Contacts of the strand formed by residues 184 - 191 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16B LEU* 3.2 39.0 - - + +
19B ILE* 3.6 21.5 - - + -
20B ALA* 3.9 11.9 - - + +
23B ILE* 5.2 0.2 - - + -
144B ASP 2.8 13.4 + - - +
145B PHE* 2.9 16.9 - - + +
146B ALA 2.8 24.9 + - - -
183B ILE* 1.3 70.9 - - - +
185B PRO* 1.3 68.7 - - + +
186B ILE* 5.8 0.4 - - + -
226B GLY 3.3 21.5 - - - +
227B THR* 3.9 10.5 - - - +
228B LEU* 4.6 9.0 - - + +
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Residues in contact with PRO 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ALA 4.4 1.3 - - - +
174B TYR* 3.5 24.9 - - + +
175B ALA* 3.8 36.3 - - + +
178B CYS* 3.8 9.9 - - + -
179B GLN* 3.8 8.5 - - + -
183B ILE 3.2 8.3 - - - +
184B VAL* 1.3 84.7 - - - +
186B ILE* 1.3 62.7 + - - +
187B VAL* 3.6 2.7 + - + +
226B GLY 3.2 17.0 - - - +
227B THR* 3.6 12.7 - - + -
228B LEU 3.2 21.3 + - - -
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Residues in contact with ILE 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B ILE* 3.8 20.4 - - + -
78B ILE* 4.1 14.4 - - + -
145B PHE* 3.6 36.3 - - + -
146B ALA 2.8 18.5 + - - +
147B LYS* 4.3 5.4 - - + -
148B TRP 3.7 7.4 + - - -
174B TYR* 2.9 17.6 + - - -
184B VAL* 5.1 0.9 - - + +
185B PRO* 1.3 71.9 - - - +
187B VAL* 1.3 62.9 + - - +
188B GLU* 3.4 4.5 + - + +
228B LEU* 3.4 25.1 - - + +
230B LYS* 3.4 37.9 - - + +
269B THR* 4.5 5.2 - - - +
301B SER* 4.9 0.7 - - - +
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Residues in contact with VAL 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU* 3.5 37.2 - - + -
174B TYR* 4.4 7.6 - - + -
175B ALA* 4.5 19.5 - - + -
185B PRO 4.3 6.7 - - - +
186B ILE* 1.3 71.6 - - - +
188B GLU* 1.3 57.9 + - - +
189B PRO* 3.1 10.4 - - + +
213B VAL* 3.9 17.9 - - + -
214B TYR* 5.7 1.6 - - - +
217B LEU* 4.4 20.0 - - + -
227B THR* 4.8 7.2 - - - -
228B LEU 2.8 16.5 + - - +
229B LEU* 3.4 8.7 - - + +
230B LYS 3.0 20.5 + - - -
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Residues in contact with GLU 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B LYS* 2.8 36.6 + - + +
148B TRP 3.3 14.4 + - - +
149B ARG* 3.3 31.3 - - + +
150B CYS* 3.0 24.4 + - - +
171B LEU* 4.0 4.7 - - - +
186B ILE* 3.4 7.2 + - + +
187B VAL* 1.3 73.1 - - - +
189B PRO* 1.3 58.8 - - - +
190B GLU* 3.3 14.7 + - - +
230B LYS* 3.3 39.8 - - + +
271B LEU* 3.7 12.6 - - + +
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Residues in contact with PRO 189 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B CYS* 4.2 7.6 - - + +
152B LEU* 5.6 5.2 - - + -
171B LEU* 3.8 17.9 - - + -
187B VAL* 3.1 17.7 - - + +
188B GLU* 1.3 82.4 - - - +
190B GLU* 1.3 62.1 + - - +
191B ILE* 3.4 8.9 + - - +
209B VAL* 4.2 11.7 - - + +
210B LEU* 4.0 26.5 - - + -
213B VAL* 4.1 14.1 - - + -
229B LEU* 3.8 10.3 - - + -
230B LYS 3.8 6.7 - - - +
231B PRO* 4.5 5.3 - - + +
232B ASN* 3.6 8.7 + - - -
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Residues in contact with GLU 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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149B ARG* 2.4 31.3 + - - +
150B CYS 3.2 16.8 + - - +
151B VAL* 3.4 3.6 - - - +
152B LEU* 2.8 26.8 + - - +
188B GLU* 3.3 17.9 + - - +
189B PRO* 1.3 72.3 - - - +
191B ILE* 1.3 70.4 + - - +
192B LEU* 3.2 23.8 + - + +
193B PRO* 4.7 4.7 - - - +
232B ASN* 4.0 3.1 - - + +
271B LEU* 3.7 39.8 - - + +
273B GLY* 5.0 5.7 - - - -
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Residues in contact with ILE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 3.6 22.0 - - + +
154B ILE* 3.5 38.4 - - + -
189B PRO 4.2 5.4 - - - +
190B GLU* 1.3 75.2 - - - +
192B LEU* 1.3 64.9 + - - +
193B PRO* 3.7 2.9 - - - +
202B CYS* 5.2 4.0 - - - -
205B VAL* 3.7 4.9 - - + -
206B THR* 3.4 42.4 - - + +
209B VAL* 3.6 25.1 - - + -
232B ASN* 2.7 37.5 - - - +
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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
------------------------------------------------------------
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