Contacts of the strand formed by residues 233 - 243 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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130A ALA 4.8 0.2 - - - +
131A LEU* 3.6 23.1 - - + +
132A HIS* 2.8 53.1 + - - +
133A HIS* 3.0 25.4 + - + +
94C GLY* 3.1 23.4 + - - +
96C HIS* 5.2 3.5 + - - -
213C VAL* 4.0 6.6 - - + +
214C CYS 3.7 2.9 - - - -
215C PHE* 3.3 26.8 - - + -
231C ILE* 4.4 5.4 - - + +
232C GLY* 1.3 73.1 - - - -
234C LYS* 1.3 63.8 + - - +
343C ASP* 4.6 2.4 - - - +
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Residues in contact with LYS 234 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91C LEU 4.6 4.5 + - - -
92C LEU 3.4 26.1 + - - +
93C SER 4.7 4.5 - - - +
94C GLY* 4.1 13.9 - - - -
96C HIS* 5.9 0.4 - - - -
213C VAL* 3.2 4.4 - - - -
214C CYS* 2.9 34.2 + - - +
216C HIS* 4.6 9.4 - - + +
232C GLY 4.6 5.6 - - - +
233C GLU* 1.3 78.7 - - - +
235C THR* 1.3 60.9 + - - +
236C GLU* 3.5 16.3 + - + +
341C ASP* 2.7 42.5 + - - +
343C ASP* 3.6 16.1 - - - +
344C ARG* 3.6 25.6 - - - +
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Residues in contact with THR 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107C ARG* 2.9 33.2 + - - +
211C ILE* 4.2 10.8 - - + -
212C GLY* 3.3 16.4 - - - +
213C VAL* 3.7 14.3 - - + +
234C LYS* 1.3 70.4 - - - +
236C GLU* 1.3 62.4 + - - +
341C ASP* 4.1 1.2 - - - +
342C LEU* 3.2 45.9 + - + +
343C ASP* 2.7 24.1 + - - +
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Residues in contact with GLU 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183C GLU 4.2 4.5 - - - +
184C ASN* 4.3 2.9 - - - +
185C LEU* 3.4 6.5 - - + +
211C ILE* 3.3 1.1 - - - -
212C GLY 2.3 56.9 + - - +
214C CYS* 3.1 28.2 - - - +
216C HIS* 3.3 25.2 + - - -
234C LYS* 3.5 14.4 + - + +
235C THR* 1.3 76.4 - - - +
237C ALA* 1.3 58.0 + - - +
238C SER 4.1 0.4 - - - -
339C ASN* 3.7 34.9 + - - +
340C GLY 3.6 6.3 - - - +
341C ASP* 4.7 9.7 - - - +
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Residues in contact with ALA 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C TRP* 3.7 29.1 + - + +
210C GLN 3.4 4.9 - - - -
211C ILE* 3.6 26.2 - - + -
235C THR 4.1 0.6 + - - -
236C GLU* 1.3 73.0 - - - +
238C SER* 1.3 61.2 + - - +
339C ASN* 3.7 1.2 - - - -
340C GLY* 3.1 32.1 + - - +
342C LEU* 4.1 15.4 - - + +
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Residues in contact with SER 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C TRP* 3.8 7.5 - - - -
185C LEU* 3.9 25.7 + - - +
186C LEU* 4.9 0.8 + - - -
208C LEU 3.9 1.2 + - - +
209C ALA* 3.4 3.6 - - - -
210C GLN* 2.6 39.2 + - - +
236C GLU 4.1 0.4 - - - -
237C ALA* 1.3 75.3 - - - +
239C LEU* 1.3 62.5 + - - +
240C VAL* 4.3 13.5 - - - +
337C SER* 5.7 1.1 - - - -
338C VAL 3.3 13.5 - - - -
339C ASN* 3.7 17.7 - - - -
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Residues in contact with LEU 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114C TRP* 4.4 7.1 - - + -
118C VAL* 3.4 21.1 - - + -
125C VAL* 4.4 16.4 - - + -
207C GLY* 4.2 15.7 - - - -
208C LEU 4.1 6.3 - - - +
209C ALA* 4.7 0.4 - - - +
238C SER* 1.3 74.5 - - - +
240C VAL* 1.3 79.6 + - - +
241C TRP* 4.2 11.2 - - + +
255C TRP* 3.4 48.5 - - + -
259C ARG* 6.0 2.0 - - - -
336C LEU 3.6 2.3 - - - +
337C SER* 3.6 0.5 - - - -
338C VAL* 2.7 51.7 + - + +
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Residues in contact with VAL 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186C LEU* 3.4 31.4 - - + -
189C ALA* 3.7 24.0 - - + -
190C LEU* 4.1 10.8 - - + -
207C GLY* 3.3 3.1 - - - -
208C LEU* 3.1 30.2 + - + +
238C SER* 4.3 11.9 - - - +
239C LEU* 1.3 80.2 - - - +
241C TRP* 1.3 59.5 + - - +
242C PHE* 3.5 37.4 + - + -
335C VAL* 4.9 5.4 - - + -
336C LEU 3.8 4.5 - - - +
337C SER* 4.7 0.9 - - - +
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Residues in contact with TRP 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C ARG* 5.1 2.2 - - - -
124C GLN* 3.7 31.0 - - + -
125C VAL* 3.9 14.6 - - + -
205C PRO* 3.8 23.3 - - + -
206C TYR* 3.2 8.3 - - - -
207C GLY* 2.9 37.7 - - - -
239C LEU* 3.8 13.2 - - + -
240C VAL* 1.3 69.5 - - - +
242C PHE* 1.3 63.0 + - - +
243C THR* 3.5 16.4 + - + +
251C TRP* 3.1 40.1 - + + -
255C TRP* 2.9 45.1 - + - +
334C CYS 3.0 3.8 - - - +
335C VAL* 4.8 0.2 - - - -
336C LEU* 3.0 48.5 + - + +
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Residues in contact with PHE 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190C LEU* 3.4 17.5 - - + -
193C TYR* 3.5 52.3 - + + -
204C LEU* 4.9 2.5 - - + -
205C PRO* 3.0 20.9 - - - +
206C TYR* 3.4 32.3 + + + +
208C LEU* 3.9 25.8 - - + -
240C VAL* 3.5 25.6 - - + -
241C TRP* 1.3 69.7 - - - +
243C THR* 1.3 69.5 + - - +
311C LEU* 4.4 2.5 - - + -
333C PRO* 4.0 12.1 - - + -
334C CYS 3.5 2.7 - - - -
335C VAL* 3.4 34.3 - - + -
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Residues in contact with THR 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204C LEU* 4.0 3.6 - - - -
205C PRO* 3.4 14.6 - - + -
241C TRP* 3.5 23.3 - - + +
242C PHE* 1.3 82.6 - - - +
244C PRO* 1.3 82.1 + - - +
248C SER* 3.8 14.7 - - - -
251C TRP* 3.4 23.7 - - + +
333C PRO* 2.8 11.4 - - - +
334C CYS* 2.6 42.3 + - - +
336C LEU* 5.2 3.6 - - + +
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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