Contacts of the strand formed by residues 172 - 180 (chain J) in PDB entry 2VWE
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 172 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105J GLU* 3.0 37.4 + - - +
136J ASN 2.8 10.8 - - - +
138J PHE* 2.9 58.0 + - + +
139J TYR* 3.7 25.8 - + - -
140J PRO* 5.0 0.2 - - + -
141J LYS* 3.6 45.3 - - + -
162J TRP* 5.6 0.4 - - + -
163J THR* 3.7 19.3 - - - +
164J GLU* 4.3 1.1 - - - -
165J GLN* 3.0 48.2 + - + -
171J THR* 1.3 72.8 - - - +
173J SER* 1.3 61.4 + - - +
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Residues in contact with SER 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J ASN* 2.2 38.6 - - - -
138J PHE* 3.5 5.4 - - - -
162J TRP* 3.6 1.6 - - - +
163J THR* 2.6 43.8 + - - -
172J TYR* 1.3 72.0 - - - +
174J MET* 1.3 58.0 + - - +
164L HIS* 3.4 16.1 + - - -
166L PHE* 2.6 32.4 - - - -
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Residues in contact with MET 174 (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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134J PHE* 4.1 0.5 - - - -
135J LEU* 2.7 55.0 + - + +
138J PHE* 3.8 3.1 - - + -
143J ILE* 3.6 18.8 - - + -
145J VAL* 3.6 24.7 - - + -
160J ASP* 3.4 35.2 - - + +
161J SER 3.2 11.2 - - - +
162J TRP* 3.6 44.0 - - + +
173J SER* 1.3 73.9 + - - +
175J SER* 1.3 81.6 + - - +
176J SER 3.9 2.0 - - - +
166L PHE* 3.5 6.3 - - - -
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Residues in contact with SER 175 (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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132J VAL* 5.0 1.1 - - - -
133J CYS 4.0 3.6 - - - -
134J PHE* 3.5 22.2 - - - -
159J LEU 2.9 13.9 - - - +
160J ASP* 3.4 2.1 - - - -
161J SER* 3.0 27.1 + - - -
174J MET* 1.3 77.6 - - - +
176J SER* 1.3 60.6 + - - +
177J THR* 3.9 5.9 + - - -
166L PHE* 3.6 12.5 - - - -
178L SER* 2.9 28.1 + - - -
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Residues in contact with SER 176 (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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132J VAL* 3.4 1.4 - - - -
133J CYS* 2.9 43.8 + - - -
145J VAL* 3.5 21.3 - - - +
147J TRP* 2.7 40.1 + - - -
158J VAL* 3.6 2.6 - - - +
159J LEU 3.3 3.6 - - - -
160J ASP* 3.0 18.7 + - - -
174J MET* 3.9 4.6 - - - +
175J SER* 1.3 70.7 - - - +
177J THR* 1.3 59.2 + - - +
178J LEU 3.9 0.2 - - - -
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Residues in contact with THR 177 (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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130J SER* 4.5 6.5 - - - -
131J VAL 3.8 2.2 - - - -
132J VAL* 3.9 20.1 - - + +
147J TRP* 4.8 0.2 - - - -
157J GLY 2.9 6.8 - - - +
158J VAL* 4.5 0.4 - - - -
159J LEU* 2.8 54.3 + - - +
175J SER* 4.6 4.0 + - - -
176J SER* 1.3 70.8 + - - +
178J LEU* 1.3 59.5 + - - +
179J THR* 3.6 12.9 + - - +
141L LEU* 3.9 36.0 - - + +
143L LYS* 6.1 0.4 - - + -
171L GLN* 5.8 0.2 - - - +
176L THR* 4.5 7.6 - - + +
178L SER* 4.4 9.0 + - - -
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Residues in contact with LEU 178 (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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130J SER* 3.3 4.5 - - - -
131J VAL* 2.9 42.6 + - + +
147J TRP* 3.6 47.8 - - + +
149J ILE* 4.0 16.8 - - + -
154J ARG* 4.0 15.7 - - + +
156J ASN 3.8 17.7 - - - +
157J GLY* 3.4 4.3 - - - -
158J VAL* 3.7 26.5 - - + +
176J SER 3.7 1.4 + - - -
177J THR* 1.3 69.2 - - - +
179J THR* 1.3 59.6 + - - +
180J LEU* 3.7 26.8 + - + +
191J TYR* 5.9 0.2 - - + -
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Residues in contact with THR 179 (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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123J GLN* 5.6 0.9 - - - +
129J ALA 5.9 0.2 - - - +
130J SER* 3.5 20.2 + - - +
154J ARG* 5.2 0.3 + - - -
156J ASN 4.6 1.4 - - - +
157J GLY* 3.0 25.4 + - - -
177J THR* 4.3 8.5 + - - +
178J LEU* 1.3 71.7 - - - +
180J LEU* 1.3 75.0 + - - +
143L LYS* 3.3 31.6 + - + +
171L GLN* 3.2 23.1 + - - -
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Residues in contact with LEU 180 (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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128J GLY* 4.3 2.4 - - - -
129J ALA 2.7 34.4 + - - +
131J VAL* 4.0 20.2 - - + -
149J ILE* 3.8 24.0 - - + -
154J ARG* 3.2 40.6 - - - +
178J LEU* 3.8 15.9 - - + +
179J THR* 1.3 83.9 - - - +
181J THR* 1.3 67.2 + - - +
184J GLU* 5.2 2.9 - - - +
185J TYR* 3.8 32.1 - - + +
191J TYR* 4.6 1.3 - - + -
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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