Contacts of the helix formed by residues 185 - 197 (chain A) in PDB entry 2ATW
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 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150A GLU* 5.2 0.7 - - - +
166A TYR* 3.7 31.7 - + + -
168A VAL* 4.0 11.9 - - + +
182A SER* 3.2 14.5 + - - +
183A ARG 3.6 0.8 - - - -
184A THR* 1.3 80.8 + - - +
186A PRO* 1.3 72.5 - - + +
187A ASN* 2.8 56.0 + - + -
188A LEU* 2.8 33.1 + - - +
212A ARG* 3.3 4.9 + - - -
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Residues in contact with PRO 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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184A THR 3.3 6.5 - - - +
185A HIS* 1.3 100.3 - - + +
187A ASN* 1.3 63.3 + - - +
189A VAL* 2.9 27.7 + - - +
190A ARG* 3.5 3.9 + - - +
210A VAL* 4.2 25.2 - - + +
212A ARG* 4.0 23.6 - - + +
315A ARG* 5.5 6.7 - - - +
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Residues in contact with ASN 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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166A TYR* 3.2 33.9 + - + -
185A HIS* 2.8 31.9 + - + -
186A PRO* 1.3 72.6 - - - +
188A LEU* 1.3 64.7 + - - +
189A VAL 3.1 0.2 - - - -
190A ARG* 3.6 33.6 - - + +
191A LYS* 3.0 28.0 + - + +
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Residues in contact with LEU 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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114A ILE* 4.1 20.2 - - + -
164A ARG 4.0 23.3 - - - +
165A CYS 4.2 8.3 - - - -
166A TYR* 4.2 15.8 - - + -
182A SER 4.2 2.0 - - - +
183A ARG* 3.8 37.9 - - - +
185A HIS* 2.8 17.4 + - - +
187A ASN* 1.3 78.3 - - - +
189A VAL* 1.3 56.7 + - - +
191A LYS* 3.5 1.2 + - - +
192A LEU* 3.0 54.2 + - + +
212A ARG* 4.2 2.5 - - - +
250A LEU* 3.8 19.1 - - + -
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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
----------------------------------------------------------
186A PRO 2.9 10.3 + - - +
188A LEU* 1.3 75.9 - - - +
190A ARG* 1.3 64.4 + - - +
192A LEU* 3.4 6.5 + - - +
193A PHE* 3.1 37.7 + - + -
207A ILE* 6.3 0.2 - - + -
210A VAL* 4.6 6.3 - - + -
212A ARG* 3.6 37.0 - - - +
218A SER* 3.9 14.1 - - - +
220A ILE* 3.9 28.3 - - + -
246A VAL* 5.0 0.2 - - + -
250A LEU* 3.9 22.0 - - + -
255A ILE* 5.3 1.8 - - + -
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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
----------------------------------------------------------
186A PRO 3.5 0.8 + - - +
187A ASN* 3.2 37.2 + - + +
189A VAL* 1.3 78.6 - - - +
191A LYS* 1.3 60.9 + - + +
193A PHE* 3.3 4.5 + - - +
194A SER* 3.0 26.2 + - - -
200A ILE* 5.0 0.5 - - - +
207A ILE* 3.1 50.1 + - + +
208A VAL 4.1 4.6 + - - -
209A ALA* 3.8 22.4 - - - +
210A VAL* 3.7 31.1 - - + +
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Residues in contact with LYS 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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112A GLY 3.4 24.6 + - - -
113A GLU* 4.6 1.3 - - - +
114A ILE* 3.7 43.7 - - + +
166A TYR* 4.3 11.7 - - + -
187A ASN* 3.0 19.8 + - + +
188A LEU* 3.8 2.5 - - - +
190A ARG* 1.3 77.0 - - + +
192A LEU* 1.3 66.7 + - - +
194A SER* 3.1 10.1 + - - +
195A LEU* 3.0 24.6 + - - +
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Residues in contact with LEU 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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114A ILE* 3.7 9.4 - - + -
164A ARG* 3.6 37.0 - - + +
188A LEU* 3.0 29.3 + - + +
189A VAL 4.0 2.7 - - - +
191A LYS* 1.3 74.8 - - - +
193A PHE* 1.3 57.6 + - - +
195A LEU* 3.0 10.3 + - + +
196A GLU* 2.9 32.3 + - + +
246A VAL* 4.1 18.2 - - + -
249A GLU* 3.6 23.6 - - + -
250A LEU* 3.5 41.7 - - + -
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Residues in contact with PHE 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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189A VAL* 3.1 33.7 + - + +
190A ARG 3.7 7.6 - - - +
192A LEU* 1.3 77.9 - - - +
194A SER* 1.3 56.0 + - - +
196A GLU 4.4 0.4 - - - +
197A VAL* 2.8 52.0 + - + +
200A ILE* 3.8 19.5 - - + -
207A ILE* 3.9 6.1 - - + -
220A ILE* 3.9 29.4 - - + -
235A CYS* 3.6 23.6 - - + -
243A VAL* 3.9 25.1 - - + -
246A VAL* 3.8 32.1 - - + -
255A ILE* 4.0 14.4 - - + -
257A ILE* 4.1 4.5 - - + -
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Residues in contact with SER 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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190A ARG 3.0 13.3 + - - -
191A LYS* 3.1 14.8 + - - -
193A PHE* 1.3 76.9 - - - +
195A LEU* 1.3 64.9 + - - +
197A VAL 3.6 5.7 + - - +
200A ILE* 3.8 21.3 - - - +
201A ALA* 3.3 36.0 - - - +
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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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114A ILE* 4.0 22.0 - - + -
164A ARG* 3.9 34.3 - - - +
191A LYS 3.0 13.3 + - - +
192A LEU* 3.2 12.1 - - + +
194A SER* 1.3 82.4 - - - +
196A GLU* 1.3 67.5 + - - +
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Residues in contact with GLU 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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164A ARG* 5.2 10.2 + - - -
192A LEU* 2.9 19.8 + - + +
193A PHE 3.1 2.2 + - - +
195A LEU* 1.3 86.9 - - - +
197A VAL* 1.3 65.8 + - + +
198A PRO* 3.6 8.9 - - - +
242A ARG* 3.8 31.2 + - + +
245A ASN* 3.3 36.1 + - + +
246A VAL* 3.9 20.6 - - + +
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Residues in contact with VAL 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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193A PHE* 2.8 43.1 + - + +
194A SER 3.6 5.3 - - - +
195A LEU 3.5 1.6 - - - -
196A GLU* 1.3 81.4 - - + +
198A PRO* 1.3 69.4 - - - +
199A GLU* 3.4 21.3 - - + +
200A ILE* 2.9 37.9 + - + +
201A ALA 2.9 10.2 + - - -
234A ALA* 3.5 29.4 - - + +
235A CYS* 4.1 8.5 - - - +
242A ARG* 4.2 5.4 - - + +
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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