Contacts of the helix formed by residues 239 - 250 (chain B) in PDB entry 5GRH
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 ASN 239 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A LYS* 4.3 11.3 - - - +
176A ILE* 5.5 3.8 - - - +
206A ASP* 4.2 7.6 + - - +
97B ARG* 6.1 0.4 - - - +
128B ARG* 3.2 28.1 + - - +
134B GLU* 5.0 3.4 + - - -
135B TYR* 5.6 3.8 + - - -
233B MET* 6.6 0.4 - - - -
235B ASN* 5.5 3.1 + - - -
236B LEU 4.1 4.8 + - - -
237B TYR 3.4 0.8 - - - -
238B GLY* 1.3 78.9 + - - +
240B ILE* 1.3 65.1 + - - +
241B VAL* 3.3 2.7 - - - +
242B ASN* 3.0 32.8 + - + +
243B ASN* 2.8 34.6 + - - +
272B ARG* 6.4 0.6 - - - +
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Residues in contact with ILE 240 (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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205A LEU* 3.9 26.9 - - + -
206A ASP* 5.5 0.9 - - - +
209A CYS* 4.1 26.8 - - - +
228A TYR* 5.4 3.6 - - + -
231A ILE* 3.6 36.8 - - + -
232A LEU* 5.4 2.2 - - + +
235A LEU* 5.5 1.8 - - + -
214B VAL* 5.5 1.6 - - + -
218B THR* 3.7 28.3 - - + -
237B TYR* 3.0 29.3 + - + +
238B GLY 3.2 0.8 + - - +
239B ASN* 1.3 76.9 - - - +
241B VAL* 1.3 60.4 + - + +
243B ASN* 3.3 1.2 + - - +
244B VAL* 2.9 35.5 + - + +
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Residues in contact with VAL 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B ILE* 3.9 15.7 - - + -
180B VAL* 4.6 12.1 - - + -
214B VAL* 4.6 13.9 - - + -
217B THR* 4.7 6.5 - - + -
218B THR* 5.2 3.1 - - + -
221B LEU* 4.4 6.7 - - + -
231B MET* 3.5 30.5 - - + -
233B MET* 3.7 32.8 - - + -
237B TYR* 6.0 1.8 - - + -
239B ASN* 3.3 0.8 - - - +
240B ILE* 1.3 80.2 - - + +
242B ASN* 1.3 62.5 + - - +
244B VAL* 3.6 4.3 + - - +
245B CYS* 3.1 30.5 + - - -
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Residues in contact with ASN 242 (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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105B ASN* 4.7 1.1 + - - +
107B ILE* 3.8 29.9 - - + +
109B CYS* 4.4 3.5 - - - -
126B ILE* 3.3 37.5 - - - +
128B ARG* 3.4 21.3 - - - +
233B MET* 5.7 2.3 - - - -
239B ASN* 3.0 39.2 + - + +
240B ILE 3.3 0.6 - - - -
241B VAL* 1.3 77.4 - - - +
243B ASN* 1.3 61.2 - - - +
245B CYS* 3.5 2.9 + - - +
246B ALA* 3.0 26.2 + - - +
270B ALA* 5.6 2.7 - - - +
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Residues in contact with ASN 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A ASP* 3.0 49.2 + - + +
207A THR* 4.7 0.6 - - - +
209A CYS* 4.6 1.3 - - + -
210A LEU* 3.6 33.0 - - + +
239B ASN* 2.8 31.5 + - - +
240B ILE 3.9 1.8 - - - +
242B ASN* 1.3 76.9 - - - +
244B VAL* 1.3 66.4 + - - +
245B CYS 3.2 0.9 - - - -
246B ALA* 3.2 5.7 + - - +
247B GLY 2.9 19.4 + - - -
270B ALA 5.9 0.4 + - - -
271B THR* 5.1 12.1 + - - +
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Residues in contact with VAL 244 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A CYS* 3.9 17.9 - - + -
213A VAL* 3.8 29.5 - - + +
235A LEU* 4.0 21.3 - - + -
218B THR* 5.0 2.5 - - + +
221B LEU* 3.6 37.0 - - + -
222B VAL* 5.0 1.3 - - + -
240B ILE* 2.9 29.1 + - + +
241B VAL 4.0 3.1 - - - +
243B ASN* 1.3 75.6 - - - +
245B CYS* 1.3 59.2 + - - +
247B GLY 3.4 0.3 + - - -
248B LEU* 3.0 32.0 + - + +
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Residues in contact with CYS 245 (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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109B CYS* 3.4 29.6 - - + -
122B ILE* 5.8 0.6 - - + +
124B ILE* 4.0 24.2 - - + -
126B ILE* 3.8 14.6 - - + -
221B LEU* 3.7 24.5 - - - -
231B MET* 5.1 0.7 - - - -
241B VAL* 3.1 27.6 + - - +
242B ASN 3.7 1.6 - - - +
244B VAL* 1.3 76.9 - - - +
246B ALA* 1.3 62.2 + - - +
248B LEU* 3.4 21.1 - - + +
249B VAL* 3.4 12.5 + - - +
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Residues in contact with ALA 246 (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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210A LEU* 4.2 9.6 - - + -
107B ILE* 6.5 0.2 - - + -
109B CYS* 3.8 2.4 - - - -
242B ASN 3.0 17.2 + - - +
243B ASN* 3.2 9.8 + - - +
245B CYS* 1.3 73.9 - - - +
247B GLY* 1.3 64.3 - - - +
248B LEU 3.2 0.5 + - - -
249B VAL* 3.3 10.2 + - - +
250B GLY 3.3 0.5 + - - -
251B GLY* 2.9 30.1 + - - +
252B PRO* 4.9 4.0 - - + -
255B VAL* 4.2 25.8 - - + -
270B ALA* 5.7 4.5 - - + -
271B THR* 6.5 0.7 - - - -
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Residues in contact with GLY 247 (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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210A LEU* 3.5 30.2 - - - +
213A VAL* 3.7 9.7 - - - +
214A GLN* 3.5 24.0 + - - +
117B THR* 5.1 1.7 - - - +
243B ASN 2.9 12.6 + - - -
244B VAL 3.8 2.0 - - - -
246B ALA* 1.3 76.4 - - - +
248B LEU* 1.3 62.4 + - - +
249B VAL 3.5 0.2 + - - -
250B GLY* 3.6 6.8 + - - -
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Residues in contact with LEU 248 (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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110A TYR* 4.3 0.7 - - - +
213A VAL* 3.2 26.2 - - + +
117B THR* 3.5 22.2 + - - +
119B HIS* 3.9 28.9 + - + +
122B ILE* 3.9 21.4 - - + +
124B ILE* 5.4 0.4 - - + -
221B LEU* 3.5 39.7 - - + +
222B VAL* 4.7 2.0 - - - -
225B PRO* 3.8 16.6 - - + -
244B VAL* 3.0 16.5 + - + +
245B CYS* 3.4 21.1 - - + +
247B GLY* 1.3 79.0 - - - +
249B VAL* 1.3 60.6 + - - +
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Residues in contact with VAL 249 (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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109B CYS* 4.0 15.0 - - + +
110B LYS 4.0 22.7 - - - +
111B SER* 4.0 8.7 - - - +
112B LEU* 4.8 8.3 + - - +
115B VAL* 4.0 8.7 - - - +
117B THR* 3.7 12.9 + - - +
122B ILE* 4.0 31.4 - - + -
245B CYS 3.4 13.2 + - - +
246B ALA 3.3 9.8 + - - +
248B LEU* 1.3 79.0 - - + +
250B GLY* 1.3 59.1 + - - +
251B GLY 4.7 0.4 - - - +
254B LEU* 3.8 12.4 - - + +
255B VAL* 3.9 22.0 - - + -
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Residues in contact with GLY 250 (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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214A GLN* 3.0 17.7 + - - -
115B VAL* 4.3 5.8 - - - -
117B THR* 3.9 11.9 - - - +
246B ALA 3.3 0.6 + - - -
247B GLY 3.6 2.7 + - - -
248B LEU 3.4 3.2 + - - -
249B VAL* 1.3 82.3 - - - +
251B GLY* 1.3 58.7 + - - +
254B LEU* 3.3 18.8 - - - +
326B ASP 5.3 2.1 - - - +
327B ILE* 4.2 12.5 - - - +
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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