Contacts of the strand formed by residues 184 - 191 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16L LEU* 3.2 39.9 - - + +
19L ILE* 3.6 21.3 - - + -
20L ALA* 3.9 12.3 - - + +
23L ILE* 5.2 0.2 - - + -
144L ASP 2.8 13.0 + - - +
145L PHE* 2.9 15.7 - - + +
146L ALA 2.8 25.8 + - - -
183L ILE* 1.3 69.9 - - - +
185L PRO* 1.3 67.6 - - - +
186L ILE* 5.8 0.2 - - + -
226L GLY 3.3 23.6 - - - +
227L THR* 3.9 11.7 - - - -
228L LEU* 4.6 8.7 - - + +
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Residues in contact with PRO 185 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146L ALA 3.9 1.3 - - - +
174L TYR* 3.5 24.0 - - + +
175L ALA* 3.8 35.7 - - + +
178L CYS* 3.8 9.6 - - + -
179L GLN* 3.8 8.5 - - + -
183L ILE 3.2 7.6 - - - +
184L VAL* 1.3 85.5 - - - +
186L ILE* 1.3 62.6 + - - +
187L VAL* 3.6 2.7 + - + -
226L GLY 3.2 17.0 - - - +
227L THR* 3.6 12.9 - - + -
228L LEU 3.2 20.8 + - - -
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Residues in contact with ILE 186 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30L ILE* 3.8 20.4 - - + -
78L ILE* 4.1 14.1 - - + -
145L PHE* 3.6 35.9 - - + -
146L ALA 2.8 18.7 + - - +
147L LYS* 4.3 6.3 - - + -
148L TRP 3.7 7.4 + - - -
174L TYR* 2.9 17.8 + - - -
184L VAL* 5.1 0.7 - - + +
185L PRO* 1.3 73.1 - - - +
187L VAL* 1.3 61.6 + - - +
188L GLU* 3.4 4.7 + - + +
228L LEU* 3.4 23.8 - - + +
230L LYS* 3.4 38.8 - - + +
269L THR* 4.5 4.5 - - - +
301L SER* 4.9 1.1 - - - +
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Residues in contact with VAL 187 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171L LEU* 3.5 37.2 - - + -
174L TYR* 4.4 7.2 - - + -
175L ALA* 4.5 19.1 - - + -
185L PRO 4.3 6.1 - - - +
186L ILE* 1.3 72.3 - - - +
188L GLU* 1.3 57.0 + - - +
189L PRO* 3.1 10.9 - - + +
213L VAL* 3.9 18.4 - - + -
214L TYR* 5.7 1.8 - - - +
217L LEU* 4.4 19.1 - - + -
227L THR* 4.8 8.1 - - - -
228L LEU 2.8 16.3 + - - +
229L LEU* 3.4 8.2 - - + +
230L LYS 3.0 20.1 + - - -
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Residues in contact with GLU 188 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147L LYS* 2.8 36.5 + - + +
148L TRP 3.3 14.9 + - - +
149L ARG* 3.3 30.1 - - + +
150L CYS* 3.0 24.3 + - - +
171L LEU* 4.0 4.9 - - - +
186L ILE* 3.4 6.8 + - + +
187L VAL* 1.3 72.8 - - - +
189L PRO* 1.3 58.5 - - - +
190L GLU* 3.3 14.7 + - - +
230L LYS* 3.3 40.5 - - + +
271L LEU* 3.7 12.5 - - + +
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Residues in contact with PRO 189 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150L CYS* 4.1 7.6 - - + +
152L LEU* 5.6 4.7 - - + -
171L LEU* 3.8 17.7 - - + -
187L VAL* 3.1 17.7 - - + +
188L GLU* 1.3 81.1 - - - +
190L GLU* 1.3 62.2 + - - +
191L ILE* 3.4 8.2 + - - +
209L VAL* 4.2 11.2 - - + +
210L LEU* 4.0 26.5 - - + -
213L VAL* 4.1 14.8 - - + -
229L LEU* 3.8 9.9 - - + -
230L LYS 3.8 7.0 - - - +
231L PRO* 4.5 5.6 - - + +
232L ASN* 3.6 9.0 + - - -
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Residues in contact with GLU 190 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149L ARG* 2.4 31.9 + - + +
150L CYS 3.2 16.6 + - - +
151L VAL* 3.4 3.8 - - - +
152L LEU* 2.8 27.4 + - - +
188L GLU* 3.3 16.9 + - - +
189L PRO* 1.3 71.4 - - - +
191L ILE* 1.3 69.4 + - - +
192L LEU* 3.2 24.5 + - + +
193L PRO* 4.7 5.0 - - - +
232L ASN* 4.0 3.8 - - + +
271L LEU* 3.7 38.6 - - + +
273L GLY* 5.0 5.8 - - - -
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Residues in contact with ILE 191 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L LEU* 3.6 22.7 - - + +
154L ILE* 3.5 37.9 - - + -
189L PRO 4.2 5.4 - - - +
190L GLU* 1.3 73.1 - - - +
192L LEU* 1.3 66.4 + - - +
193L PRO* 3.7 3.1 - - - +
202L CYS* 5.2 4.5 - - - -
205L VAL* 3.7 5.2 - - + -
206L THR* 3.4 42.8 - - + +
209L VAL* 3.6 25.1 - - + -
232L ASN* 2.7 37.1 - - - +
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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