Contacts of the strand formed by residues 173 - 183 (chain O) in PDB entry 2D2I
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 173 (chain O).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164O ALA* 4.4 6.3 - - + +
167O LEU* 4.0 21.3 - - + -
168O HIS* 2.9 32.3 + - + +
172O GLY* 1.3 71.6 - - - -
174O ILE* 1.3 57.8 + - - +
175O LYS* 3.7 24.9 - - - +
226O LEU* 3.6 23.6 - - + -
229O LYS* 2.7 34.2 + - + -
230O LEU* 4.5 8.5 - - + -
249O VAL* 3.6 38.1 - - + -
250O GLN 4.0 2.0 - - - -
251O VAL* 4.3 4.3 - - + -
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Residues in contact with ILE 174 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172O GLY 4.4 0.4 - - - +
173O ILE* 1.3 76.2 - - - +
175O LYS* 1.3 68.1 + - + +
229O LYS* 3.3 27.3 - - - +
250O GLN* 3.0 42.0 + - + +
251O VAL 3.4 27.4 - - - +
252O GLU* 3.9 22.2 - - + +
308O ASP* 5.5 0.4 - - - +
306P ASP* 4.7 8.4 - - - +
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Residues in contact with LYS 175 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173O ILE* 3.7 7.8 - - - +
174O ILE* 1.3 80.3 - - - +
176O GLY* 1.3 59.3 + - - +
229O LYS* 3.3 12.8 - - - -
249O VAL* 3.6 2.1 - - - -
250O GLN* 2.7 64.7 + - + +
250P GLN* 6.5 0.2 - - - -
305P MET* 3.6 24.5 - - + +
306P ASP* 2.9 42.6 + - + +
308P ASP* 2.6 31.4 + - - -
309P LEU* 3.8 19.3 - - + -
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Residues in contact with GLY 176 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175O LYS* 1.3 79.4 - - - +
177O THR* 1.3 61.4 + - - -
229O LYS 2.9 6.1 + - - +
230O LEU* 3.7 17.7 - - - -
231O ASN 3.4 8.7 + - - -
248O VAL 3.1 13.5 - - - -
249O VAL* 3.9 2.7 - - - -
250O GLN 4.7 0.2 - - - -
305P MET* 3.4 23.1 - - - +
309P LEU* 4.8 6.3 - - - -
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Residues in contact with THR 177 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176O GLY* 1.3 75.0 - - - -
178O MET* 1.3 70.9 + - - +
230O LEU* 4.5 1.3 - - - +
231O ASN 3.2 13.4 + - - -
247O LEU* 3.2 5.2 - - - +
248O VAL* 2.9 37.3 + - + +
248P VAL* 3.5 41.3 - - + -
303P LEU* 4.1 11.2 - - - +
309P LEU* 4.2 11.4 - - + -
311P LYS* 3.2 26.9 + - + +
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Residues in contact with MET 178 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156O THR* 4.3 14.1 - - + -
160O LEU* 3.9 32.5 - - + -
177O THR* 1.3 81.2 + - - +
179O THR* 1.3 72.0 + - - +
180O THR* 4.0 9.4 - - + +
213O THR* 3.6 24.0 - - + +
215O ALA* 4.9 1.1 - - + -
216O ALA* 4.2 8.5 - - + -
230O LEU* 6.1 1.3 - - + -
231O ASN 3.0 14.1 + - - +
232O GLY* 2.9 26.7 - - - -
233O ILE 3.0 25.5 + - - +
245O VAL* 4.8 5.4 - - + -
246O ASP 3.2 13.9 - - - +
247O LEU* 3.8 13.9 - - + -
311P LYS* 4.0 5.5 + - - +
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Residues in contact with THR 179 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178O MET* 1.3 77.9 + - - +
180O THR* 1.3 66.2 + - - +
181O THR* 4.0 5.3 + - - +
233O ILE* 3.3 21.8 - - + +
235O LEU* 4.0 28.5 - - + -
244O VAL 3.9 0.7 - - - +
245O VAL* 3.6 1.0 - - - -
246O ASP* 2.9 40.8 + - - +
246P ASP* 2.4 31.3 + - + +
311P LYS* 3.0 17.5 + - - -
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Residues in contact with THR 180 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156O THR* 4.1 20.9 - - + +
178O MET* 4.3 8.3 - - + -
179O THR* 1.3 75.9 - - - +
181O THR* 1.3 57.5 + - - +
182O HIS* 3.4 14.9 + - + -
213O THR* 4.8 3.8 - - - +
233O ILE 3.0 7.9 + - - +
234O ALA* 3.3 25.7 - - + +
235O LEU 2.7 32.6 + - - -
244O VAL 3.3 8.6 + - - -
245O VAL* 4.3 3.1 - - - -
316O TYR* 2.9 25.6 + - - -
3339O SO4 5.5 1.1 - - - +
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Residues in contact with THR 181 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179O THR* 4.0 5.5 + - - +
180O THR* 1.3 70.0 - - - +
182O HIS* 1.3 57.2 + - - +
235O LEU* 3.3 12.3 - - + +
237O VAL* 3.8 33.2 - - + -
243O SER* 3.5 3.8 - - - -
244O VAL* 3.0 42.6 + - + +
181P THR* 3.7 18.1 + - + -
208P ILE* 4.0 15.9 - - + +
235P LEU* 3.8 11.3 - - + +
237P VAL* 4.4 10.5 - - + -
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Residues in contact with HIS 182 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155O CYS* 3.5 25.7 - - - -
156O THR* 3.9 7.2 + - - -
180O THR* 3.7 14.8 - - + +
181O THR* 1.3 73.8 - - - +
183O SER* 1.3 81.0 + - - +
185O THR* 4.2 8.5 - - + -
234O ALA* 5.2 0.9 - - + -
235O LEU 2.8 9.9 + - - +
236O ARG* 3.3 38.1 + - - +
237O VAL* 2.7 36.3 + - - +
243O SER* 3.3 15.8 + - - -
316O TYR* 3.3 23.6 + - - -
318O ASN* 3.9 20.0 - - + +
3340O SO4 5.1 1.1 - - - -
3341O NAP 4.7 0.7 - - - -
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Residues in contact with SER 183 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182O HIS* 1.3 94.3 + - - +
184O TYR* 1.3 64.6 + - - +
236O ARG* 3.4 5.7 + - - -
237O VAL 3.8 0.7 - - - -
239O THR* 2.9 32.9 + - - -
240O PRO 3.8 1.8 - - - -
241O ASN* 3.0 28.2 + - - -
242O VAL 2.7 26.6 + - - -
243O SER* 3.2 9.7 + - - -
318O ASN* 4.3 4.9 - - - -
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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