Contacts of the strand formed by residues 271 - 279 (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 ILE 271 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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179J PRO* 5.1 5.4 - - + -
180J VAL 3.4 13.7 - - - +
181J TYR* 3.8 13.2 - - + +
182J LYS* 4.0 4.3 - - - +
191J VAL* 4.5 5.4 - - + -
214J LEU* 4.1 16.8 - - + -
256J PHE* 6.0 2.5 - - + -
260J SER* 5.5 0.4 - - - +
266J MET* 3.6 36.1 - - + -
269J ARG 3.2 19.1 - - - +
270J PRO* 1.3 76.3 - - - +
272J LEU* 1.3 63.5 + - - +
273J ILE* 4.3 17.3 - - + -
291J GLU* 3.2 12.2 - - - +
292J GLY 3.1 41.6 + - - +
294J ILE* 5.3 4.0 - - + -
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Residues in contact with LEU 272 (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* 3.9 25.1 - - + +
178J MET 3.9 0.2 - - - +
179J PRO* 4.1 1.2 - - - +
180J VAL* 2.7 57.7 + - + +
181J TYR 3.8 8.7 - - - +
182J LYS* 4.3 24.5 - - + -
271J ILE* 1.3 75.2 - - - +
273J ILE* 1.3 64.4 + - - +
274J ILE* 3.7 25.5 + - + +
289J SER* 4.8 7.9 - - - +
290J PHE 3.1 20.0 - - - +
291J GLU* 3.9 4.9 - - + +
292J GLY 4.2 0.9 - - - +
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Residues in contact with ILE 273 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151J LEU* 4.3 12.1 - - + -
177J ALA* 5.5 1.8 - - + -
178J MET 3.6 2.9 - - - +
179J PRO* 5.4 1.1 - - + -
215J ILE* 4.2 21.1 - - + -
254J TYR* 6.5 1.1 - - + -
256J PHE* 3.9 29.4 - - + -
271J ILE* 4.3 20.2 - - + -
272J LEU* 1.3 75.8 - - - +
274J ILE* 1.3 63.8 + - - +
275J ILE* 4.1 17.4 + - + -
288J ARG 3.9 0.2 - - - +
289J SER* 3.1 25.6 - - - -
290J PHE* 2.7 46.4 + - + +
292J GLY* 4.5 9.6 - - - -
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Residues in contact with ILE 274 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116J PRO* 4.4 7.2 - - + +
117J SER 3.8 19.3 - - - +
118J ASN* 3.6 26.5 - - + -
176J ARG 3.7 1.6 - - - +
177J ALA 3.6 0.3 - - - -
178J MET* 2.7 56.3 + - + +
180J VAL* 4.6 12.8 - - + -
272J LEU* 3.7 25.4 - - + +
273J ILE* 1.3 78.1 - - - +
275J ILE* 1.3 61.2 + - - +
276J THR* 4.0 13.4 + - + +
287J ARG* 5.4 2.9 - - + -
288J ARG 3.4 14.8 - - - +
289J SER* 4.0 9.0 - - - -
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Residues in contact with ILE 275 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127J PHE* 5.3 11.0 - - + -
129J VAL* 4.9 8.1 - - + -
161J ILE* 3.4 33.7 - - + -
163J ILE* 5.3 5.8 - - + -
175J ILE* 3.4 29.6 - - + -
176J ARG 3.0 3.6 - - - -
177J ALA* 4.0 19.3 - - + -
254J TYR* 4.7 7.4 - - + +
273J ILE* 4.1 17.9 - - + -
274J ILE* 1.3 74.7 - - - +
276J THR* 1.3 71.8 - - - +
277J LEU 5.1 0.9 - - - +
286J GLY 4.6 0.7 - - - +
287J ARG* 3.7 0.3 - - - -
288J ARG* 3.2 35.3 + - + +
290J PHE* 4.4 10.8 - - + -
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Residues in contact with THR 276 (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* 4.6 0.2 - - - -
176J ARG* 2.7 53.5 + - - +
178J MET* 5.2 5.9 - - + +
274J ILE* 4.4 15.0 + - + +
275J ILE* 1.3 86.7 - - - +
277J LEU* 1.3 64.9 + - - +
278J GLU* 3.4 7.4 + - - +
284J VAL* 4.2 13.0 - - + -
286J GLY 4.7 0.4 - - - -
287J ARG* 3.7 35.9 - - + +
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Residues in contact with LEU 277 (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* 3.4 42.1 - - + -
163J ILE* 5.7 0.2 - - + -
165J VAL* 6.3 1.3 - - + -
169J PRO* 5.5 8.7 - - + -
173J THR* 3.1 40.4 - - + +
174J ALA 3.5 3.1 - - - +
175J ILE* 4.1 17.5 - - + -
240J TYR* 4.7 9.6 - - + -
276J THR* 1.3 71.0 - - - +
278J GLU* 1.3 68.4 + - - +
279J MET* 4.9 0.7 - - + +
283J GLN 3.0 1.0 - - - +
284J VAL* 3.0 31.4 - - - +
285J LEU* 3.6 29.0 + - + +
286J GLY 4.0 3.8 + - - +
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Residues in contact with GLU 278 (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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173J THR* 4.6 0.2 - - - -
174J ALA* 2.8 52.5 + - + +
176J ARG* 3.1 44.8 + - + +
237J VAL* 5.4 2.7 - - + -
276J THR* 3.4 8.7 + - - +
277J LEU* 1.3 80.2 - - - +
279J MET* 1.3 65.9 + - - +
280J ARG 3.2 22.3 - - - +
281J ASP* 4.6 2.3 + - - +
282J GLY 3.8 14.1 - - - +
283J GLN 3.3 6.3 - - - +
284J VAL* 6.0 1.3 - - + -
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Residues in contact with MET 279 (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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170J PRO* 3.3 34.1 - - + -
171J PRO 5.0 7.2 - - - +
172J GLY 4.2 6.7 - - - +
173J THR* 4.6 7.4 - - - +
277J LEU* 4.9 0.4 - - + +
278J GLU* 1.3 88.9 - - - +
280J ARG* 1.3 70.8 + - - +
281J ASP* 2.9 1.9 + - - -
282J GLY* 3.4 26.4 + - - +
283J GLN 3.7 10.3 + - - +
285J LEU* 3.8 27.1 - - + -
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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