Contacts of the strand formed by residues 205 - 213 (chain J) in PDB entry 1DU3
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 GLN 205 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95H ASP 3.6 9.1 + - - +
96H SER* 3.5 17.4 - - - -
97H PRO* 5.5 0.2 - - + -
98H GLU* 3.3 14.2 + - - +
99H MET* 3.0 30.8 + - - +
101H ARG* 3.3 23.6 - - - +
203J ASP* 5.0 0.4 - - - +
204J LYS* 1.3 75.3 - - - +
206J MET* 1.3 52.6 + - - +
207J VAL* 3.7 10.2 + - + +
227J ARG 3.6 5.4 - - - -
261J THR* 2.5 29.5 + - - -
262J ASN* 3.0 11.3 + - - +
237K TYR* 2.5 47.2 + - + +
239K LEU* 4.2 7.9 - - + -
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Residues in contact with MET 206 (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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190J PHE* 3.3 48.0 - - + -
192J PHE* 3.9 9.9 - - + -
204J LYS* 4.1 11.9 - - + +
205J GLN* 1.3 73.4 - - - +
207J VAL* 1.3 60.3 + - - +
226J ALA* 3.3 2.1 - - - -
227J ARG* 2.9 34.6 + - + +
228J ASN* 3.7 8.1 - - - +
229J SER* 3.2 45.8 - - - +
240J TYR* 3.7 35.7 - - + -
242J ILE* 3.8 9.6 - - + +
261J THR* 3.5 3.6 - - - -
262J ASN* 4.5 7.0 - - + +
265J LEU* 5.2 0.9 - - + -
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Residues in contact with VAL 207 (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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97H PRO* 5.4 0.7 - - + -
98H GLU* 3.8 27.1 - - + -
190J PHE* 4.2 4.9 - - - -
205J GLN* 3.9 15.3 - - + +
206J MET* 1.3 81.1 - - - +
208J GLN* 1.3 61.3 - - - +
209J TYR* 3.5 37.3 - - + +
224J LYS* 4.4 3.4 - - + -
225J SER 3.3 20.2 - - - +
226J ALA* 3.7 13.2 - - + -
227J ARG 5.3 0.2 - - - +
242J ILE* 4.8 0.7 - - - -
260J VAL* 3.3 8.9 - - - +
261J THR* 3.3 34.9 + - + -
239K LEU* 5.9 0.2 - - + -
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Residues in contact with GLN 208 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186J SER* 3.2 48.4 + - - +
188J THR* 3.4 20.8 - - + +
207J VAL* 1.3 72.8 - - - +
209J TYR* 1.3 62.7 + - - +
210J ILE* 3.4 9.3 - - - +
224J LYS* 3.3 2.1 - - - -
225J SER 3.0 20.3 + - - -
242J ILE* 3.3 31.7 - - + +
244J GLN* 3.0 40.9 + - - +
258J VAL* 3.9 17.7 - - + -
259J SER 3.6 4.0 - - - +
260J VAL* 4.0 2.2 - - + -
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Residues in contact with TYR 209 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97H PRO* 3.3 24.4 - - - +
98H GLU* 3.7 9.9 - - - +
147J LEU* 3.5 39.8 - - + +
148J GLY 4.2 2.7 - - - -
207J VAL* 3.5 36.3 - - + +
208J GLN* 1.3 75.5 - - - +
210J ILE* 1.3 62.1 + - - +
211J TYR* 3.4 26.2 + + + -
221J LEU* 3.8 15.5 - - + -
223J MET 3.6 2.9 - - - -
224J LYS* 3.7 27.6 - - + -
257J PHE 3.8 0.3 - - - +
258J VAL* 3.4 4.7 - - - +
259J SER* 2.8 45.1 + - - +
260J VAL* 4.6 0.2 - - - -
261J THR* 3.9 14.6 - - + -
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Residues in contact with ILE 210 (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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184J ILE* 3.9 23.3 - - + -
185J TYR* 4.4 4.9 - - - -
186J SER* 4.2 14.6 - - - +
208J GLN* 3.4 28.5 - - - +
209J TYR* 1.3 72.8 - - - +
211J TYR* 1.3 60.5 + - - +
221J LEU* 3.7 1.1 - - - +
222J LEU* 2.7 50.8 + - + +
223J MET* 3.0 26.8 + - + +
244J GLN* 3.5 20.0 - - + +
256J ILE* 5.0 2.0 - - + -
257J PHE 3.3 8.3 - - - +
258J VAL* 4.2 12.8 - - + -
275J PHE* 4.9 2.5 - - + -
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Residues in contact with TYR 211 (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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146J ALA* 3.5 18.8 - - + -
147J LEU* 2.7 42.0 + - - +
209J TYR* 3.4 26.5 - - + -
210J ILE* 1.3 75.2 - - - +
212J LYS* 1.3 61.8 + - - +
219J PRO* 4.0 16.6 - - + -
220J ILE 3.4 6.5 - - - -
221J LEU* 3.6 38.6 - - + +
222J LEU* 4.3 1.1 - - - -
256J ILE* 3.2 8.0 - - - +
257J PHE* 2.9 67.4 + + + +
259J SER* 3.8 12.6 - - - -
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Residues in contact with LYS 212 (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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211J TYR* 1.3 76.4 - - - +
213J TYR* 1.3 64.4 + - - +
214J THR* 4.0 21.8 + - - +
218J ASP 4.5 0.3 - - - +
219J PRO* 3.4 6.1 - - - +
220J ILE* 2.9 53.7 + - + +
222J LEU* 3.8 33.4 - - + -
248J PHE* 6.3 0.2 - - - +
249J GLU 4.2 14.8 + - - -
250J LEU* 3.7 21.9 - - + +
251J LYS* 6.1 1.8 - - - +
254J ASP* 4.5 9.9 + - - +
255J ARG 3.1 10.1 - - - +
256J ILE* 4.1 5.8 - - + -
160K GLY* 4.8 12.0 + - - -
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Residues in contact with TYR 213 (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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146J ALA* 5.7 0.3 - - - +
150J LYS* 5.3 2.7 - - - -
173J GLU* 3.9 13.7 - - - -
212J LYS* 1.3 71.8 - - - +
214J THR* 1.3 63.5 + - - +
216J TYR 4.6 4.9 - - - -
217J PRO 3.7 17.0 - - - -
218J ASP 4.3 2.9 - - - -
219J PRO* 3.6 41.8 - - + +
253J ASN 4.4 0.9 - - - +
254J ASP* 3.5 5.2 - - - -
255J ARG* 2.6 75.9 + - + +
257J PHE* 3.3 35.4 - + - -
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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