Contacts of the strand formed by residues 192 - 203 (chain A) in PDB entry 2NTC
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 HIS 192 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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133A GLU 5.3 3.1 - - - -
134A ASP* 4.5 5.9 + - - -
135A PRO* 4.0 20.0 - - + +
162A TYR* 4.1 13.0 + - + -
163A THR 3.1 11.2 - - - +
164A THR* 4.2 13.7 - - + +
165A LYS* 4.6 7.6 - - - +
188A ASN* 3.9 2.6 - - - +
189A SER* 2.6 40.8 + - - +
190A TYR 3.0 15.1 + - - -
191A ASN* 1.3 83.0 + - + +
193A ASN* 1.3 69.4 + - - +
220A PHE* 3.0 34.9 - + + -
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Residues in contact with ASN 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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161A ILE 3.9 0.3 - - - +
162A TYR* 3.5 4.8 - - - -
163A THR* 3.1 30.7 + - - +
164A THR 4.1 3.3 - - - +
165A LYS* 3.6 21.2 - - - +
168A ALA* 3.5 23.2 - - + +
186A ARG* 3.1 33.5 + - + +
187A HIS 3.1 15.0 + - - +
188A ASN* 3.5 15.2 + - - -
189A SER 4.4 0.7 - - - +
192A HIS* 1.3 89.5 + - - +
194A ILE* 1.3 66.6 + - - +
244A ILE* 3.5 10.6 - - - +
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Residues in contact with ILE 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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138A PHE* 4.1 15.5 - - + -
139A PRO* 4.3 3.6 - - + -
142A LEU* 3.7 25.6 - - + -
160A ALA* 4.9 0.2 - - + -
161A ILE 3.2 8.7 - - - +
162A TYR* 3.3 27.1 - - + -
186A ARG* 3.5 1.4 - - - -
187A HIS* 2.7 47.7 + - + -
188A ASN 5.1 0.7 - - - +
189A SER* 3.1 28.9 - - - +
193A ASN* 1.3 74.1 - - - +
195A LEU* 1.3 73.7 + - - +
232A MET* 4.7 4.3 - - + -
236A LEU* 3.9 26.5 - - + -
241A PHE* 4.2 1.1 - - + -
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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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159A PHE 4.0 0.2 - - - +
160A ALA* 3.2 6.1 - - - +
161A ILE* 2.9 51.5 + - + +
163A THR* 5.0 2.0 - - + -
168A ALA* 3.8 25.1 - - + +
171A LEU* 3.6 37.2 - - + -
172A TYR* 4.0 17.0 - - + +
175A ILE* 4.7 4.0 - - + -
184A ILE* 4.9 3.4 - - + -
185A SER 3.4 5.4 - - - +
186A ARG* 3.7 33.7 - - + -
193A ASN 5.7 0.2 - - - +
194A ILE* 1.3 76.0 - - - +
196A PHE* 1.3 61.7 + - - +
197A PHE* 4.1 11.7 - - + -
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Residues in contact with PHE 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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158A CYS* 3.5 22.2 - - - -
159A PHE 3.6 6.3 - - - -
160A ALA* 4.6 1.3 - - + +
183A PHE* 3.9 5.4 - + - -
184A ILE* 3.3 1.9 - - - +
185A SER* 2.9 50.6 + - - +
187A HIS* 4.0 1.8 - - - +
194A ILE* 4.0 2.1 + - + -
195A LEU* 1.3 73.5 - - - +
197A PHE* 1.3 63.8 + - - +
198A LEU* 3.2 34.5 - - + -
226A VAL* 4.7 1.8 - - + -
229A GLU 3.8 22.7 - - - -
232A MET* 3.8 27.8 - - + -
233A TYR* 4.0 8.1 - + + -
236A LEU* 4.0 21.3 - - + -
252A LEU* 3.6 21.3 - - + -
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Residues in contact with PHE 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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158A CYS* 3.5 4.0 - - - -
159A PHE* 3.0 64.7 + + + -
161A ILE* 3.9 16.4 - - + -
175A ILE* 3.8 40.2 - - + -
179A TYR* 5.0 2.9 - + - -
181A VAL* 4.1 5.8 - - + -
183A PHE 3.2 14.4 - - - +
184A ILE* 3.7 15.9 - - + -
195A LEU* 4.1 13.2 - - + -
196A PHE* 1.3 84.5 - - - +
198A LEU* 1.3 65.4 + - - +
199A THR* 4.0 19.5 - - + -
208A ILE* 3.8 25.8 - - + -
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Residues in contact with LEU 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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157A ALA* 3.2 12.1 - - + +
158A CYS* 4.0 8.3 - - + -
181A VAL* 3.3 13.5 - - - +
182A THR* 3.2 32.3 + - - +
183A PHE* 3.0 14.7 + - + +
196A PHE* 3.2 40.8 - - + -
197A PHE* 1.3 73.9 - - - +
199A THR* 1.3 64.4 + - - +
229A GLU* 5.1 7.6 - - + -
252A LEU* 4.2 19.7 - - + -
257A PHE* 4.1 26.7 - - + -
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Residues in contact with THR 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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157A ALA* 3.1 31.8 + - - +
159A PHE* 3.8 9.6 - - + -
179A TYR* 4.0 24.2 - - + +
181A VAL* 4.6 1.1 - - + -
182A THR* 4.3 3.7 + - - +
197A PHE* 4.0 22.2 - - + -
198A LEU* 1.3 80.1 - - - +
200A PRO* 1.3 73.9 - - - +
201A HIS 2.7 23.5 + - - -
203A HIS* 3.7 15.4 - - + -
208A ILE* 5.8 0.2 - - + -
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Residues in contact with PRO 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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157A ALA* 5.5 0.7 - - - -
179A TYR 3.5 11.9 - - - +
180A SER* 3.2 31.0 - - - +
182A THR* 3.7 21.9 - - + -
199A THR* 1.3 83.6 - - - +
201A HIS* 1.3 83.1 + - + +
203A HIS* 6.0 0.2 - - - +
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Residues in contact with HIS 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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156A LEU 4.0 0.9 - - - +
157A ALA* 4.1 2.5 - - - +
199A THR* 2.7 32.1 + - - +
200A PRO* 1.3 100.9 - - + +
202A ARG* 1.3 66.3 + - - +
203A HIS* 3.5 16.3 - - + +
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Residues in contact with ARG 202 (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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154A ARG* 4.4 21.2 - - - +
155A THR* 2.7 49.2 + - - +
156A LEU* 3.1 14.1 - - - +
157A ALA* 5.1 4.0 - - + -
201A HIS* 1.3 77.1 - - - +
203A HIS* 1.3 63.7 + - - +
15W G 3.2 22.7 - - - +
16W C 3.9 22.3 + - - +
17W C 5.3 11.8 + - - +
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Residues in contact with HIS 203 (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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155A THR* 3.2 6.5 - - - -
156A LEU 2.8 29.0 + - - -
159A PHE* 3.3 10.2 - + + -
179A TYR* 3.4 37.5 + + - +
199A THR* 3.7 17.9 - - + -
201A HIS* 3.5 33.2 + - + +
202A ARG* 1.3 78.9 + - - +
204A ARG* 1.3 62.0 + - - +
205A VAL 3.8 0.3 + - - -
207A ALA* 5.0 0.2 - - + -
208A ILE* 3.1 28.0 - - + -
15W G 2.9 29.9 + - - +
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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