Contacts of the helix formed by residues 185 - 195 (chain A) in PDB entry 3NKO
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 MET 185 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A PHE* 3.7 30.5 - - + -
177A TYR* 3.6 23.8 - - + +
178A MET* 4.1 19.3 - - - +
180A LYS* 4.6 7.9 - - + -
181A GLY* 2.8 11.3 + - - +
184A VAL* 1.3 90.4 - - + +
186A PRO* 1.3 61.3 - - - +
188A ILE* 3.9 16.4 - - + -
189A GLU* 2.8 28.5 + - + +
328A LEU* 3.6 34.5 - - + +
332A ASP* 3.1 17.2 - - + +
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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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144A VAL* 3.5 24.3 - - + +
182A SER* 3.4 31.0 - - - +
183A LYS 4.9 1.1 - - - +
184A VAL 3.4 7.9 - - - +
185A MET* 1.3 89.9 - - - +
187A ASN* 1.3 63.9 + - - +
189A GLU* 3.4 1.7 + - - +
190A LYS* 3.0 19.4 + - - +
332A ASP* 3.1 16.2 - - + +
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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
----------------------------------------------------------
143A TRP* 3.4 18.1 - - + +
144A VAL* 3.3 33.2 + - - +
186A PRO* 1.3 78.7 - - - +
188A ILE* 1.3 63.0 + - - +
190A LYS* 3.2 4.5 + - - +
191A LEU* 3.0 24.3 + - - +
332A ASP* 3.0 37.3 + - - +
333A LYS* 5.1 1.8 - - - +
335A VAL* 3.9 19.2 - - + -
336A GLY* 3.3 26.5 - - - +
340A ASP* 5.4 0.5 - - - +
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Residues in contact with ILE 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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173A PHE* 4.7 0.7 - - + -
178A MET* 3.8 33.2 - - + -
185A MET* 3.9 29.2 - - + +
187A ASN* 1.3 69.0 - - - +
189A GLU* 1.3 61.5 + - - +
191A LEU* 3.2 10.7 + - + +
192A ARG* 2.9 27.0 + - - +
331A ILE* 4.2 8.1 - - + -
332A ASP* 2.8 35.8 + - - +
335A VAL* 3.8 21.5 - - + -
355A PHE* 3.7 36.1 - - + -
488A VAL* 5.4 1.1 - - + +
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Residues in contact with GLU 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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178A MET* 4.4 4.4 - - - +
181A GLY* 3.9 16.6 - - - -
182A SER* 3.7 30.1 - - - +
185A MET* 2.8 19.8 + - + +
186A PRO 3.8 3.8 - - - +
188A ILE* 1.3 77.3 - - - +
190A LYS* 1.3 57.5 + - - +
192A ARG* 2.6 46.1 + - - -
193A SER* 2.8 38.0 + - - +
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Residues in contact with LYS 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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143A TRP* 2.8 62.7 + - + +
144A VAL* 4.2 10.5 - - + +
146A ASP* 2.8 34.7 + - - +
147A ASP 4.0 3.2 + - - -
148A CYS* 3.5 31.4 - - - +
186A PRO 3.0 15.0 + - - +
187A ASN* 3.6 7.9 - - - +
188A ILE 3.2 0.2 - - - -
189A GLU* 1.3 73.8 - - - +
191A LEU* 1.3 66.3 + - - +
193A SER* 3.8 5.6 - - - -
194A CYS* 2.9 24.8 + - + +
490A TYR* 4.6 6.4 + - + -
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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
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143A TRP* 3.7 19.7 - - + -
187A ASN 3.0 15.3 + - - +
188A ILE* 3.2 12.3 + - + +
190A LYS* 1.3 78.1 - - - +
192A ARG* 1.3 56.0 + - - +
195A GLY* 2.9 24.4 + - - -
335A VAL* 3.9 25.1 - - + -
339A MET* 4.4 10.8 - - + -
353A VAL* 4.6 18.4 - - + -
355A PHE* 4.6 18.6 - - + -
488A VAL* 3.4 22.3 - - + +
490A TYR* 3.6 37.6 - - + -
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Residues in contact with ARG 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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178A MET* 3.8 39.6 + - + -
188A ILE 2.9 16.2 + - - +
189A GLU* 2.6 40.3 + - - +
191A LEU* 1.3 77.3 - - - +
193A SER* 1.3 79.5 + - - +
195A GLY 3.9 7.8 + - - +
197A HIS* 3.2 73.1 + - + +
488A VAL* 3.8 10.5 - - + -
1014A EDO 3.7 23.7 - - - -
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Residues in contact with SER 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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148A CYS* 4.9 0.2 - - - -
189A GLU* 2.8 28.5 + - - +
190A LYS* 3.6 6.6 + - - -
192A ARG* 1.3 97.5 - - - +
194A CYS* 1.3 72.8 + - - +
197A HIS* 5.5 0.2 - - - -
497A ARG* 3.4 33.4 + - - +
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Residues in contact with CYS 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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148A CYS* 2.0 55.4 - - + -
190A LYS 2.9 12.9 + - - +
193A SER* 1.3 90.1 - - - +
195A GLY* 1.3 60.4 + - - +
490A TYR* 4.2 13.0 - - + -
496A TYR* 3.5 6.2 - - + -
497A ARG* 2.9 33.5 + - - -
1011A EDO 3.2 17.9 - - - -
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Residues in contact with GLY 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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191A LEU 2.9 17.4 + - - -
192A ARG 4.0 7.9 - - - +
193A SER 3.5 0.2 - - - -
194A CYS* 1.3 78.3 - - - +
196A THR* 1.3 59.5 + - - -
197A HIS* 5.2 0.2 + - - -
489A GLY 3.5 8.1 - - - -
490A TYR* 3.9 2.8 - - - -
495A LYS 3.5 6.3 - - - -
497A ARG* 3.1 5.2 + - - -
498A THR 3.1 23.2 + - - +
1011A EDO 3.6 17.0 - - - -
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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