Contacts of the strand formed by residues 209 - 216 (chain D) in PDB entry 4BGG
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 THR 209 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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207D ASP 5.6 0.3 - - - -
208D ILE* 1.3 74.2 - - - +
210D LEU* 1.3 69.2 + - - +
211D LEU* 3.4 15.7 + - + +
225D GLY* 3.1 5.1 - - - -
226D SER* 2.9 45.0 + - - -
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Residues in contact with LEU 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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208D ILE 4.0 2.6 + - - -
209D THR* 1.3 75.5 - - - +
211D LEU* 1.3 62.7 + - - +
223D TRP* 3.8 32.7 - - + -
224D ARG 4.1 4.7 - - - -
225D GLY* 4.4 2.0 - - - -
234D VAL* 6.2 3.4 - - + -
236D ILE* 6.4 1.3 - - + -
280D TRP* 5.8 8.5 - - + -
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Residues in contact with LEU 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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209D THR* 3.4 23.5 + - + +
210D LEU* 1.3 77.9 - - - +
212D GLU* 1.3 60.5 + - - +
223D TRP* 4.2 5.8 - - - -
224D ARG* 2.9 50.4 + - - +
225D GLY 4.3 2.7 - - - -
226D SER* 4.0 24.7 - - - +
231D ASN* 4.5 2.0 - - - +
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Residues in contact with GLU 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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211D LEU* 1.3 79.5 - - - +
213D CYS* 1.3 64.6 + - - +
214D VAL* 3.5 18.3 + - + +
223D TRP* 3.2 9.3 - - - -
224D ARG* 2.7 75.6 + - + +
285D TYR* 4.2 2.4 + - - -
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Residues in contact with CYS 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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212D GLU* 1.3 75.8 - - - +
214D VAL* 1.3 60.8 + - - +
215D GLY 3.5 28.3 - - - -
216D LYS* 4.6 6.3 - - - -
221D GLU* 4.5 11.2 - - - -
222D VAL 3.7 6.5 - - - -
223D TRP* 3.3 36.6 - - + -
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Residues in contact with VAL 214 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
212D GLU* 3.9 24.7 - - + +
213D CYS* 1.3 76.7 - - - +
215D GLY* 1.3 56.3 + - - +
222D VAL* 2.9 39.3 + - + +
223D TRP* 4.2 6.7 - - - +
224D ARG 4.3 1.6 - - - +
285D TYR* 3.8 22.9 - - + +
1000D 844 3.6 63.4 - - + +
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Residues in contact with GLY 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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213D CYS* 3.5 11.3 - - - -
214D VAL* 1.3 81.9 - - - +
216D LYS* 1.3 57.6 + - - -
219D TYR* 3.3 15.7 - - - -
221D GLU* 3.3 2.9 - - - -
222D VAL* 2.9 31.8 + - - -
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Residues in contact with LYS 216 (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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213D CYS* 4.6 7.4 - - - -
215D GLY* 1.3 74.3 - - - +
217D GLY* 1.3 58.1 + - - +
219D TYR* 3.4 8.1 + - - -
220D GLY 3.5 6.7 - - - +
221D GLU* 4.3 15.3 - - + +
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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