Contacts of the strand formed by residues 231 - 243 (chain B) in PDB entry 2G4C
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 231 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94B GLY 4.4 1.6 - - - +
95B CYS* 3.7 13.0 - - - -
145B PHE* 3.4 36.1 - - + -
181B LEU* 5.1 2.7 - - + -
215B PHE* 4.2 24.7 - - + -
216B HIS 4.1 8.5 - - - +
217B PRO* 4.9 0.9 - - + -
229B LYS 4.9 2.5 - - - +
230B SER* 1.3 81.5 - - - +
232B GLY* 1.3 61.9 + - - +
233B GLU 4.2 0.3 + - - -
133D HIS* 2.9 51.5 + - + +
135D PRO* 4.8 8.7 - - + -
147D LEU* 4.1 17.5 - - + -
179D GLY* 6.1 1.8 - - - -
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Residues in contact with GLY 232 (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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93B SER 3.5 16.8 - - - -
94B GLY 3.5 10.1 - - - -
95B CYS* 4.1 2.0 - - - -
214B CYS 3.5 0.7 - - - +
215B PHE* 3.2 8.4 - - - +
216B HIS* 2.7 44.6 + - - -
218B VAL* 4.3 1.0 - - - +
230B SER 4.3 0.4 + - - -
231B ILE* 1.3 76.2 - - - +
233B GLU* 1.3 61.9 + - - -
234B LYS* 5.4 1.6 - - - -
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Residues in contact with GLU 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B GLY* 3.0 22.6 + - - +
96B HIS* 4.6 7.2 + - - +
213B VAL* 3.9 6.5 - - + +
214B CYS 3.5 3.4 - - - -
215B PHE* 3.5 28.9 - - + -
231B ILE 4.2 0.2 + - - -
232B GLY* 1.3 74.3 - - - -
234B LYS* 1.3 67.4 + - - +
343B ASP* 4.4 4.4 - - - +
131D LEU* 3.7 23.8 - - + +
132D HIS* 2.8 48.4 + - - +
133D HIS* 2.9 32.6 + - + +
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Residues in contact with LYS 234 (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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91B LEU 5.4 0.4 + - - -
92B LEU* 2.9 28.8 + - - +
93B SER* 4.3 11.9 - - - +
94B GLY* 4.5 4.8 - - - +
212B GLY 3.5 1.4 - - - +
213B VAL* 3.0 4.5 - - - -
214B CYS* 2.6 42.4 + - - +
216B HIS* 3.6 31.0 - - + +
232B GLY 5.4 0.7 - - - -
233B GLU* 1.3 80.6 - - - +
235B THR* 1.3 61.1 + - - +
236B GLU* 3.5 7.0 + - + -
341B ASP* 3.2 36.5 + - - +
343B ASP* 3.6 8.7 - - + +
344B ARG* 3.1 18.0 - - - +
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Residues in contact with THR 235 (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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107B ARG* 3.0 29.4 + - - +
211B ILE* 4.1 15.0 - - + -
212B GLY* 3.3 8.5 - - - +
213B VAL* 3.7 17.2 - - - +
234B LYS* 1.3 70.4 - - - +
236B GLU* 1.3 61.0 + - - +
341B ASP* 4.0 1.2 - - - -
342B LEU* 2.9 52.4 + - + +
343B ASP* 2.8 19.6 + - - +
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Residues in contact with GLU 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B GLU 3.6 5.0 - - - +
184B ASN* 4.2 4.9 - - - +
185B LEU* 3.7 8.0 + - + +
211B ILE* 3.1 3.5 - - - +
212B GLY 2.6 42.4 + - - +
214B CYS* 3.3 34.6 - - + +
216B HIS* 3.3 26.2 + - - -
234B LYS* 4.0 9.6 - - + +
235B THR* 1.3 80.0 - - - +
237B ALA* 1.3 61.0 + - - +
339B ASN* 3.2 25.8 - - - +
340B GLY 3.3 8.8 - - - +
341B ASP* 4.2 13.9 - - - +
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Residues in contact with ALA 237 (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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114B TRP* 3.5 41.2 + - + +
210B GLN 3.5 4.5 - - - -
211B ILE* 3.6 16.2 - - + -
235B THR 4.2 0.4 + - - -
236B GLU* 1.3 72.9 - - - +
238B SER* 1.3 59.4 + - - +
301B GLU* 5.0 0.2 - - - +
338B VAL* 3.8 1.0 - - - +
339B ASN* 3.5 5.1 - - - +
340B GLY* 3.0 33.1 + - - +
342B LEU* 4.2 11.9 - - + -
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Residues in contact with SER 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TRP* 4.1 4.6 - - - -
185B LEU* 3.6 35.5 - - - +
186B LEU* 4.5 0.9 + - - -
208B LEU 3.6 2.3 - - - +
209B ALA* 3.2 3.1 - - - +
210B GLN* 2.6 41.2 + - - +
237B ALA* 1.3 75.2 - - - +
239B LEU* 1.3 61.1 + - - +
240B VAL* 4.0 17.5 - - - +
337B SER* 5.0 0.9 + - - -
338B VAL 3.4 7.7 + - - -
339B ASN* 3.7 17.6 + - - -
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Residues in contact with LEU 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
114B TRP* 4.2 16.0 - - + -
118B VAL* 3.5 30.5 - - + -
125B VAL* 4.1 11.7 - - + -
207B GLY* 4.0 23.3 - - - -
208B LEU 3.8 4.5 - - - +
209B ALA* 4.3 0.9 - - + +
238B SER* 1.3 72.7 - - - +
240B VAL* 1.3 69.1 + - - +
241B TRP* 3.9 11.0 + - + +
255B TRP* 3.6 38.6 - - + +
259B ARG* 6.4 0.2 - - - -
337B SER* 3.8 1.0 - - - -
338B VAL* 2.9 49.1 + - + +
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Residues in contact with VAL 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B LEU* 4.5 15.3 - - + -
189B ALA* 3.5 28.9 - - + -
190B LEU* 4.2 6.7 - - + -
207B GLY* 3.1 5.5 - - - -
208B LEU 3.1 31.5 + - - +
238B SER* 4.0 13.9 - - - +
239B LEU* 1.3 78.3 - - - +
241B TRP* 1.3 61.6 + - - +
242B PHE* 3.9 24.1 + - + -
335B VAL* 3.6 29.8 - - + -
336B LEU 3.6 4.3 - - - +
337B SER* 4.6 5.2 - - - +
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Residues in contact with TRP 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122B ARG* 5.2 0.7 - - - -
124B GLN* 3.5 31.4 - - - -
125B VAL* 3.7 17.9 - - + -
205B PRO* 3.8 24.6 - - + +
206B TYR* 4.2 4.5 - - - -
207B GLY* 3.2 37.7 - - - -
239B LEU* 3.9 13.9 + - + +
240B VAL* 1.3 72.2 - - - +
242B PHE* 1.3 61.1 + - - +
243B THR* 3.4 30.2 + - + -
251B TRP* 3.2 43.0 - + + -
255B TRP* 3.7 35.0 - + + +
334B CYS 3.4 1.0 - - - +
335B VAL* 3.8 2.1 - - - -
336B LEU* 3.0 45.0 + - + +
338B VAL* 6.2 0.7 - - + -
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Residues in contact with PHE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
189B ALA 4.6 4.7 - - - -
190B LEU* 4.2 13.5 - - + -
193B TYR* 3.4 45.8 - + + -
204B LEU* 3.7 10.2 - - + +
205B PRO* 3.2 22.2 - - - +
206B TYR* 3.0 63.7 + + + +
208B LEU* 3.7 25.1 - - + -
240B VAL* 3.9 27.6 - - + -
241B TRP* 1.3 73.3 - - - +
243B THR* 1.3 56.2 + - - +
311B LEU* 4.5 4.0 - - + -
333B PRO* 4.1 8.3 - - + -
334B CYS 3.8 4.7 - - - -
335B VAL* 4.3 14.8 - - + -
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Residues in contact with THR 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205B PRO* 3.7 4.3 - - - -
241B TRP* 3.7 23.1 - - + +
242B PHE* 1.3 74.8 - - - +
244B PRO* 1.3 77.6 + - - +
247B THR* 3.7 0.7 - - - -
248B SER* 3.6 19.8 + - - +
251B TRP* 3.0 29.5 - - + -
333B PRO* 4.2 2.2 - - - -
334B CYS* 2.6 44.2 + - + +
336B LEU* 4.1 13.5 - - + -
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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