Contacts of the strand formed by residues 191 - 197 (chain D) in PDB entry 3EBL
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 ARG 191 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112D PRO* 3.6 10.9 - - - +
113D PHE 3.9 13.8 + - - +
114D PRO* 3.4 4.3 - - - +
115D VAL 2.9 25.3 + - - +
182D MET 4.6 1.8 + - - -
183D ARG* 5.2 0.8 - - - +
187D ASP* 2.7 43.6 + - - +
189D GLN 4.2 3.6 - - - +
190D ALA* 1.3 75.1 - - - +
192D VAL* 1.3 59.2 + - - +
193D PHE* 4.0 2.1 - - - -
219D CYS* 3.8 20.6 - - - -
352D LEU* 2.9 45.8 + - + +
353D TYR* 3.8 33.8 + - - +
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Residues in contact with VAL 192 (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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115D VAL* 3.4 8.7 - - + +
117D ILE* 3.8 24.0 - - + -
173D LEU* 3.8 11.2 - - + -
176D VAL* 4.1 12.6 - - + -
177D MET* 3.5 39.0 - - + -
190D ALA* 3.7 12.9 + - + -
191D ARG* 1.3 74.4 - - - +
193D PHE* 1.3 76.6 - - - +
194D LEU* 4.3 5.4 - - + -
217D LYS 4.7 4.7 + - - +
218D VAL* 3.6 5.2 - - + -
219D CYS* 2.8 36.8 + - - +
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Residues in contact with PHE 193 (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 PRO* 3.7 26.7 - - + -
115D VAL 2.8 10.2 + - - +
116D ILE* 3.4 8.5 - - + -
117D ILE 2.8 26.9 + - - -
191D ARG 4.0 5.6 - - - -
192D VAL* 1.3 84.0 - - - +
194D LEU* 1.3 59.5 + - - +
219D CYS* 3.5 28.5 - - + -
220D GLY* 3.2 22.7 - - - +
222D ILE* 4.2 14.1 - - + -
347D PHE* 4.0 15.0 - + - -
348D LEU* 3.7 42.8 - - + -
351D ASN* 3.9 22.9 - - + -
352D LEU* 4.5 5.4 - - + -
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Residues in contact with LEU 194 (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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117D ILE* 3.6 31.9 - - + -
119D PHE* 4.4 7.9 - - + -
173D LEU* 4.5 4.9 - - + -
192D VAL* 4.3 4.5 - - + -
193D PHE* 1.3 75.1 - - - +
195D SER* 1.3 60.9 + - - +
204D ALA* 3.6 19.2 - - + +
207D VAL* 3.7 21.8 - - + -
208D ALA* 3.6 39.9 - - + +
218D VAL* 3.9 21.1 - - + -
220D GLY 3.0 5.9 + - - +
221D ASN* 3.2 13.5 - - - +
222D ILE* 2.8 24.1 + - - +
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Residues in contact with SER 195 (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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116D ILE* 3.6 26.5 - - - -
117D ILE 2.9 9.3 + - - +
118D PHE* 3.8 13.4 - - - -
119D PHE* 2.9 29.0 + - - -
141D PHE* 4.0 11.5 - - - -
194D LEU* 1.3 75.8 - - - +
196D GLY* 1.3 57.8 + - - +
204D ALA* 4.0 7.5 - - - +
222D ILE* 3.0 30.6 + - - +
224D LEU* 4.2 2.9 - - - +
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Residues in contact with GLY 196 (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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118D PHE* 3.6 8.5 - - - -
119D PHE 3.2 14.4 - - - -
195D SER* 1.3 78.9 + - - +
197D ASP* 1.3 58.9 + - - -
200D GLY 3.6 10.0 + - - -
201D GLY* 3.4 14.7 - - - -
204D ALA* 4.3 2.6 - - - +
222D ILE 3.1 4.6 + - - +
223D LEU* 3.6 0.9 - - - -
224D LEU* 2.9 25.8 + - - -
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Residues in contact with ASP 197 (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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118D PHE* 3.5 9.3 - - + -
119D PHE 3.5 0.8 + - - -
121D GLY* 2.8 25.3 + - - -
134D TYR* 2.7 37.5 + - - -
196D GLY* 1.3 74.3 - - - -
198D SER* 1.3 72.0 + - - +
200D GLY* 2.8 13.9 + - - -
224D LEU* 3.0 18.4 - - + +
329D TYR* 2.5 40.1 + - + +
401D GA4 3.3 4.5 - - - +
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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