Contacts of the helix formed by residues 188 - 201 (chain A) in PDB entry 5HJS
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 ASN 188 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A GLN 3.9 0.8 + - - +
187A LEU* 1.3 76.0 - - - +
189A ASP* 1.3 65.7 + - - +
190A ALA* 3.3 5.6 + - - +
191A GLU* 3.0 35.3 + - - +
192A PHE* 3.2 24.5 + - - -
228A TYR* 2.7 25.1 + - - -
232A HIS* 3.4 27.6 + - + -
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Residues in contact with ASP 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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54A VAL* 3.7 22.5 - - + +
58A GLN* 3.1 22.7 + - - +
140A ARG* 3.6 28.9 + - - +
188A ASN* 1.3 76.7 - - - +
190A ALA* 1.3 58.4 + - - +
192A PHE* 3.4 1.0 + - - -
193A ALA* 2.9 30.7 + - - +
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Residues in contact with ALA 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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50A ILE* 3.6 23.1 - - + -
54A VAL* 3.6 15.3 - - + +
188A ASN* 3.3 2.2 + - - +
189A ASP* 1.3 78.0 - - - +
191A GLU* 1.3 59.1 + - - +
193A ALA* 3.5 2.1 + - - +
194A LEU* 3.0 35.4 + - - +
228A TYR* 3.5 36.3 - - + +
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Residues in contact with GLU 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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186A GLN 4.4 0.3 - - - +
187A LEU* 3.4 19.5 - - + -
188A ASN* 3.0 30.0 + - - +
190A ALA* 1.3 74.9 - - - +
192A PHE* 1.4 58.2 + - - +
194A LEU* 3.5 1.6 + - - +
195A LEU* 3.0 32.7 + - - +
225A LEU* 4.1 11.9 - - + +
228A TYR* 3.7 18.5 - - + -
229A VAL* 3.8 5.1 - - + +
232A HIS* 2.7 37.0 + - - +
233A HIS* 4.1 1.9 + - - -
243A MET* 3.5 39.2 - - + +
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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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136A LEU* 3.7 35.2 - - + -
139A SER* 3.7 3.4 - - - -
140A ARG* 3.7 62.6 - - + +
182A MET* 3.6 33.0 - - + -
187A LEU* 3.6 32.5 - - + +
188A ASN 3.2 26.1 + - - +
191A GLU* 1.4 75.1 - - - +
193A ALA* 1.4 56.9 - - - +
195A LEU* 3.4 4.4 + - + +
196A ILE* 2.9 38.6 + - + +
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Residues in contact with ALA 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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50A ILE* 6.4 0.2 - - + -
53A LEU* 4.0 31.9 - - + +
54A VAL* 4.6 3.4 - - + -
57A GLN* 3.7 20.1 + - + +
107A PHE* 3.9 13.0 - - + -
189A ASP 2.9 19.0 + - - +
190A ALA* 3.8 6.1 - - - +
192A PHE* 1.4 74.0 - - - +
194A LEU* 1.3 58.9 + - + +
196A ILE* 3.6 3.7 + - - +
197A ALA* 3.1 26.7 + - - +
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Residues in contact with LEU 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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49A MET* 4.1 15.0 - - + -
50A ILE* 3.9 30.3 - - + -
53A LEU* 4.0 12.6 - - + -
190A ALA 3.0 25.4 + - - +
193A ALA* 1.3 75.4 - - + +
195A LEU* 1.3 59.8 + - - +
197A ALA* 3.2 3.9 + - - +
198A ILE* 2.9 34.6 + - - +
221A TYR* 4.0 33.5 - - + +
224A ALA* 4.2 1.8 - - + +
225A LEU* 3.9 42.2 - - + -
228A TYR* 4.6 4.9 - - + -
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Residues in contact with LEU 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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136A LEU* 4.3 23.8 - - + -
182A MET* 4.7 3.4 - - + -
187A LEU* 3.5 30.5 - - + -
191A GLU 3.0 18.2 + - - +
192A PHE* 3.8 5.8 - - + +
194A LEU* 1.3 75.9 - - - +
196A ILE* 1.4 58.2 + - - +
198A ILE* 3.4 6.4 + - + +
199A SER* 2.9 28.9 + - - -
225A LEU* 4.1 19.1 - - + -
243A MET* 3.6 37.5 - - + +
244A LEU* 4.4 0.9 - - + +
246A LYS* 5.0 3.1 - - + -
247A LEU* 3.9 28.7 - - + +
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Residues in contact with ILE 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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57A GLN* 3.7 15.9 - - - +
107A PHE* 3.6 24.2 - - + -
133A VAL* 3.6 27.8 - - + +
136A LEU* 3.8 27.1 - - + -
137A GLU* 3.3 30.5 - - + +
140A ARG* 4.1 6.3 - - - +
192A PHE* 2.9 25.0 + - + +
193A ALA 3.7 4.5 - - - +
194A LEU 3.2 0.2 - - - -
195A LEU* 1.4 74.8 - - - +
197A ALA* 1.4 62.5 + - - +
199A SER* 3.1 5.9 + - - -
200A ILE* 3.0 32.8 + - + +
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Residues in contact with ALA 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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53A LEU* 4.4 0.4 - - + -
107A PHE* 4.7 0.2 - - - -
111A LEU* 3.8 31.9 - - + -
193A ALA 3.1 15.1 + - - +
194A LEU* 3.2 8.3 + - - +
196A ILE* 1.4 75.1 - - - +
198A ILE* 1.4 60.4 + - - +
200A ILE* 3.4 1.2 + - - +
201A PHE* 3.1 31.8 + - - -
221A TYR* 3.6 32.3 - - + -
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Residues in contact with ILE 198 (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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194A LEU 2.9 27.2 + - - +
195A LEU* 3.7 7.6 - - + +
197A ALA* 1.4 71.5 - - - +
199A SER* 1.3 62.1 + - - +
201A PHE* 3.5 6.1 + - - -
202A SER* 3.6 0.7 + - - -
218A GLN* 3.0 37.2 + - + +
221A TYR* 3.8 20.9 - - + +
222A VAL* 3.9 28.7 - - + -
225A LEU* 3.7 30.1 - - + -
244A LEU* 4.0 5.4 - - + -
247A LEU* 3.5 25.1 - - + -
245B MET* 3.6 18.1 - - + +
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Residues in contact with SER 199 (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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129A SER* 4.3 1.2 - - - -
132A GLU* 3.1 35.5 + - - +
133A VAL* 4.3 10.1 - - - +
136A LEU* 4.7 8.3 - - - -
195A LEU 2.9 14.7 + - - -
196A ILE* 3.1 11.0 + - - -
198A ILE* 1.3 76.8 - - - +
200A ILE* 1.3 60.0 + - - +
202A SER* 2.7 22.6 + - - -
205A ARG* 3.0 16.7 + - - +
247A LEU* 4.8 13.0 - - - -
250A LEU* 4.8 1.0 - - - +
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Residues in contact with ILE 200 (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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104A ILE* 4.6 10.1 - - + -
107A PHE* 4.6 4.0 - - + -
108A ALA* 4.3 13.2 - - + -
111A LEU* 3.9 24.7 - - + -
114A PHE* 4.0 32.8 - - + -
125A LEU* 3.3 29.3 - - + +
126A LEU* 4.8 4.3 - - + -
129A SER* 3.6 21.4 - - - +
133A VAL* 4.0 11.2 - - + -
196A ILE* 3.0 38.9 + - + +
197A ALA 3.4 4.0 + - - +
199A SER* 1.3 76.8 - - - +
201A PHE* 1.3 60.0 + - + +
202A SER* 3.0 7.3 + - - -
205A ARG* 4.9 1.0 + - - -
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Residues in contact with PHE 201 (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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111A LEU* 3.8 17.9 - - + -
112A PRO 4.0 4.9 - - - -
114A PHE* 3.7 40.6 - + + -
117A LEU* 3.9 17.5 - - + -
125A LEU* 4.1 10.3 - - + -
197A ALA 3.1 23.3 + - - +
198A ILE 3.7 5.4 - - - -
200A ILE* 1.3 73.1 - - + +
202A SER* 1.3 56.9 + - - +
203A ALA 3.7 1.0 + - - -
214A VAL* 3.5 22.2 - - + +
217A LEU* 3.7 28.3 - - + -
218A GLN* 3.2 33.3 - - + +
221A TYR* 3.4 35.4 - + - -
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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