Contacts of the helix formed by residues 195 - 206 (chain A) in PDB entry 4GEK
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 ILE 195 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18A TRP* 4.0 25.4 - - + -
23A ARG* 4.8 16.2 - - + +
24A VAL* 4.0 25.6 - - + +
27A VAL* 3.9 22.0 - - + -
31A MET* 3.8 28.7 - - + -
193A LEU* 4.1 12.1 - - + +
194A GLU* 1.3 78.2 - - - +
196A SER* 1.3 62.9 + - - +
197A GLN 3.4 1.1 - - - -
198A LYS* 3.2 24.0 + - + -
199A ARG* 2.9 25.3 + - + +
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Residues in contact with SER 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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190A TYR* 3.0 54.8 + - - -
191A SER* 3.6 12.8 + - - -
193A LEU* 2.8 22.4 + - - -
194A GLU 3.1 0.6 + - - -
195A ILE* 1.3 81.8 - - - +
197A GLN* 1.3 64.1 + - - +
199A ARG* 3.3 1.2 + - - -
200A SER* 2.9 28.2 + - - -
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Residues in contact with GLN 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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194A GLU 4.2 5.3 + - - +
195A ILE 3.4 0.6 - - - -
196A SER* 1.3 81.9 + - - +
198A LYS* 1.3 59.9 + - + +
200A SER* 3.3 10.2 + - - -
201A MET* 2.9 42.1 + - - +
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Residues in contact with LYS 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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18A TRP* 3.6 22.0 - - + +
23A ARG* 3.9 26.9 - - - +
194A GLU* 5.2 2.5 + - - +
195A ILE* 3.2 21.2 + - + +
197A GLN* 1.3 79.3 - - + +
199A ARG* 1.3 57.6 + - - +
201A MET* 3.2 18.9 + - - +
202A LEU 2.9 24.6 + - - -
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Residues in contact with ARG 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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18A TRP* 3.5 21.7 - - + -
20A PHE* 4.3 0.4 - - - -
31A MET* 3.6 43.2 - - + +
32A ILE* 3.9 10.6 - - - +
35A SER* 4.6 4.6 + - - +
36A VAL* 4.9 5.7 - - - +
136A GLN* 5.1 3.2 - - - +
137A PHE* 4.8 1.4 - - - -
190A TYR* 3.5 20.2 - - + +
195A ILE 2.9 16.7 + - - +
196A SER* 4.4 2.5 - - - -
198A LYS* 1.3 77.7 - - - +
200A SER* 1.3 61.4 + - - +
202A LEU* 3.2 26.6 + - - +
203A GLU* 3.0 49.8 + - - +
206A MET* 5.8 2.0 - - - +
235A PHE* 6.2 0.8 - - - -
302A GEK 2.5 45.2 + - - -
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Residues in contact with SER 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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185A LYS* 4.6 9.1 + - - +
190A TYR* 2.8 28.7 + - - -
196A SER 2.9 14.9 + - - -
197A GLN* 3.5 11.4 - - - -
199A ARG* 1.3 77.5 - - - +
201A MET* 1.3 58.7 - - - +
203A GLU* 3.2 8.2 + - - +
204A ASN* 2.9 43.0 + - - +
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Residues in contact with MET 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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197A GLN* 2.9 28.6 + - - +
198A LYS* 3.2 21.7 + - - +
200A SER* 1.3 73.8 - - - +
202A LEU* 1.3 66.3 + - - +
204A ASN* 3.1 22.0 + - - +
205A VAL* 3.3 17.5 + - - +
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Residues in contact with LEU 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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18A TRP* 3.6 51.1 - - + +
137A PHE* 3.9 24.2 - - + -
198A LYS 2.9 12.4 + - - +
199A ARG* 3.3 42.4 - - - +
201A MET* 1.3 76.1 - - - +
203A GLU* 1.3 63.6 + - + +
205A VAL* 3.1 17.0 + - + +
206A MET* 3.0 30.8 + - + +
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Residues in contact with GLU 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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35A SER* 4.3 15.1 + - - +
36A VAL* 5.8 0.5 - - - +
165A LYS* 2.8 44.4 + - - +
181A HIS* 3.5 17.0 - - - -
185A LYS* 5.1 4.0 + - - -
190A TYR* 4.7 2.3 + - - -
199A ARG* 3.0 49.1 + - - +
200A SER* 3.2 9.4 + - - +
202A LEU* 1.3 76.6 - - + +
204A ASN* 1.3 64.0 + - - +
205A VAL 3.2 1.0 + - - -
206A MET* 3.4 33.5 + - + +
235A PHE* 4.1 5.0 - - - -
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Residues in contact with ASN 204 (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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200A SER* 2.9 31.7 + - - +
201A MET* 3.4 14.6 - - - +
202A LEU 3.1 0.6 - - - -
203A GLU* 1.3 79.4 - - - +
205A VAL* 1.3 65.1 + - + +
206A MET 4.8 1.4 - - - +
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Residues in contact with VAL 205 (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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201A MET 3.3 11.8 + - - +
202A LEU* 3.4 21.3 - - + +
204A ASN* 1.3 84.4 - - + +
206A MET* 1.3 64.8 + - - +
207A LEU* 3.5 15.3 + - - +
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Residues in contact with MET 206 (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 GLN* 3.7 47.8 - - - +
137A PHE* 4.3 15.3 - - + -
165A LYS* 3.8 28.9 - - + -
199A ARG* 5.8 2.5 - - - +
202A LEU* 3.0 31.9 + - + +
203A GLU* 3.4 28.0 + - + +
204A ASN 4.8 1.2 - - - +
205A VAL* 1.3 81.0 - - - +
207A LEU* 1.3 63.8 + - - +
208A THR* 3.7 21.6 + - + +
235A PHE* 6.0 0.2 - - + -
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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