Contacts of the strand formed by residues 173 - 181 (chain J) in PDB entry 3VD1
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 173 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169J PRO* 4.7 1.8 - - + +
170J PRO* 2.4 35.4 + - - +
171J PRO* 2.9 3.4 + - - -
172J GLY* 1.3 83.7 + - - +
174J ALA* 1.3 77.5 + - - +
239J PRO* 4.2 13.0 - - - +
240J TYR* 3.3 40.8 + - + +
277J LEU* 3.1 30.5 - - + +
278J GLU 3.8 5.8 - - - -
279J MET* 4.6 7.6 - - - +
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Residues in contact with ALA 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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172J GLY 4.9 1.6 - - - +
173J THR* 1.3 81.4 - - - +
175J ILE* 1.3 64.0 + - - +
237J VAL* 5.2 9.0 - - + -
238J VAL 3.8 9.9 - - - +
239J PRO* 4.2 4.3 - - + -
240J TYR 4.1 2.7 - - - +
276J THR 3.9 0.2 - - - +
277J LEU* 3.5 5.4 - - - +
278J GLU* 2.8 46.9 + - + +
279J MET 5.3 1.8 - - - +
280J ARG* 5.6 2.2 - - - +
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Residues in contact with ILE 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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127J PHE* 5.1 0.7 - - + -
163J ILE* 3.3 33.2 - - + -
174J ALA* 1.3 78.4 - - - +
176J ARG* 1.3 66.2 + - - +
236J VAL 3.6 1.7 - - - +
237J VAL* 3.0 7.4 - - - -
238J VAL* 2.8 44.1 + - + +
240J TYR* 4.1 26.5 - - + -
250J THR* 5.4 0.7 - - - +
252J ILE* 4.3 16.4 - - + -
254J TYR* 4.4 11.9 - - - +
275J ILE* 3.4 26.9 - - + -
276J THR 3.8 2.9 - - - +
277J LEU* 4.1 16.8 - - + -
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Residues in contact with ARG 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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175J ILE* 1.3 77.9 - - - +
177J ALA* 1.3 63.4 + - - +
178J MET* 4.4 16.1 - - + +
226J VAL* 4.8 20.4 + - - +
228J ASP* 6.0 0.4 + - - -
235J SER* 3.4 31.7 - - - +
236J VAL 3.8 3.1 - - - -
237J VAL* 3.7 22.1 - - + +
274J ILE 3.7 0.3 - - - +
275J ILE* 3.0 4.7 - - - +
276J THR* 2.7 54.0 + - - +
278J GLU* 3.1 36.6 + - - +
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Residues in contact with ALA 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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176J ARG* 1.3 72.3 - - - +
178J MET* 1.3 55.0 + - - +
179J PRO* 4.3 1.4 - - - +
215J ILE* 4.3 14.1 - - + +
235J SER* 2.3 29.5 + - - -
236J VAL* 3.3 29.2 + - + +
254J TYR* 3.4 32.1 + - + +
273J ILE* 5.5 1.8 - - + -
274J ILE 3.8 2.0 - - - -
275J ILE* 4.0 12.3 - - + -
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Residues in contact with MET 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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116J PRO* 5.4 11.2 - - + -
176J ARG* 4.4 19.1 - - + +
177J ALA* 1.3 74.2 - - - +
179J PRO* 1.3 79.1 - - + +
180J VAL* 4.2 7.9 - - + -
215J ILE* 4.0 5.0 - - - +
233J ARG* 4.6 30.7 - - + -
234J GLN 5.0 1.8 - - - +
235J SER* 3.3 13.9 - - - +
272J LEU 3.9 0.2 - - - +
273J ILE* 3.6 4.9 - - - +
274J ILE* 2.7 59.4 + - + +
276J THR* 5.2 6.3 - - + +
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Residues in contact with PRO 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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177J ALA 4.3 2.2 - - - +
178J MET* 1.3 90.6 - - + +
180J VAL* 1.3 71.5 + - - +
190J VAL* 5.8 0.8 - - + +
191J VAL* 2.7 37.6 - - + +
214J LEU* 4.2 18.6 - - + +
215J ILE* 3.8 28.9 - - + +
233J ARG* 4.3 1.4 + - - -
234J GLN* 3.7 24.7 - - + +
235J SER* 5.1 0.4 - - - -
271J ILE* 5.1 4.9 - - + -
272J LEU 4.1 3.1 - - - +
273J ILE* 5.2 1.1 - - + -
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Residues in contact with VAL 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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116J PRO* 4.0 22.9 - - + -
178J MET* 4.2 12.1 + - + -
179J PRO* 1.3 84.1 - - - +
181J TYR* 1.3 78.5 + - + +
187J VAL* 4.2 20.4 - - + +
191J VAL* 3.7 8.2 - - + +
233J ARG* 3.1 32.3 - - - +
271J ILE* 3.4 6.6 - - - +
272J LEU* 2.7 55.4 + - + +
274J ILE* 4.6 6.0 - - + +
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Residues in contact with TYR 181 (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 ASN* 5.8 0.3 + - - -
180J VAL* 1.3 88.9 - - + +
182J LYS* 1.3 62.5 + - - +
183J LYS* 3.5 18.3 + - + +
186J HIS* 3.6 23.1 - + + -
187J VAL* 4.1 16.8 - - - +
189J ASP* 3.2 29.0 - - + +
190J VAL 4.3 2.6 + - - -
191J VAL* 3.3 34.9 - - + +
192J LYS 4.9 0.2 + - - -
265J GLY 4.3 2.9 + - - -
266J MET* 4.1 6.2 + - + -
269J ARG* 3.4 52.6 + - + -
270J PRO 3.5 15.5 - - - +
271J ILE* 3.8 13.7 - - + +
272J LEU* 3.8 9.4 - - - +
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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