Contacts of the strand formed by residues 233 - 243 (chain D) 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 GLU 233 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130B ALA 4.9 0.2 - - - +
131B LEU* 3.6 23.0 - - + +
132B HIS* 2.8 48.9 + - - +
133B HIS* 3.0 25.6 + - + +
94D GLY* 3.0 23.5 + - - +
96D HIS* 5.2 3.8 + - - -
213D VAL* 4.0 7.9 - - + +
214D CYS 3.7 2.7 - - - -
215D PHE* 3.3 32.3 - - + -
231D ILE* 4.4 4.9 - - + +
232D GLY* 1.3 72.3 - - - -
234D LYS* 1.3 64.0 + - - +
343D ASP* 4.6 2.3 - - - +
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Residues in contact with LYS 234 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91D LEU 4.6 4.1 + - - -
92D LEU* 3.4 26.5 + - - +
93D SER 4.7 4.0 - - - +
94D GLY* 4.1 14.6 - - - -
96D HIS* 5.9 0.4 - - - -
213D VAL* 3.3 3.7 - - - -
214D CYS 2.9 33.0 + - - +
216D HIS* 4.6 9.2 - - + +
232D GLY 4.6 5.4 - - - +
233D GLU* 1.3 78.0 - - - +
235D THR* 1.3 63.2 + - - +
236D GLU* 3.5 17.3 + - + +
341D ASP* 2.7 42.5 + - - +
343D ASP* 3.6 15.7 - - - +
344D ARG* 3.6 25.6 - - - +
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Residues in contact with THR 235 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D ARG* 2.9 33.5 + - - +
211D ILE* 4.2 20.4 - - + -
212D GLY* 3.4 16.4 - - - +
213D VAL* 3.7 14.5 - - + +
234D LYS* 1.3 71.5 - - - +
236D GLU* 1.3 63.0 + - - +
341D ASP* 4.1 1.0 - - - +
342D LEU* 3.2 35.4 + - + +
343D ASP* 2.7 23.3 + - - -
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Residues in contact with GLU 236 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183D GLU 4.2 4.7 - - - +
184D ASN* 4.3 2.8 - - - +
185D LEU* 3.3 7.1 - - + +
211D ILE* 3.3 1.6 - - - -
212D GLY 2.4 56.0 + - - +
214D CYS* 3.1 28.1 - - - +
216D HIS* 3.3 24.7 + - - -
234D LYS* 3.5 14.7 + - + +
235D THR* 1.3 76.2 - - - +
237D ALA* 1.3 58.2 + - - +
339D ASN* 3.6 35.5 + - - +
340D GLY 3.6 5.8 - - - +
341D ASP* 4.7 9.5 - - + +
342D LEU* 5.2 0.2 - - - -
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Residues in contact with ALA 237 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D TRP* 3.7 28.8 + - + +
210D GLN 3.4 5.4 - - - -
211D ILE* 3.5 27.4 - - + -
235D THR 4.1 1.0 + - - -
236D GLU* 1.3 72.3 - - - +
238D SER* 1.3 62.0 + - - +
338D VAL 4.8 0.2 - - - -
339D ASN* 3.7 1.0 - - - -
340D GLY* 3.1 32.2 + - - +
342D LEU* 4.2 14.8 - - + +
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Residues in contact with SER 238 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D TRP* 3.7 7.9 - - - -
185D LEU* 3.9 25.3 + - - +
186D LEU 4.9 0.8 + - - -
189D ALA* 5.9 0.3 - - - +
208D LEU 3.9 1.2 + - - +
209D ALA* 3.4 4.2 - - - -
210D GLN* 2.6 38.0 + - - +
236D GLU 4.1 0.4 - - - -
237D ALA* 1.3 76.3 - - - +
239D LEU* 1.3 60.6 + - - +
240D VAL* 4.3 13.7 - - - +
337D SER* 5.7 1.1 - - - -
338D VAL 3.3 13.0 - - - -
339D ASN* 3.7 17.5 - - - -
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Residues in contact with LEU 239 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114D TRP* 4.4 7.3 - - + -
118D VAL* 3.4 21.5 - - + +
125D VAL* 4.4 15.9 - - + -
207D GLY* 4.2 15.3 - - - -
208D LEU 4.1 6.5 - - - +
209D ALA* 4.6 1.1 - - - +
238D SER* 1.3 74.0 - - - +
240D VAL* 1.3 77.9 + - - +
241D TRP* 4.2 11.9 - - + +
255D TRP* 3.4 49.6 - - + -
259D ARG* 6.0 1.6 - - - -
336D LEU 3.6 1.9 - - - +
337D SER* 3.6 1.2 - - - -
338D VAL* 2.7 51.1 + - + +
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Residues in contact with VAL 240 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D LEU* 3.4 31.0 - - + -
189D ALA* 3.7 20.9 - - + -
190D LEU* 4.1 10.1 - - + -
207D GLY* 3.4 2.9 - - - -
208D LEU* 3.1 31.1 + - + +
238D SER* 4.3 12.3 - - - +
239D LEU* 1.3 79.7 - - - +
241D TRP* 1.3 59.7 + - - +
242D PHE* 3.5 37.6 + - + -
335D VAL* 4.9 5.2 - - + -
336D LEU 3.8 4.7 - - - +
337D SER* 4.7 1.3 - - - +
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Residues in contact with TRP 241 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D ARG* 5.1 2.7 - - - -
124D GLN* 3.7 30.1 - - + -
125D VAL* 3.9 15.3 - - + -
205D PRO* 3.8 21.5 - - + -
206D TYR* 3.2 9.0 - - - -
207D GLY* 2.9 36.1 - - - -
239D LEU* 3.8 12.7 - - + -
240D VAL* 1.3 70.6 - - - +
242D PHE* 1.3 63.0 + - - +
243D THR* 3.5 17.1 + - + +
251D TRP* 3.1 40.0 - + + -
255D TRP* 2.9 46.4 - + - +
334D CYS 3.1 3.6 - - - +
336D LEU* 3.0 48.1 + - + +
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Residues in contact with PHE 242 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D LEU* 3.4 17.7 - - + -
193D TYR* 3.5 52.7 - + + -
204D LEU* 4.9 2.7 - - + -
205D PRO* 3.0 21.9 - - - +
206D TYR* 3.4 32.0 + + + +
208D LEU* 3.9 26.0 - - + -
240D VAL* 3.5 25.4 - - + -
241D TRP* 1.3 68.6 - - - +
243D THR* 1.3 68.4 + - - +
311D LEU* 4.4 2.5 - - + -
333D PRO* 4.0 12.6 - - + -
334D CYS 3.5 3.4 - - - -
335D VAL* 3.4 34.3 - - + -
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Residues in contact with THR 243 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D LEU* 4.0 2.9 - - - -
205D PRO* 3.4 15.0 - - + -
241D TRP* 3.5 22.9 - - + +
242D PHE* 1.3 82.4 - - - +
244D PRO* 1.3 80.7 + - - +
248D SER* 3.8 15.1 - - - -
251D TRP* 3.4 23.5 - - + +
333D PRO* 2.9 12.0 - - - +
334D CYS* 2.6 41.5 + - - +
336D LEU* 5.2 4.4 - - + +
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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