Contacts of the strand formed by residues 192 - 199 (chain J) in PDB entry 3EO1
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 VAL 192 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150J LYS* 6.3 1.1 - - + -
151J VAL* 3.3 1.0 - - - +
152J ASP* 2.9 53.8 + - - +
191J LYS* 1.3 78.1 - - + +
193J TYR* 1.3 80.0 + - - +
194J ALA* 5.5 2.0 - - + -
209J SER* 5.1 8.3 - - - -
210J PHE 4.1 3.8 - - - +
211J ASN* 3.6 23.6 - - - +
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Residues in contact with TYR 193 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121J PRO* 5.7 0.2 - - + -
133J VAL* 4.5 18.2 - - + -
149J TRP* 5.9 2.5 - + + -
150J LYS 3.1 12.1 - - - -
151J VAL* 3.4 33.1 - - + +
180J LEU* 5.7 5.4 - - + -
182J LEU* 5.8 4.0 - - - +
186J ASP 3.9 4.9 + - - -
187J TYR* 3.1 61.9 + + - +
190J HIS* 4.5 9.1 - - + +
191J LYS 4.5 6.3 - - - -
192J VAL* 1.3 85.5 - - - +
194J ALA* 1.3 60.5 + - - +
209J SER* 3.2 4.6 - - - -
210J PHE* 2.7 75.8 + + + +
212J ARG* 5.9 3.6 - - + -
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Residues in contact with ALA 194 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118J ILE* 4.5 3.1 - - - -
149J TRP* 3.0 12.9 - - - +
150J LYS* 2.7 51.6 + - + -
192J VAL* 5.5 2.5 - - + -
193J TYR* 1.3 77.1 - - - +
195J CYS* 1.3 61.1 + - - +
196J GLU 3.5 0.7 - - - -
207J THR* 3.6 16.4 - - + -
208J LYS 3.4 7.0 - - - +
209J SER* 3.3 20.9 - - - +
210J PHE* 4.7 0.8 - - - -
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Residues in contact with CYS 195 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116J VAL* 4.4 4.5 - - + +
118J ILE* 3.8 18.0 - - + +
135J CYS* 2.0 52.9 - - + -
147J VAL* 3.4 24.5 - - - -
148J GLN 4.3 2.5 - - - -
149J TRP* 4.4 10.8 - - + +
194J ALA* 1.3 68.6 - - - +
196J GLU* 1.3 64.6 + - - +
197J VAL* 3.2 12.5 + - - +
207J THR* 3.9 11.9 - - - -
208J LYS 3.0 11.0 + - - -
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Residues in contact with GLU 196 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J VAL* 3.6 0.3 - - - +
148J GLN* 2.7 55.5 + - + +
149J TRP 4.2 0.2 - - - +
150J LYS* 3.1 35.2 - - + +
194J ALA 3.5 3.4 - - - -
195J CYS* 1.3 72.6 - - - +
197J VAL* 1.3 78.5 + - - +
198J THR* 4.6 7.5 - - - +
205J PRO* 4.7 8.7 - - - +
207J THR* 3.1 29.7 + - + +
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Residues in contact with VAL 197 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114J PRO* 5.1 6.1 - - + -
116J VAL* 3.7 22.0 - - + -
137J LEU* 4.3 9.6 - - + -
146J LYS 4.0 4.7 - - - -
147J VAL* 3.6 29.2 - - + -
195J CYS* 3.3 22.0 - - - +
196J GLU* 1.3 86.7 - - - +
198J THR* 1.3 70.1 + - - +
199J HIS* 5.2 1.6 - - + +
202J LEU* 5.3 0.7 - - + -
205J PRO* 3.7 8.5 - - - +
206J VAL* 3.1 48.6 + - + +
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Residues in contact with THR 198 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144J GLU 4.6 0.2 - - - +
145J ALA* 4.1 3.0 - - - -
146J LYS* 3.4 50.8 + - + +
196J GLU* 4.6 7.9 - - - +
197J VAL* 1.3 82.2 - - - +
199J HIS* 1.3 61.6 + - - +
200J GLN* 3.9 9.5 + - - +
202J LEU* 5.4 0.2 - - - -
205J PRO* 4.5 16.3 - - - +
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Residues in contact with HIS 199 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111J VAL* 4.1 0.2 - - + -
112J ALA 3.8 9.3 + - - -
114J PRO* 3.7 28.5 - - + +
137J LEU* 5.5 1.8 - - + -
140J PHE* 3.6 28.2 - + + -
141J TYR 3.0 43.0 + - - -
142J PRO* 4.0 3.0 - - + -
143J ARG 4.4 0.4 + - - -
144J GLU* 3.1 23.0 + - + +
145J ALA* 4.5 6.1 - - + +
197J VAL* 5.2 1.0 - - + +
198J THR* 1.3 74.4 - - - +
200J GLN* 1.3 58.6 + - - +
201J GLY* 2.7 51.8 + - - -
202J LEU* 3.1 25.5 + - + +
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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