Contacts of the helix formed by residues 197 - 210 (chain A) in PDB entry 1JVN
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 SER 197 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124A TRP* 3.4 20.1 - - - -
142A ARG 4.4 0.2 - - - +
143A TYR* 3.6 15.2 - - - +
144A TYR 3.0 23.6 + - - -
193A HIS 2.5 24.3 + - - -
194A PRO* 3.1 11.2 + - - +
196A LYS* 1.3 77.5 - - - +
198A GLY* 1.3 65.0 + - - +
200A ALA* 3.5 9.2 + - - +
201A GLY* 3.1 17.6 + - - -
550A ASP* 3.5 5.1 - - - +
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Residues in contact with GLY 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124A TRP* 4.4 0.8 - - - -
194A PRO 3.9 1.6 + - - +
196A LYS 3.7 0.6 + - - -
197A SER* 1.3 76.1 - - - +
199A LYS* 1.3 57.3 + - - -
201A GLY* 3.0 2.6 + - - -
202A LEU* 2.9 30.6 + - - +
287A TYR* 3.7 18.6 - - - -
324A PHE* 2.9 23.3 + - - +
325A VAL* 4.7 0.2 - - - +
548A ARG* 4.2 9.9 - - - -
550A ASP* 3.6 4.7 - - - -
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Residues in contact with LYS 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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24A LEU* 6.5 0.7 - - - -
198A GLY* 1.3 68.3 - - - -
200A ALA* 1.3 58.7 + - - +
202A LEU* 3.0 16.9 + - + +
203A ASN* 2.8 59.4 + - - +
206A GLU* 5.7 2.0 - - - -
287A TYR* 4.0 5.3 + - - -
550A ASP* 2.7 16.5 + - - +
551A GLU* 3.3 31.0 + - - +
552A GLU* 3.7 32.8 + - + +
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Residues in contact with ALA 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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141A LYS* 4.0 24.9 - - + -
142A ARG 3.8 17.7 - - - +
143A TYR* 3.6 11.2 + - + -
197A SER 3.7 8.7 - - - +
198A GLY 3.3 0.2 - - - -
199A LYS* 1.3 76.3 - - - +
201A GLY* 1.3 59.8 + - - +
203A ASN* 3.5 13.1 - - - +
204A VAL* 3.4 25.3 + - - +
550A ASP* 3.1 19.9 + - + +
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Residues in contact with GLY 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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143A TYR* 4.6 2.2 - - - -
194A PRO* 2.8 45.3 - - - +
197A SER* 3.1 13.4 + - - -
198A GLY 3.0 4.8 + - - -
200A ALA* 1.3 75.0 - - - +
202A LEU* 1.3 64.0 + - - +
203A ASN 3.2 0.2 - - - -
204A VAL* 3.1 11.9 + - - -
205A ILE* 3.1 11.6 + - - +
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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
----------------------------------------------------------
20A ALA* 3.8 39.9 - - + +
23A HIS* 3.7 20.2 - - + +
24A LEU* 3.8 13.9 - - + +
194A PRO 3.7 1.9 + - - +
195A GLU* 5.6 0.7 - - - -
198A GLY 2.9 16.8 + - - +
199A LYS* 3.0 17.5 + - + +
201A GLY* 1.3 75.3 - - - +
203A ASN* 1.3 58.8 + - - +
205A ILE* 3.3 8.5 + - + +
206A GLU* 2.9 30.9 + - - +
324A PHE* 4.2 15.5 - - + -
552A GLU* 3.6 38.1 - - + +
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Residues in contact with ASN 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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141A LYS* 4.8 14.1 - - - +
199A LYS* 2.8 50.8 + - - +
200A ALA* 3.5 15.1 - - - +
201A GLY 3.2 0.2 - - - -
202A LEU* 1.3 78.2 - - - +
204A VAL* 1.3 52.4 + - + +
206A GLU* 3.4 14.1 + - - +
207A ASN* 2.8 49.1 + - - +
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Residues in contact with VAL 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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80A MET* 4.4 9.0 - - + -
135A PHE 4.0 15.2 - - - +
136A GLY 5.2 1.1 - - - -
137A LEU* 3.9 17.9 - - + -
143A TYR* 3.7 25.1 - - + +
188A PHE* 3.6 32.2 - - + -
190A THR* 4.4 7.4 - - + -
192A PHE* 4.5 4.3 - - + -
194A PRO* 4.4 4.0 - - + -
200A ALA 3.4 15.0 - - - +
201A GLY 3.1 8.8 + - - +
203A ASN* 1.3 73.6 - - + +
205A ILE* 1.3 60.7 + - - +
207A ASN* 3.3 3.5 + - - +
208A PHE* 3.0 26.9 + - - +
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Residues in contact with ILE 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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17A LEU* 4.3 11.2 - - + -
20A ALA* 4.0 22.9 - - + -
21A ILE* 4.5 13.2 - - + -
24A LEU* 3.6 16.6 - - + -
46A ILE* 5.2 6.7 - - + -
80A MET* 4.5 10.8 - - + -
194A PRO* 3.6 31.0 - - + -
195A GLU* 3.9 14.4 - - + +
201A GLY 3.1 11.9 + - - +
202A LEU* 3.6 9.0 - - + +
204A VAL* 1.3 74.2 - - - +
206A GLU* 1.3 59.7 + - - +
208A PHE* 3.1 7.2 + - - +
209A LEU* 2.9 42.3 + - + +
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Residues in contact with GLU 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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24A LEU* 3.6 31.6 - - + +
26A TYR* 5.7 1.1 - - + +
199A LYS* 5.7 1.7 - - - -
202A LEU 2.9 16.6 + - - +
203A ASN* 3.7 17.7 - - - +
205A ILE* 1.3 76.3 - - - +
207A ASN* 1.3 59.4 + - - +
209A LEU* 3.3 5.2 + - - -
210A LYS* 2.8 71.6 + - + +
212A GLN* 4.8 6.1 - - - +
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Residues in contact with ASN 207 (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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135A PHE* 3.1 30.5 + - - +
136A GLY* 3.5 5.5 + - - -
203A ASN* 2.8 34.3 + - - +
204A VAL* 3.6 2.4 - - - +
205A ILE 3.3 0.2 - - - -
206A GLU* 1.3 78.7 - - - +
208A PHE* 1.3 57.2 + - - +
211A GLN* 3.0 7.1 + - - -
212A GLN* 2.9 64.7 + - - +
214A PRO* 3.2 29.9 - - - +
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Residues in contact with PHE 208 (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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44A ARG* 4.1 8.6 + - + -
45A LEU 3.8 7.2 - - - -
46A ILE* 4.3 6.7 - - + -
78A PRO* 3.5 20.6 - - + -
79A ILE 3.5 40.2 - - - -
80A MET* 3.5 30.3 - - + -
135A PHE* 3.6 10.0 - + - -
186A ASN 4.8 1.1 - - - -
188A PHE* 3.8 27.1 - + + -
204A VAL 3.0 13.7 + - - +
205A ILE 3.1 6.5 + - - +
207A ASN* 1.3 76.6 - - - +
209A LEU* 1.3 83.5 + - + +
211A GLN* 2.9 50.8 + - - +
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Residues in contact with LEU 209 (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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4A VAL* 3.6 33.0 - - + -
21A ILE* 4.4 7.9 - - + -
24A LEU* 4.4 7.6 - - + -
26A TYR* 3.5 52.1 + - + +
44A ARG* 2.6 40.8 + - + +
46A ILE* 4.5 3.4 - - + -
205A ILE* 2.9 35.4 + - + +
206A GLU 3.3 3.3 + - - +
208A PHE* 1.3 96.4 - - + +
210A LYS* 1.3 57.5 + - - +
476B SER* 5.8 0.7 - - - -
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Residues in contact with LYS 210 (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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24A LEU 5.5 3.0 + - - -
26A TYR* 3.3 25.4 - - - +
44A ARG* 4.5 3.3 + - - +
206A GLU* 2.8 52.1 + - + +
209A LEU* 1.3 75.0 - - - +
211A GLN* 1.3 71.2 + - - +
212A GLN* 3.4 30.2 + - - +
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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