Contacts of the strand formed by residues 196 - 204 (chain A) in PDB entry 1JG4
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 GLN 196 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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167A GLY* 3.9 17.2 - - - -
188A PRO* 3.7 9.6 - - + +
189A VAL 3.5 8.7 - - - +
190A GLY 4.1 9.6 - - - +
191A SER 3.1 28.3 + - - +
192A TYR 3.4 8.7 + - - -
193A HIS* 3.8 6.1 - - - +
194A LEU 3.8 2.6 - - - +
195A TRP* 1.3 78.3 - - - +
197A GLU* 1.3 58.1 + - - +
215A GLY* 3.2 6.8 - - - -
216A VAL* 2.8 39.8 + - + +
217A ALA* 3.6 4.5 - - - -
218A PHE* 2.8 52.8 + - - +
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Residues in contact with GLU 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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188A PRO* 3.4 0.3 - - - +
189A VAL 2.8 35.5 + - - +
196A GLN* 1.3 73.9 - - - +
198A LEU* 1.3 64.3 + - - +
199A LEU* 3.3 14.3 + - + +
212A ASN* 3.3 39.1 - - + +
214A GLY* 2.8 38.6 + - - -
215A GLY* 3.9 4.5 + - - -
216A VAL* 4.3 2.0 - - - -
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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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79A MET* 4.5 10.5 - - - -
82A ILE* 4.3 10.1 - - + -
83A MET* 4.1 31.6 - - + -
86A ILE* 4.2 13.5 - - + -
186A ILE* 4.0 22.4 - - + -
187A ILE 3.9 13.2 - - - +
188A PRO* 4.3 9.4 - - + -
197A GLU* 1.3 70.8 - - - +
199A LEU* 1.3 61.9 + - - +
212A ASN* 3.7 1.4 - - - -
213A HIS* 2.7 55.1 + - + +
214A GLY 2.9 16.7 + - - +
216A VAL* 4.1 12.2 - - + +
218A PHE* 4.9 3.8 - - + -
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Residues in contact with LEU 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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171A ILE* 4.1 22.0 - - + -
185A LEU 3.6 0.9 - - - +
186A ILE* 3.3 9.2 - - - +
187A ILE* 2.8 41.0 + - + +
189A VAL* 3.6 30.3 - - + -
197A GLU* 3.8 24.2 - - + +
198A LEU* 1.3 74.8 - - - +
200A GLU* 1.3 60.3 + - - +
201A VAL* 3.9 10.5 - - + -
210A ILE* 4.3 9.9 - - + -
211A LYS 3.7 2.0 - - - +
212A ASN* 2.9 36.8 - - - +
213A HIS* 4.6 1.6 - - - -
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Residues in contact with GLU 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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86A ILE* 3.7 23.1 - - + +
184A LYS* 2.8 25.4 + - + -
185A LEU 3.6 3.6 - - - +
186A ILE* 4.7 2.2 - - + +
199A LEU* 1.3 72.8 - - - +
201A VAL* 1.3 60.4 + - - +
202A ARG* 2.8 40.8 + - + +
209A LYS 3.6 1.2 - - - +
210A ILE* 3.3 4.7 - - - +
211A LYS* 2.9 48.5 + - + +
213A HIS* 2.7 35.7 + - + +
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Residues in contact with VAL 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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171A ILE* 3.7 25.6 - - + -
176A ILE* 3.6 20.2 - - + -
179A LEU* 4.1 1.4 - - - +
184A LYS* 3.2 3.4 - - - -
185A LEU* 2.7 52.8 + - + +
187A ILE* 4.5 8.5 - - + -
199A LEU* 4.1 15.7 - - + -
200A GLU* 1.3 76.4 - - - +
202A ARG* 1.3 61.4 + - - +
203A LYS 4.0 0.5 + - - -
208A ILE* 3.3 32.5 - - + -
209A LYS 3.4 2.5 - - - -
210A ILE* 4.2 8.5 - - + -
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Residues in contact with ARG 202 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182A GLY 5.6 2.5 - - - +
183A GLY 3.5 6.3 - - - +
184A LYS* 3.6 28.5 - - + +
200A GLU* 2.8 34.6 + - + +
201A VAL* 1.3 76.2 - - - +
203A LYS* 1.3 61.1 + - - +
204A THR* 3.6 16.1 + - + +
207A GLY 3.7 0.3 - - - +
208A ILE* 3.3 7.2 - - - +
209A LYS* 2.7 50.6 + - + +
211A LYS* 6.0 1.4 - - - +
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Residues in contact with LYS 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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176A ILE* 3.0 30.9 + - + +
177A GLU* 3.3 16.3 + - - +
179A LEU* 3.0 45.3 + - + +
180A LYS 4.0 7.9 - - - +
181A ILE* 3.7 11.7 - - + +
182A GLY* 2.6 35.2 + - - -
183A GLY 3.0 10.4 + - - +
201A VAL 4.0 1.0 + - - -
202A ARG* 1.3 68.6 - - - +
204A THR* 1.3 60.6 + - - +
208A ILE* 3.9 20.6 - - + -
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Residues in contact with THR 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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181A ILE* 4.9 2.2 - - - -
182A GLY* 4.7 7.0 - - - +
202A ARG* 4.2 20.2 - - + +
203A LYS* 1.3 83.1 - - - +
205A LYS* 1.3 70.8 + - - +
206A ASP* 3.1 22.2 + - - +
207A GLY* 2.6 41.8 + - - +
208A ILE* 5.4 0.5 - - - +
209A LYS* 4.0 12.7 - - + +
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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