARG 3.0 15.6 + - - +
180D SER* 2.8 15.1 + - - +
181D VAL 2.8 1.0 + - - -
182D ASP* 1.3 76.6 - - - +
184D SER* 1.3 60.7 + - - +
185D LEU 3.1 0.7 - - - -
186D LEU* 2.8 33.3 + - + +
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Residues in contact with SER 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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180D SER 2.9 14.6 + - - -
181D VAL* 3.4 11.4 + - - -
183D ARG* 1.3 70.0 - - - +
185D LEU* 1.3 57.1 + - - +
186D LEU 2.6 16.8 + - - -
187D LEU* 2.7 38.9 + - - +
190D TRP* 4.6 1.4 - - - -
247D PRO* 4.1 13.2 - - - +
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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* 2.7 20.5 + - + +
182D ASP 4.1 0.4 - - - +
184D SER* 1.3 74.0 + - - +
186D LEU* 1.3 54.0 + - - +
187D LEU 2.7 11.8 + - - -
188D GLN 3.9 0.3 + - - -
190D TRP* 3.2 48.6 - - + +
191D GLN* 3.7 22.0 + - + +
234D TYR* 3.3 45.1 - - + +
243D TYR* 4.1 11.7 - - + -
244D PRO* 4.1 15.3 - - + -
247D PRO* 3.7 24.0 - - + -
248D PHE* 4.1 12.8 - - + -
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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