Contacts of the strand formed by residues 206 - 215 (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 TYR 206 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124D GLN* 3.3 25.4 - - + +
126D PHE* 4.8 6.7 - + - -
193D TYR* 2.9 53.1 + + - -
196D CYS* 3.2 22.6 + - + +
197D LEU* 3.5 22.6 + - + +
200D VAL* 4.2 14.4 - - + -
203D ARG 4.0 17.5 - - - +
204D LEU* 4.7 4.5 - - + -
205D PRO* 1.3 77.4 - - - +
207D GLY* 1.3 64.1 + - - +
208D LEU* 3.5 24.0 - - + -
241D TRP* 3.2 8.5 - - - -
242D PHE* 3.4 27.5 + + + -
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Residues in contact with GLY 207 (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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124D GLN 3.4 8.9 + - - +
125D VAL* 3.3 8.0 - - - -
126D PHE 2.9 20.3 + - - -
206D TYR* 1.3 75.8 - - - +
208D LEU* 1.3 71.7 + - - +
209D ALA 4.0 0.2 - - - -
239D LEU* 4.2 4.7 - - - -
240D VAL 3.4 11.4 - - - -
241D TRP* 2.9 21.4 - - - -
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Residues in contact with LEU 208 (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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126D PHE* 3.4 15.0 - - + +
127D PRO 5.8 0.2 - - - +
128D VAL* 3.9 18.5 - - + +
189D ALA* 3.4 38.3 - - + +
192D HIS* 3.5 24.7 - - + -
193D TYR* 4.1 2.0 - - - +
196D CYS* 4.2 15.5 - - + -
206D TYR* 3.5 20.2 - - + -
207D GLY* 1.3 84.3 - - - +
209D ALA* 1.3 63.4 + - - +
210D GLN* 5.0 0.3 - - - +
238D SER* 3.9 3.3 + - - +
239D LEU* 4.2 2.1 - - - +
240D VAL* 3.1 31.2 + - - +
242D PHE* 3.9 17.0 - - + -
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Residues in contact with ALA 209 (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* 4.2 5.6 - - + -
115D TRP* 3.7 15.4 - - + -
119D VAL* 3.6 32.1 - - + -
125D VAL* 3.7 12.7 - - + +
126D PHE 3.0 8.4 + - - +
127D PRO* 3.8 1.7 - - - +
128D VAL* 3.0 29.1 + - - +
208D LEU* 1.3 73.4 - - - +
210D GLN* 1.3 63.4 + - - +
238D SER 3.4 8.1 - - - +
239D LEU* 4.6 3.8 - - + +
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Residues in contact with GLN 210 (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 0.9 - - - -
115D TRP* 4.1 6.0 - - - -
128D VAL* 3.7 29.0 - - + +
129D ASP* 4.3 0.3 - - - -
130D ALA* 2.9 40.5 + - - +
182D ARG* 4.5 1.7 + - - -
185D LEU* 3.7 48.4 + - + +
189D ALA* 4.8 4.6 - - - +
208D LEU 5.0 0.4 - - - +
209D ALA* 1.3 79.9 - - - +
211D ILE* 1.3 68.4 + - - +
212D GLY* 5.4 0.2 - - - -
237D ALA* 3.4 1.0 - - - -
238D SER* 2.6 41.6 + - - +
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Residues in contact with ILE 211 (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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111D ALA* 3.7 35.2 - - + +
114D TRP* 3.7 28.0 - - + -
115D TRP* 4.2 12.6 - - + -
185D LEU* 4.3 0.4 - - - -
210D GLN* 1.3 80.8 - - - +
212D GLY* 1.3 60.6 + - - +
235D THR* 4.2 10.1 - - + -
236D GLU 3.3 4.5 - - - +
237D ALA* 3.5 20.2 - - + -
342D LEU* 3.8 20.0 - - + -
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Residues in contact with GLY 212 (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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132D HIS* 6.0 0.2 - - - -
182D ARG* 4.5 9.2 - - - -
185D LEU* 3.7 10.8 - - - +
210D GLN* 5.4 0.4 - - - -
211D ILE* 1.3 79.1 - - - +
213D VAL* 1.3 62.7 + - - -
214D CYS* 4.2 0.7 - - - -
235D THR* 4.1 3.8 - - - -
236D GLU* 2.4 54.2 + - - +
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Residues in contact with VAL 213 (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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132B HIS* 3.4 37.0 - - + +
107D ARG* 5.7 0.9 - - - +
132D HIS* 4.2 6.8 + - - +
182D ARG* 2.5 34.6 + - - +
212D GLY* 1.3 74.9 - - - -
214D CYS* 1.3 68.1 + - - +
215D PHE* 4.2 12.9 - - + -
233D GLU* 4.0 24.0 - - + +
234D LYS 3.3 10.8 - - - +
235D THR* 3.7 20.9 - - + +
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Residues in contact with CYS 214 (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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182D ARG* 3.6 16.2 - - - +
183D GLU 3.3 11.2 - - - +
184D ASN* 3.7 19.5 - - - -
185D LEU* 4.1 11.7 - - - -
212D GLY 4.2 0.2 - - - -
213D VAL* 1.3 79.0 - - - +
215D PHE* 1.3 63.3 + - - +
216D HIS* 3.3 26.0 + - + -
232D GLY 3.5 0.3 - - - +
233D GLU* 3.7 1.7 - - - -
234D LYS 2.9 28.9 + - - +
236D GLU* 3.1 27.8 - - - +
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Residues in contact with PHE 215 (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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132B HIS* 3.7 24.0 - + + -
133B HIS* 5.4 2.0 - + + -
181B LEU* 5.2 2.5 - - + -
215B PHE* 5.0 4.5 - + - -
132D HIS* 4.4 29.2 - + + -
145D PHE* 4.3 12.4 + - + -
181D LEU* 3.6 48.7 - - + +
182D ARG* 3.0 17.2 + - + +
183D GLU* 3.5 14.0 - - - +
213D VAL* 4.2 16.4 - - + -
214D CYS* 1.3 72.9 - - - +
216D HIS* 1.3 63.5 + - - +
231D ILE* 4.5 15.3 - - + -
232D GLY 3.3 5.6 - - - +
233D GLU* 3.3 43.5 - - + -
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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