Contacts of the helix formed by residues 173 - 186 (chain A) in PDB entry 5HAN
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 ARG 173 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A GLY 3.5 0.8 + - - -
172A LEU* 1.3 76.7 - - - +
174A PRO* 1.3 75.0 - - + +
175A GLN 3.4 2.0 - - - -
176A PRO* 3.3 20.9 - - + +
177A PHE* 3.0 20.2 + - - +
202A PHE* 3.3 21.5 - - + +
203A ALA* 4.6 0.7 - - - -
62B ASP* 3.5 17.6 + - - +
64B PHE* 3.4 61.0 - - + +
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Residues in contact with PRO 174 (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 ARG* 1.3 87.0 - - + +
175A GLN* 1.3 57.7 + - - +
177A PHE* 3.4 6.9 - - + +
178A ALA* 3.0 27.7 + - - +
202A PHE 3.7 11.7 - - - +
203A ALA* 4.0 8.5 - - - -
204A PRO* 4.1 4.5 - - + -
207A ASP* 3.9 35.2 - - + +
208A THR* 3.6 27.5 - - - +
211A ALA* 3.7 6.8 - - + +
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Residues in contact with GLN 175 (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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174A PRO* 1.3 72.1 - - - +
176A PRO* 1.4 72.1 - - + +
177A PHE 3.1 1.1 - - - -
178A ALA* 3.0 16.1 + - - +
179A ASN* 2.8 57.3 + - - +
211A ALA* 4.3 12.8 - - - +
214A ASP* 5.3 5.9 + - - +
218A ARG* 4.6 7.3 + - - -
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Residues in contact with PRO 176 (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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172A LEU* 3.9 24.2 - - + +
173A ARG* 3.3 32.8 - - + +
175A GLN* 1.4 92.5 - - + +
177A PHE* 1.4 60.2 + - - +
179A ASN* 3.5 13.6 + - + +
180A ALA* 3.2 21.7 + - - +
62B ASP* 4.8 9.4 - - - +
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Residues in contact with PHE 177 (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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166A ILE* 3.5 30.0 - - + +
172A LEU* 3.8 25.7 - - + +
173A ARG 3.0 20.1 + - - +
174A PRO* 3.4 8.1 - - + +
176A PRO* 1.4 75.3 - - - +
178A ALA* 1.4 60.8 + - - +
180A ALA* 3.3 7.3 + - - +
181A CYS* 3.2 30.4 + - - -
193A ASN* 3.5 22.2 - - - -
197A GLN* 3.3 28.7 - - + -
208A THR* 3.8 17.9 - - + -
212A VAL* 3.6 31.4 - - + -
229A PHE* 4.0 8.1 - + - -
231A PHE* 5.9 0.2 - + - -
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Residues in contact with ALA 178 (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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174A PRO 3.0 15.1 + - - +
175A GLN* 3.0 13.3 + - - +
177A PHE* 1.4 75.1 - - - +
179A ASN* 1.3 61.6 + - - +
181A CYS* 3.2 11.6 + - - +
182A TYR* 2.9 26.2 + - - +
211A ALA* 3.4 39.9 - - + +
212A VAL* 4.0 1.8 - - + +
215A ALA* 3.4 10.4 - - + +
218A ARG* 5.0 1.1 - - - +
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Residues in contact with ASN 179 (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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175A GLN* 2.8 48.9 + - - +
176A PRO* 3.7 10.8 - - + +
178A ALA* 1.3 72.6 - - - +
180A ALA* 1.3 56.1 + - - +
182A TYR* 3.4 6.4 + - - +
183A ASP* 3.0 39.3 + - - +
218A ARG* 4.3 8.5 + - - +
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Residues in contact with ALA 180 (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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166A ILE* 4.2 9.2 - - + -
167A LYS 5.4 0.4 - - - +
172A LEU* 4.5 8.7 - - + -
176A PRO 3.2 11.2 + - - +
177A PHE 3.5 9.6 - - - +
179A ASN* 1.3 75.1 - - - +
181A CYS* 1.4 65.2 + - - +
183A ASP* 3.8 6.6 - - - +
184A PHE* 3.1 25.3 + - - +
398A PHE* 3.7 26.1 - - + -
60B THR* 4.2 17.5 - - + -
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Residues in contact with CYS 181 (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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166A ILE* 3.7 13.0 - - - -
177A PHE* 3.2 44.6 + - - -
178A ALA* 3.2 8.9 + - - +
180A ALA* 1.4 73.2 - - - +
182A TYR* 1.3 64.5 + - - +
184A PHE 3.3 1.4 + - - -
185A TRP* 2.9 42.8 + - + +
191A ILE* 3.4 17.4 - - + +
212A VAL* 4.1 7.9 - - + -
215A ALA* 4.5 2.2 - - + -
229A PHE* 3.8 17.3 - - - -
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Residues in contact with TYR 182 (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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178A ALA 2.9 16.5 + - - +
179A ASN* 3.7 5.4 - - - +
181A CYS* 1.3 76.0 - - - +
183A ASP* 1.4 75.8 + - - +
185A TRP* 3.2 9.3 + - - +
186A LEU* 3.2 45.7 + - + +
215A ALA* 3.8 12.5 - - + +
218A ARG* 3.5 42.1 + - + +
219A ALA* 3.5 36.1 - - + +
222A LYS* 3.6 27.5 - - - +
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Residues in contact with ASP 183 (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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179A ASN* 3.0 26.9 + - - +
180A ALA* 3.8 7.5 - - - +
182A TYR* 1.4 88.6 - - - +
184A PHE* 1.3 63.5 + - - +
186A LEU* 3.3 15.5 + - - +
398A PHE* 5.5 0.7 - - + -
404A GLY* 4.7 7.9 + - - +
405A ALA* 3.3 34.5 - - + +
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Residues in contact with PHE 184 (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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162A VAL* 4.0 11.0 - - + -
163A GLY 3.5 23.3 - - - -
164A THR* 3.4 28.3 - - + -
180A ALA 3.1 17.2 + - - +
181A CYS 3.8 2.7 - - - +
183A ASP* 1.3 76.3 - - - +
185A TRP* 1.3 60.2 + + - +
187A GLY 2.9 7.8 + - - -
188A GLY* 2.9 39.7 + - - -
189A ASP 4.1 0.2 - - - -
190A PHE 3.3 20.2 - - - -
191A ILE* 3.6 14.4 - - + -
397A ALA* 4.0 13.0 - - + -
398A PHE* 4.1 11.9 - + + -
404A GLY* 3.7 15.8 - - - +
408A ALA* 3.3 35.1 - - + +
411A LEU* 4.4 1.6 - - + -
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Residues in contact with TRP 185 (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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181A CYS* 2.9 37.4 + - + +
182A TYR 3.7 0.9 - - - +
184A PHE* 1.3 76.2 - + - +
186A LEU* 1.3 59.0 + - - +
187A GLY 3.1 0.8 + - - -
188A GLY 3.3 7.1 - - - +
189A ASP 3.4 14.3 + - - -
191A ILE* 3.4 18.7 - - + +
212A VAL* 3.9 13.5 - - + -
215A ALA 4.0 6.1 - - - -
216A MET* 3.5 48.0 - - + -
219A ALA* 3.7 17.9 - - + -
223A THR* 4.0 0.7 - - - +
227A LYS* 2.8 56.5 + - + +
228A LEU 3.2 32.6 + - - -
229A PHE* 3.7 28.5 - + + -
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Residues in contact with LEU 186 (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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182A TYR* 3.2 52.7 + - + +
183A ASP* 3.5 17.7 - - - +
184A PHE 3.1 1.2 + - - -
185A TRP* 1.3 76.5 - - - +
187A GLY* 1.3 56.8 + - - +
219A ALA* 4.8 2.0 - - - -
222A LYS* 3.8 21.8 - - + -
223A THR* 3.9 22.7 - - + +
227A LYS* 4.9 0.8 + - - -
405A ALA* 4.1 13.9 - - + -
409A LYS* 4.5 7.7 + - - -
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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