Contacts of the helix formed by residues 177 - 197 (chain A) in PDB entry 4UML
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 177 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133A TYR* 3.6 32.1 - - + +
175A GLY 3.3 8.7 - - - +
176A TYR* 1.3 93.3 - - + +
178A LEU* 1.3 65.7 + - - +
179A GLU 3.3 2.0 + - - +
180A ASP* 3.3 22.9 + - - +
181A ALA 3.0 18.9 + - - -
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Residues in contact with LEU 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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168A VAL* 4.7 3.4 - - + -
170A ASN* 3.8 18.6 - - - +
176A TYR 3.2 6.4 + - - +
177A PRO* 1.3 71.4 - - - +
179A GLU* 1.3 59.3 + - - +
181A ALA* 3.3 4.0 + - - +
182A THR* 2.8 45.1 + - - +
210A LEU* 3.9 28.9 - - + +
211A GLU* 3.8 27.8 - - + -
214A THR* 3.8 21.3 - - + +
215A TYR* 5.2 0.4 - - + -
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Residues in contact with GLU 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PRO* 3.3 0.8 - - - +
178A LEU* 1.3 79.8 - - - +
180A ASP* 1.3 64.5 + - - +
182A THR* 3.2 4.2 + - - -
183A HIS* 3.1 35.2 + - + +
214A THR* 4.0 23.5 + - + +
217A LYS* 2.7 42.8 + - - +
218A LEU* 3.8 11.3 - - + +
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Residues in contact with ASP 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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133A TYR* 4.9 2.8 + - - -
138A ARG* 4.9 12.0 + - - -
142A GLU* 5.9 3.1 - - + +
176A TYR* 4.0 14.8 - - + +
177A PRO* 3.3 27.1 + - - +
179A GLU* 1.3 79.6 - - - +
181A ALA* 1.3 61.4 + - - +
183A HIS* 3.2 20.8 + - - +
184A ILE* 3.3 17.6 + - + +
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Residues in contact with ALA 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
145A LEU* 3.8 18.5 - - + +
149A TYR* 5.1 0.2 - - - -
170A ASN* 3.5 39.6 - - - +
176A TYR* 3.7 13.7 - - + -
177A PRO 3.0 16.7 + - - +
178A LEU 3.5 2.7 - - - +
180A ASP* 1.3 77.0 - - - +
182A THR* 1.3 57.8 + - - +
184A ILE* 3.2 5.8 + - - +
185A ALA* 3.0 26.7 + - - +
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Residues in contact with THR 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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170A ASN* 5.6 0.6 + - - -
178A LEU* 2.8 27.2 + - - +
179A GLU 3.2 5.3 + - - -
181A ALA* 1.3 74.1 - - - +
183A HIS* 1.3 64.3 + - - +
185A ALA* 3.7 5.7 - - - +
186A LEU* 3.0 37.3 + - + +
214A THR* 3.6 14.9 - - + +
215A TYR* 3.7 44.0 + - + -
218A LEU* 3.7 17.3 - - + -
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Residues in contact with HIS 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 GLU* 3.1 40.8 + - + +
180A ASP* 3.2 14.3 + - - +
182A THR* 1.3 75.4 - - - +
184A ILE* 1.3 59.8 + - + +
187A ARG* 2.9 42.9 + - - +
218A LEU* 3.7 21.1 - - + +
221A LEU* 3.7 22.9 - - + -
222A TYR* 2.6 33.9 + - - +
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Residues in contact with ILE 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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142A GLU* 4.2 21.8 - - + +
145A LEU* 4.1 13.9 - - + +
146A TYR* 3.9 34.5 - - + +
149A TYR* 4.8 1.8 - - + -
176A TYR* 3.2 31.0 - - + +
180A ASP* 3.6 15.3 - - + +
181A ALA 3.2 7.5 + - - +
183A HIS* 1.3 78.2 - - + +
185A ALA* 1.3 61.5 + - - +
187A ARG* 3.9 26.2 - - - +
188A THR* 2.6 36.2 + - - +
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Residues in contact with ALA 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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149A TYR* 3.3 44.7 - - + +
170A ASN* 6.0 0.4 - - - +
181A ALA 3.0 13.3 + - - +
182A THR* 3.7 7.2 - - - +
184A ILE* 1.3 77.7 - - - +
186A LEU* 1.3 63.5 + - + +
188A THR* 3.9 1.4 - - - -
189A VAL* 3.1 29.7 + - - +
205A PHE* 4.7 6.1 - - + -
215A TYR* 4.1 15.5 - - + +
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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 THR* 3.0 29.1 + - + +
185A ALA* 1.3 71.7 - - - +
187A ARG* 1.3 60.9 + - - +
189A VAL* 3.4 0.5 + - - -
190A ARG* 2.8 31.0 + - - +
205A PHE* 3.7 32.5 - - + -
215A TYR* 4.0 18.2 - - + +
218A LEU* 3.6 43.3 - - + +
219A LEU* 3.8 22.4 - - + +
222A TYR* 3.6 20.2 - - + -
223A PHE* 3.9 5.9 - - + -
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Residues in contact with ARG 187 (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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46A PHE* 4.4 3.4 - - + -
146A TYR* 5.6 6.1 - - - +
183A HIS* 2.9 30.4 + - - +
184A ILE* 3.9 31.6 + - - +
186A LEU* 1.3 76.1 - - - +
188A THR* 1.3 64.7 + - - +
190A ARG* 3.3 2.1 + - - +
191A ARG* 3.0 74.7 + - - +
222A TYR* 3.6 31.1 + - + -
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Residues in contact with THR 188 (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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146A TYR* 3.4 39.1 - - + -
149A TYR* 3.8 27.3 - - + +
150A ARG* 4.0 12.1 - - - +
153A LEU* 4.5 4.7 - - + -
184A ILE* 2.6 28.1 + - - +
185A ALA 3.9 2.9 - - - -
187A ARG* 1.3 81.4 + - - +
189A VAL* 1.3 60.9 + - - +
191A ARG* 4.0 5.4 - - - +
192A PHE* 3.0 24.3 + - + +
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Residues in contact with VAL 189 (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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56A VAL* 5.1 0.2 - - + -
149A TYR* 4.6 5.6 - - + -
153A LEU* 4.2 17.7 - - + -
166A PHE* 4.1 21.1 - - + -
185A ALA 3.1 18.4 + - - +
186A LEU 4.0 1.6 - - - +
188A THR* 1.3 73.2 - - - +
190A ARG* 1.3 68.2 + - - +
192A PHE* 3.4 0.5 + - - +
193A LEU* 2.8 46.5 + - + +
203A VAL* 4.1 13.0 - - + -
205A PHE* 3.6 33.7 - - + -
223A PHE* 4.3 5.8 - - + -
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Residues in contact with ARG 190 (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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46A PHE* 3.5 28.7 - - + +
47A LEU* 2.9 34.9 + - - +
49A ASN* 3.6 22.4 - - - +
52A VAL* 4.1 5.7 - - - +
53A ASN* 4.5 4.2 + - - -
186A LEU 2.8 18.3 + - - +
187A ARG* 3.3 6.3 + - - +
189A VAL* 1.3 76.8 - - - +
191A ARG* 1.3 58.2 + - - +
193A LEU* 3.1 4.6 + - - +
194A GLU* 2.7 59.1 + - - +
222A TYR* 3.0 30.6 + - + +
223A PHE* 3.6 32.1 - - + +
224A PRO* 3.8 10.3 - - - +
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Residues in contact with ARG 191 (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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46A PHE* 4.0 28.0 - - + -
187A ARG* 3.0 60.0 + - - +
188A THR* 4.1 5.2 - - - +
190A ARG* 1.3 74.4 - - - +
192A PHE* 1.3 62.0 + - - +
194A GLU* 3.5 12.1 + - - +
195A ILE* 3.1 32.9 + - + +
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Residues in contact with PHE 192 (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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150A ARG* 5.7 0.7 - - - -
153A LEU* 3.7 60.6 - - + -
154A GLN* 4.7 2.2 - - - -
157A LYS* 3.9 14.1 - - + -
188A THR* 3.0 19.0 + - + +
189A VAL 3.8 1.6 - - - +
191A ARG* 1.3 78.1 - - - +
193A LEU* 1.3 69.5 + - + +
195A ILE 3.4 0.3 + - - -
196A HIS* 2.8 69.6 + + + +
200A ILE* 3.6 28.7 - - + -
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Residues in contact with LEU 193 (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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51A ASP* 5.6 0.5 - - - +
52A VAL* 4.0 31.4 - - + +
55A LYS* 4.3 19.3 - - + -
56A VAL* 4.0 23.3 - - + -
189A VAL* 2.8 40.6 + - + +
190A ARG 3.7 3.1 - - - +
192A PHE* 1.3 86.3 - - + +
194A GLU* 1.3 66.3 + - - +
197A GLY* 3.0 36.0 + - - +
200A ILE* 4.6 11.0 - - + -
203A VAL* 4.3 18.8 - - + -
223A PHE* 4.4 1.1 - - + -
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Residues in contact with GLU 194 (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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46A PHE* 3.7 12.6 - - - -
47A LEU 5.6 0.2 + - - -
49A ASN* 4.6 10.4 + - - +
52A VAL* 4.3 6.9 - - + +
190A ARG* 2.7 59.3 + - - +
191A ARG* 3.6 18.7 - - - +
192A PHE 3.2 0.2 - - - -
193A LEU* 1.3 79.1 - - - +
195A ILE* 1.3 70.7 + - + +
197A GLY 4.8 0.3 + - - -
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Residues in contact with ILE 195 (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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191A ARG* 3.1 21.8 + - + +
193A LEU 3.3 0.2 - - - -
194A GLU* 1.3 91.4 - - + +
196A HIS* 1.3 93.8 + - + +
197A GLY 3.5 1.8 + - - -
198A GLU 5.3 0.3 + - - -
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Residues in contact with HIS 196 (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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157A LYS* 3.4 31.2 - - + +
192A PHE* 2.8 56.5 + + + +
195A ILE* 1.3 95.3 + - + +
197A GLY* 1.3 62.5 + - - +
198A GLU 3.4 3.2 + - - -
199A THR* 3.6 19.2 - - - +
200A ILE* 4.5 1.4 - - - +
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Residues in contact with GLY 197 (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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51A ASP* 5.7 1.1 - - - -
55A LYS* 2.3 30.3 + - - -
193A LEU* 3.0 36.1 + - - -
194A GLU 4.8 0.2 + - - -
195A ILE 3.5 2.2 + - - -
196A HIS* 1.3 79.3 - - - +
198A GLU* 1.3 60.3 + - - +
200A ILE* 2.8 15.6 + - - +
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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
------------------------------------------------------------
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