Contacts of the helix formed by residues 200 - 212 (chain B) in PDB entry 1JQE
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 THR 200 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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172B VAL* 3.9 6.1 - - - -
173B VAL* 3.3 16.2 - - + -
174B SER 3.9 0.2 - - - -
175B GLY* 3.6 12.5 - - - -
180B ASP* 3.8 26.9 + - + +
183B TRP* 3.9 20.9 - - + -
198B TYR 5.3 0.7 - - - +
199B ILE* 1.3 82.9 - - - +
201B SER* 1.3 65.0 + - - +
202B ASP* 3.1 24.1 + - - +
203B ASP* 2.9 25.8 + - - +
204B LEU* 3.3 8.7 + - - +
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Residues in contact with SER 201 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS* 4.3 4.8 + - - -
172B VAL* 3.7 8.7 - - - +
173B VAL 3.0 7.7 + - - -
174B SER* 3.7 1.7 + - - -
175B GLY 3.0 20.1 + - - -
200B THR* 1.3 73.4 - - - +
202B ASP* 1.3 60.9 + - - +
204B LEU* 3.2 5.8 + - - +
205B THR* 2.8 36.1 + - - +
217B CYS* 4.3 11.9 - - - -
219B ASP* 4.6 0.7 + - - -
286B SER* 3.0 36.7 + - - -
288B ILE* 4.5 2.7 - - - -
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Residues in contact with ASP 202 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ILE* 5.2 6.0 - - - +
96A ALA* 5.5 5.7 - - - +
99A LYS* 2.5 38.6 + - - +
175B GLY* 3.2 30.1 - - - +
180B ASP* 4.4 5.7 - - - +
184B LYS* 5.0 5.5 + - - -
200B THR* 3.1 7.0 + - - +
201B SER* 1.3 77.5 + - - +
203B ASP* 1.3 62.7 + - - +
205B THR* 3.3 7.6 + - - -
206B GLN* 3.1 39.9 + - - +
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Residues in contact with ASP 203 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198B TYR 3.9 4.1 - - - +
199B ILE* 3.5 27.4 - - + -
200B THR* 2.9 35.1 + - - +
202B ASP* 1.3 78.0 - - - +
204B LEU* 1.3 59.4 + - - +
206B GLN* 3.4 15.1 + - - +
207B MET* 3.0 41.6 + - + +
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Residues in contact with LEU 204 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B LEU* 3.7 12.3 - - + -
151B ILE* 3.8 28.7 - - + -
155B LEU* 4.7 5.3 - - + +
170B ILE* 3.6 29.2 - - + -
172B VAL* 3.5 27.8 - - + -
199B ILE* 3.8 17.3 - - + -
200B THR 3.8 9.6 - - - +
201B SER 3.2 7.0 + - - +
203B ASP* 1.3 76.9 - - - +
205B THR* 1.3 61.2 + - - +
207B MET* 3.2 6.9 + - - +
208B LEU* 2.8 38.7 + - + +
288B ILE* 3.8 15.5 - - + -
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Residues in contact with THR 205 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A LYS* 5.0 6.6 + - - +
115A TRP 4.4 12.4 + - - -
201B SER* 2.8 23.3 + - - +
202B ASP* 3.3 13.9 + - - -
204B LEU* 1.3 71.9 - - - +
206B GLN* 1.3 59.5 + - - +
208B LEU* 4.2 5.6 - - - -
209B ASP* 2.8 37.3 + - - +
215B TYR* 3.5 31.4 + - + -
217B CYS* 4.4 21.5 - - + -
288B ILE* 4.5 6.7 - - + -
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Residues in contact with GLN 206 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92A ALA* 5.9 1.8 - - - +
117A LYS* 4.0 46.9 + - + +
202B ASP* 3.1 31.8 + - - +
203B ASP* 3.5 16.3 + - - +
204B LEU 3.2 0.4 - - - -
205B THR* 1.3 84.5 + - - +
207B MET* 1.3 62.9 + - + +
209B ASP* 3.6 7.2 - - - +
210B ASN* 3.0 34.1 + - - +
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Residues in contact with MET 207 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151B ILE* 3.6 40.2 - - + -
152B PRO* 3.8 29.8 - - + -
155B LEU* 4.2 10.1 - - + -
197B GLN* 5.8 1.3 - - - +
199B ILE* 4.8 5.2 - - + -
203B ASP* 3.0 30.6 + - + +
204B LEU* 3.6 11.7 - - - +
206B GLN* 1.3 77.9 - - + +
208B LEU* 1.3 56.9 + - - +
210B ASN* 3.4 9.1 + - - +
211B LEU* 2.9 35.6 + - + +
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Residues in contact with LEU 208 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B LEU* 3.9 20.4 - - + -
170B ILE* 5.4 2.2 - - + -
204B LEU* 2.8 30.9 + - + +
205B THR* 3.8 3.1 - - - +
207B MET* 1.3 71.2 - - - +
209B ASP* 1.3 65.7 + - - +
211B LEU* 3.1 3.4 + - + -
212B GLY 2.9 18.4 + - - -
213B LEU* 3.2 36.1 + - + +
215B TYR* 3.5 31.9 - - + -
288B ILE* 3.7 33.0 - - + -
290B ILE* 3.7 23.8 - - + -
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Residues in contact with ASP 209 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A TRP 4.1 2.4 - - - +
116A HIS* 2.8 45.5 + - - +
117A LYS 4.7 1.2 + - - -
118A GLU* 5.4 1.5 - - - +
126A ARG* 4.2 20.9 + - - +
205B THR 2.8 21.0 + - - +
206B GLN* 3.6 8.1 - - - +
208B LEU* 1.3 74.7 - - - +
210B ASN* 1.3 63.7 + - - +
212B GLY* 3.0 15.6 + - - -
213B LEU 5.4 0.4 - - - -
215B TYR* 2.6 27.7 + - - -
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Residues in contact with ASN 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A ARG* 2.4 44.0 + - - +
206B GLN* 3.0 28.0 + - - +
207B MET* 3.7 7.9 - - - +
209B ASP* 1.3 76.6 - - - +
211B LEU* 1.3 62.0 + - + +
212B GLY* 3.4 0.7 + - - -
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Residues in contact with LEU 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B PRO* 3.7 21.8 - - + +
155B LEU* 3.7 37.0 - - + -
156B LYS* 4.2 38.3 + - + +
207B MET 2.9 21.2 + - - +
208B LEU* 3.1 6.2 + - + +
210B ASN* 1.3 78.3 - - + +
212B GLY* 1.3 61.2 + - - +
213B LEU* 3.6 23.2 + - + +
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Residues in contact with GLY 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A LYS* 6.2 2.2 - - - -
208B LEU 2.9 4.8 + - - -
209B ASP* 3.0 14.1 + - - -
210B ASN 3.1 1.0 - - - -
211B LEU* 1.3 79.3 - - - +
213B LEU* 1.3 64.6 + - - +
214B LYS 3.9 0.7 + - - -
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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