Contacts of the helix formed by residues 187 - 200 (chain A) in PDB entry 5IWM
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 187 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100A ARG* 3.6 0.6 - - - +
101A TYR* 3.5 3.1 - - - -
186A HIS* 1.3 72.1 - - - +
188A LEU* 1.3 58.7 + - - +
189A THR* 2.9 32.4 + - - -
190A GLU* 3.1 36.8 + - - +
191A LEU* 2.9 28.7 + - - +
215A GLY 5.0 0.4 + - - -
217A ASP* 3.4 26.0 + - + +
482A ASP* 3.0 29.0 + - - -
483A ASP 3.3 20.6 + - - -
484A ARG* 3.6 4.0 - - - +
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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
----------------------------------------------------------
101A TYR* 2.7 30.7 + - + +
131A ILE* 4.1 15.5 - - + -
164A PHE* 3.8 26.5 - - + -
165A PRO* 4.2 13.5 - - + -
169A ALA* 4.4 9.4 - - + -
186A HIS 3.6 0.6 + - - -
187A ASN* 1.3 68.0 + - - +
189A THR* 1.3 61.5 + - - +
191A LEU* 4.3 4.3 - - + -
192A ILE* 3.0 46.7 + - + +
476A ILE* 4.4 12.6 - - + +
477A ARG* 5.4 0.2 - - - -
480A PHE* 3.9 35.4 - - + +
481A GLY* 4.5 5.8 - - - +
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Residues in contact with THR 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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187A ASN* 2.9 9.3 + - - -
188A LEU* 1.3 76.4 - - - +
190A GLU* 1.3 63.8 - - + +
192A ILE* 3.6 1.4 + - - +
193A ASN* 3.1 42.4 + - - +
477A ARG* 4.2 22.8 - - + -
481A GLY* 3.2 24.5 - - - -
482A ASP 3.2 15.9 + - - +
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Residues in contact with GLU 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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186A HIS* 5.9 0.3 - - - +
187A ASN* 3.1 24.9 + - - +
189A THR* 1.3 78.8 - - + +
191A LEU* 1.3 65.7 + - + +
193A ASN* 3.3 8.1 + - - +
194A GLY 3.0 17.8 + - - -
212A ASP* 3.3 24.5 - - - +
213A ILE* 3.5 17.1 - - + +
214A GLU* 3.4 26.1 + - - +
215A GLY 3.7 3.6 - - - +
484A ARG* 2.7 51.6 + - - +
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Residues in contact with LEU 191 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PRO* 3.6 27.8 - - + +
168A LEU* 3.8 27.6 - - + -
169A ALA* 3.3 40.4 - - + +
186A HIS* 3.9 17.5 - - + -
187A ASN 2.9 18.7 + - - +
188A LEU* 3.3 8.0 + - - +
190A GLU* 1.3 76.3 - - + +
192A ILE* 1.3 57.9 + - - +
194A GLY* 3.1 3.1 + - - -
195A VAL* 2.9 31.8 + - - +
213A ILE* 3.9 26.7 - - + +
352A LEU* 4.6 2.7 - - + +
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Residues in contact with ILE 192 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A PRO* 4.1 20.2 - - + -
188A LEU* 3.0 36.2 + - + +
189A THR 4.3 1.1 - - - +
191A LEU* 1.3 73.3 - - - +
193A ASN* 1.3 58.5 + - - +
195A VAL* 3.2 7.5 + - - +
196A LEU* 2.9 41.2 + - + +
473A LEU* 3.6 50.9 - - + +
474A THR 4.4 0.2 - - - +
476A ILE* 4.1 11.2 - - + -
477A ARG* 3.6 35.0 - - + +
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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
----------------------------------------------------------
189A THR* 3.1 31.3 + - - +
190A GLU* 3.6 6.9 - - - +
191A LEU 3.3 0.2 - - - -
192A ILE* 1.3 76.0 - - - +
194A GLY* 1.3 61.0 + - - +
196A LEU* 3.2 10.2 + - - +
197A SER* 3.0 26.0 + - - -
212A ASP* 3.3 22.2 + - + +
477A ARG* 3.0 34.0 + - - +
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Residues in contact with GLY 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 GLU 3.0 12.5 + - - -
191A LEU 3.1 3.8 + - - -
193A ASN* 1.3 73.8 - - - +
195A VAL* 1.3 65.0 + - - +
197A SER* 3.2 3.8 + - - -
198A LEU* 2.9 24.3 + - - +
209A LEU* 3.9 13.9 - - - +
212A ASP* 3.6 18.8 + - - +
213A ILE* 4.4 11.4 - - - -
352A LEU* 4.6 3.1 - - - -
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Residues in contact with VAL 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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165A PRO* 4.6 5.2 - - + -
191A LEU 2.9 19.4 + - - +
192A ILE* 3.5 10.3 - - - +
194A GLY* 1.3 74.1 - - - +
196A LEU* 1.3 56.9 + - - +
198A LEU* 3.3 8.9 + - - +
199A SER* 3.0 27.1 + - - -
352A LEU* 3.8 24.6 - - + +
355A TYR* 4.2 23.3 - - + -
356A LEU* 4.0 24.6 - - + +
473A LEU* 3.6 28.7 - - + -
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Residues in contact with LEU 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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192A ILE* 2.9 24.3 + - + +
193A ASN* 3.5 12.6 - - - +
194A GLY 3.2 0.2 - - - -
195A VAL* 1.3 73.5 - - - +
197A SER* 1.3 65.1 + - - +
199A SER* 2.6 22.0 + - - -
200A LYS* 3.2 28.7 + - - +
470A ARG* 4.0 42.0 - - + +
473A LEU* 4.4 15.3 - - + -
474A THR* 4.0 11.4 - - - +
477A ARG* 3.8 26.2 - - - +
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Residues in contact with SER 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 ASN 3.0 6.7 + - - -
194A GLY 3.7 3.8 - - - -
196A LEU* 1.3 75.2 - - - +
198A LEU* 1.3 61.2 + - - +
200A LYS* 3.2 12.8 + - - +
201A ASN* 3.1 23.9 + - - +
204A ILE* 3.7 22.7 - - - +
209A LEU* 5.2 0.2 - - - -
212A ASP* 2.9 27.5 + - - -
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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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194A GLY 2.9 17.8 + - - +
195A VAL* 3.5 7.0 - - - +
197A SER* 1.3 73.1 - - - +
199A SER* 1.3 61.1 + - - +
200A LYS 3.1 4.3 - - - -
201A ASN 3.1 26.8 + - - +
202A PRO* 3.6 9.9 - - + +
204A ILE* 3.7 25.0 - - + +
209A LEU* 4.5 4.7 - - + -
349A LYS* 4.1 21.3 - - + -
352A LEU* 3.7 44.6 - - + +
353A VAL* 3.8 14.6 - - + +
356A LEU* 4.1 16.2 - - + +
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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
----------------------------------------------------------
195A VAL* 3.0 12.0 + - - -
196A LEU* 2.6 26.3 + - - +
198A LEU* 1.3 75.5 - - - +
200A LYS* 1.3 57.3 + - - +
201A ASN 3.4 0.6 + - - -
202A PRO* 5.2 3.9 - - - +
356A LEU* 3.8 23.3 - - - -
466A LEU* 3.9 23.0 - - - +
470A ARG* 3.1 42.6 + - - +
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Residues in contact with LYS 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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196A LEU* 3.4 28.9 - - - +
197A SER* 3.2 12.9 + - - +
198A LEU 3.1 0.6 - - - -
199A SER* 1.3 80.7 - - - +
201A ASN* 1.3 60.2 + - - +
202A PRO* 4.2 3.6 - - - +
470A ARG* 4.1 28.0 - - - +
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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