Contacts of the strand formed by residues 184 - 191 (chain K) in PDB entry 1XFB
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 VAL 184 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16K LEU* 3.2 40.4 - - + +
19K ILE* 3.6 21.1 - - + -
20K ALA* 3.9 12.3 - - + +
23K ILE* 5.2 0.2 - - + -
144K ASP 2.8 14.0 + - - +
145K PHE* 2.9 15.7 - - + +
146K ALA 2.8 25.6 + - - -
183K ILE* 1.3 69.9 - - - +
185K PRO* 1.3 68.3 - - + +
186K ILE* 5.8 0.2 - - + -
226K GLY 3.3 22.2 - - - +
227K THR* 3.9 11.0 - - - +
228K LEU* 4.6 8.3 - - + +
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Residues in contact with PRO 185 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146K ALA 3.9 1.3 - - - +
174K TYR* 3.5 24.9 - - + +
175K ALA* 3.8 36.3 - - + +
178K CYS* 3.8 9.0 - - + -
179K GLN* 3.8 9.2 - - + -
183K ILE 3.2 7.6 - - - +
184K VAL* 1.3 85.4 - - - +
186K ILE* 1.3 62.3 + - - +
187K VAL* 3.6 3.1 + - + +
226K GLY 3.2 16.4 - - - +
227K THR* 3.6 12.9 - - + -
228K LEU 3.2 20.7 + - - -
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Residues in contact with ILE 186 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30K ILE* 3.8 20.4 - - + -
78K ILE* 4.1 14.6 - - + -
145K PHE* 3.6 36.1 - - + -
146K ALA 2.8 19.7 + - - +
147K LYS* 4.3 6.3 - - + -
148K TRP 3.7 7.3 + - - -
174K TYR* 2.9 18.0 + - - -
184K VAL* 5.1 0.7 - - + +
185K PRO* 1.3 72.6 - - - +
187K VAL* 1.3 62.3 + - - +
188K GLU* 3.4 3.9 + - + +
228K LEU* 3.4 24.2 - - + +
230K LYS* 3.4 39.0 - - + +
269K THR* 4.5 4.9 - - - +
301K SER* 4.9 0.9 - - - +
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Residues in contact with VAL 187 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171K LEU* 3.5 38.1 - - + -
174K TYR* 4.4 7.2 - - + -
175K ALA* 4.5 19.5 - - + -
185K PRO 4.3 6.7 - - - +
186K ILE* 1.3 71.2 - - - +
188K GLU* 1.3 57.0 + - - +
189K PRO* 3.0 9.9 - - + +
213K VAL* 3.9 18.4 - - + -
214K TYR* 5.7 2.0 - - - +
217K LEU* 4.4 18.8 - - + -
227K THR* 4.8 7.4 - - - -
228K LEU 2.8 16.3 + - - +
229K LEU* 3.4 8.8 - - + +
230K LYS 3.0 20.8 + - - -
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Residues in contact with GLU 188 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147K LYS* 2.8 36.4 + - + +
148K TRP 3.3 15.0 + - - +
149K ARG* 3.3 31.7 - - + +
150K CYS* 3.0 24.6 + - - +
171K LEU* 4.0 4.7 - - - +
186K ILE* 3.4 6.1 + - + +
187K VAL* 1.3 73.5 - - - +
189K PRO* 1.3 57.5 - - - +
190K GLU* 3.3 13.4 + - - +
230K LYS* 3.3 40.8 - - + +
271K LEU* 3.7 12.7 - - + +
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Residues in contact with PRO 189 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150K CYS* 4.2 7.2 - - + +
152K LEU* 5.6 5.4 - - + -
171K LEU* 3.8 17.5 - - + -
187K VAL* 3.0 17.9 - - + +
188K GLU* 1.3 82.6 - - - +
190K GLU* 1.3 61.9 + - - +
191K ILE* 3.4 8.7 + - - +
209K VAL* 4.2 11.7 - - + +
210K LEU* 4.0 25.8 - - + -
213K VAL* 4.1 15.0 - - + -
229K LEU* 3.8 9.4 - - + -
230K LYS 3.8 6.5 - - - +
231K PRO* 4.5 6.1 - - + +
232K ASN* 3.6 8.7 + - - -
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Residues in contact with GLU 190 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149K ARG* 2.4 30.9 + - - +
150K CYS 3.2 16.6 + - - +
151K VAL* 3.4 3.1 - - - +
152K LEU* 2.8 28.1 + - - +
188K GLU* 3.3 18.6 + - - +
189K PRO* 1.3 71.2 - - - +
191K ILE* 1.3 68.9 + - - +
192K LEU* 3.2 24.3 + - + +
193K PRO* 4.7 4.7 - - + +
232K ASN* 4.0 3.4 - - + +
271K LEU* 3.7 38.3 - - + +
273K GLY* 5.0 5.5 - - - -
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Residues in contact with ILE 191 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152K LEU* 3.6 22.0 - - + +
154K ILE* 3.5 37.7 - - + -
159K PRO* 5.8 0.2 - - + -
189K PRO 4.2 5.2 - - - +
190K GLU* 1.3 76.2 - - - +
192K LEU* 1.3 65.2 + - - +
193K PRO* 3.7 2.4 - - - +
202K CYS* 5.2 4.8 - - - -
205K VAL* 3.7 4.9 - - + -
206K THR* 3.4 42.2 - - + +
209K VAL* 3.6 25.4 - - + -
232K ASN* 2.7 37.2 - - - +
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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