Contacts of the helix formed by residues 172 - 190 (chain A) in PDB entry 5E0F
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 LYS 172 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A TRP* 2.9 41.2 + - - +
135A ASP* 3.1 20.9 + - - +
169A ALA* 3.0 28.1 + - + +
171A GLU* 1.3 84.7 - - + +
173A ASP* 1.3 65.2 + - - +
174A TYR* 4.2 11.1 - - - +
175A VAL* 3.1 9.5 + - + +
176A ARG* 2.9 25.3 + - - +
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Residues in contact with ASP 173 (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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171A GLU 3.6 4.0 + - - -
172A LYS* 1.3 71.3 - - - +
174A TYR* 1.3 57.9 + - - +
176A ARG* 4.1 12.4 + - - +
177A SER* 2.8 40.9 + - - -
213A LYS* 2.7 31.4 + - - -
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Residues in contact with TYR 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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130A PRO* 2.7 49.1 + - - +
131A TYR* 4.2 2.0 - + - -
135A ASP* 3.5 28.7 - - - -
172A LYS* 3.2 14.6 - - - +
173A ASP* 1.3 80.0 + - - +
175A VAL* 1.3 58.9 + - - +
177A SER* 3.2 7.7 + - - -
178A LYS* 3.0 55.7 + - + +
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Residues in contact with VAL 175 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A TYR* 4.0 20.2 - - + +
135A ASP* 3.6 43.1 - - + +
168A LEU* 4.2 8.3 - - + -
169A ALA 3.6 25.1 - - - +
170A LEU* 3.8 26.9 - - + -
172A LYS* 3.1 9.2 + - + +
174A TYR* 1.3 71.5 - - + +
176A ARG* 1.3 67.6 - - - +
177A SER 3.2 0.2 + - - -
178A LYS* 3.2 2.3 + - - +
179A ILE* 3.0 28.6 + - + +
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Residues in contact with ARG 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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170A LEU 2.8 25.9 + - - +
171A GLU* 3.4 20.2 + - - +
172A LYS 2.9 18.6 + - - +
173A ASP* 3.7 13.0 + - - +
175A VAL* 1.3 76.6 - - - +
177A SER* 1.3 58.2 + - - +
179A ILE* 3.5 2.3 + - - +
180A ALA* 2.9 28.9 + - - +
205A GLY 4.3 2.4 + - - -
206A ASP* 2.9 25.9 + - - +
209A ALA* 3.2 32.1 - - - +
210A ILE* 3.9 30.0 - - + +
213A LYS* 3.8 16.5 - - - +
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Residues in contact with SER 177 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173A ASP* 2.8 29.0 + - - -
174A TYR* 3.5 9.0 - - - -
175A VAL 3.1 0.2 - - - -
176A ARG* 1.3 75.3 - - - +
178A LYS* 1.3 63.0 + - - +
180A ALA* 3.4 1.8 + - - +
181A GLU* 2.8 29.3 + - - +
213A LYS* 3.3 26.4 + - - +
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Residues in contact with LYS 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 4.2 9.1 - - + -
129A VAL* 3.1 42.8 + - + -
130A PRO* 4.0 6.5 - - - +
131A TYR* 3.9 15.5 - - + +
174A TYR* 3.0 56.5 + - + +
175A VAL 3.2 4.0 + - - +
177A SER* 1.3 73.8 - - - +
179A ILE* 1.3 65.0 + - - +
181A GLU* 2.9 33.8 + - - +
182A TYR* 3.2 21.5 + - - +
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Residues in contact with ILE 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A TYR* 3.7 13.2 - - + +
99A ILE* 3.6 39.5 - - + +
131A TYR* 3.6 12.8 - - - +
168A LEU* 4.5 1.1 - - + -
170A LEU* 3.3 34.3 - - + -
175A VAL* 3.0 22.1 + - + +
176A ARG 3.8 3.4 - - - +
178A LYS* 1.3 77.0 - - - +
180A ALA* 1.3 57.3 + - - +
182A TYR* 3.2 8.9 + - + +
183A MET* 2.9 40.8 + - + +
210A ILE* 3.8 18.8 - - + -
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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
----------------------------------------------------------
176A ARG 2.9 17.5 + - - +
177A SER* 3.7 4.3 - - - +
179A ILE* 1.3 77.3 - - - +
181A GLU* 1.3 53.8 + - - +
183A MET* 3.9 0.6 - - - +
184A ASN* 2.7 44.9 + - - +
210A ILE* 4.3 5.3 - - + +
213A LYS* 3.5 33.9 - - + -
214A LEU* 4.0 15.9 - - + -
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Residues in contact with GLU 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A SER 2.8 17.8 + - - +
178A LYS* 2.9 42.3 + - - +
179A ILE 3.2 0.2 - - - -
180A ALA* 1.3 75.2 - - - +
182A TYR* 1.3 58.4 + - - +
184A ASN* 3.4 5.7 + - - +
185A HIS* 3.0 30.0 + - + +
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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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45A PRO* 3.4 22.5 - - - +
46A ASN* 3.4 30.2 + - + +
67A TYR* 3.7 50.5 - + + -
69A LEU* 3.7 21.5 - - + -
95A VAL* 4.0 2.4 - - - +
96A ASP 4.5 1.9 + - - -
97A ALA* 4.9 10.0 - - + -
98A VAL 5.1 2.0 - - - -
99A ILE* 4.8 14.1 - - + -
178A LYS 3.2 9.4 + - - +
179A ILE* 3.3 8.1 - - - +
181A GLU* 1.3 79.0 - - - +
183A MET* 1.3 74.5 + - + +
185A HIS* 3.2 23.2 - - - +
186A LEU* 3.2 28.2 + - + +
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Residues in contact with MET 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA* 4.8 2.9 - - + -
99A ILE* 4.7 10.3 - - + -
179A ILE* 2.9 36.9 + - + +
182A TYR* 1.3 88.3 - - + +
184A ASN* 1.3 58.8 + - - +
186A LEU* 3.3 4.5 + - - +
187A ILE* 2.9 31.2 + - - +
194A PHE* 3.6 51.1 - - + -
196A LEU* 4.1 16.8 - - + -
210A ILE* 4.0 15.0 - - - -
211A LEU* 4.4 7.0 - - + -
214A LEU* 3.7 27.6 - - + -
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Residues in contact with ASN 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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180A ALA* 2.7 29.0 + - - +
181A GLU* 4.0 5.5 - - - +
183A MET* 1.3 69.9 - - - +
185A HIS* 1.3 65.2 + - - +
187A ILE* 3.8 4.8 - - - +
188A ASP* 3.0 31.1 + - - +
213A LYS 3.2 22.0 + - - -
214A LEU* 3.3 10.3 - - - +
215A HIS* 2.8 55.4 + - + +
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Residues in contact with HIS 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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67A TYR 4.8 5.9 + - - -
68A LYS* 6.2 0.9 - - - -
69A LEU* 3.5 26.5 - - + +
76A GLU* 2.7 39.8 + - - -
80A ARG* 3.8 11.0 + - - -
181A GLU* 3.0 13.6 + - + +
182A TYR* 3.2 14.3 - - - +
184A ASN* 1.3 75.5 - - - +
186A LEU* 1.3 61.9 + - + +
188A ASP* 3.4 4.7 + - - +
189A ILE* 3.1 38.5 + - + +
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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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45A PRO* 4.2 3.6 - - + -
69A LEU* 3.9 23.8 - - + -
79A PHE* 3.5 35.9 - - + -
95A VAL* 3.8 22.0 - - + -
182A TYR* 3.2 43.6 + - + +
183A MET* 3.5 6.7 - - - +
184A ASN 3.2 0.2 - - - -
185A HIS* 1.3 74.3 - - + +
187A ILE* 1.3 66.0 + - - +
189A ILE* 3.3 5.4 + - - +
190A GLY 3.1 6.9 + - - -
191A VAL* 3.1 35.1 + - + +
194A PHE* 3.8 11.7 - - + -
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Residues in contact with ILE 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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183A MET 2.9 21.1 + - - +
184A ASN* 3.5 20.6 + - - +
186A LEU* 1.3 73.8 - - - +
188A ASP* 1.3 61.1 + - - +
190A GLY* 2.9 22.3 + - - -
191A VAL* 3.6 11.0 + - + +
194A PHE* 3.9 24.9 - - + -
214A LEU* 4.0 15.9 - - + -
215A HIS* 3.8 21.5 - - + +
216A ASN 3.3 26.5 - - - +
217A LEU* 3.9 20.9 - - + -
218A ASN* 4.0 8.8 + - - +
228A PRO* 4.3 6.3 - - + -
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Residues in contact with ASP 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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80A ARG* 5.6 1.1 + - - -
184A ASN 3.0 18.6 + - - +
185A HIS* 4.0 4.3 - - - +
187A ILE* 1.3 82.3 - - - +
189A ILE* 1.3 59.1 + - - +
215A HIS* 2.8 40.9 + - - +
216A ASN 4.7 1.9 - - - +
218A ASN* 2.8 31.8 + - - +
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Residues in contact with ILE 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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69A LEU* 3.7 30.3 - - + -
79A PHE* 4.0 9.4 - - + -
80A ARG* 3.6 57.9 - - + +
83A VAL* 3.5 33.3 - - + +
84A THR* 4.7 3.9 + - - +
185A HIS* 3.1 28.7 + - + +
186A LEU* 3.4 8.5 - - - +
187A ILE 3.2 0.2 - - - -
188A ASP* 1.3 77.6 - - + +
190A GLY* 1.3 56.0 + - - +
221A TRP* 3.6 14.6 - - - -
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Residues in contact with GLY 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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83A VAL* 3.5 10.3 - - - +
87A ASN* 2.9 25.5 + - - +
93A ILE 5.4 1.6 + - - -
186A LEU 3.1 1.0 + - - -
187A ILE 2.9 10.4 + - - -
188A ASP 4.2 0.9 - - - -
189A ILE* 1.3 79.3 - - - +
191A VAL* 1.3 69.7 + - - +
192A ALA 3.6 0.9 + - - -
218A ASN* 4.2 4.5 - - - -
221A TRP* 3.9 10.1 - - - -
222A PHE* 3.7 9.8 - - - -
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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
------------------------------------------------------------
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