Contacts of the strand formed by residues 180 - 188 (chain B) in PDB entry 1UXI
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 180 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B LEU* 3.7 1.5 - - - -
172B MET* 2.9 43.7 + - + +
173B GLY* 4.9 0.2 - - - -
178B GLU 3.3 18.6 - - - +
179B MET* 1.3 73.9 - - - +
181B PRO* 1.3 72.6 - - - +
182B LEU* 3.5 18.6 + - + +
210B ARG* 4.8 2.7 - - - +
288B GLU 4.7 2.7 - - - +
291B LEU* 3.8 50.9 - - + +
292B LEU* 4.0 9.2 - - + +
295B SER* 4.1 6.5 - - - -
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Residues in contact with PRO 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 4.2 24.5 - - + -
171B LEU* 3.7 25.1 - - + -
179B MET* 3.8 17.0 - - + +
180B VAL* 1.3 96.5 - - - +
182B LEU* 1.3 61.0 + - - +
183B PRO* 3.4 9.7 - - - +
206B VAL* 3.4 45.3 - - + +
209B THR* 4.6 4.3 - - + -
210B ARG* 4.2 7.9 - - + +
291B LEU* 5.5 2.8 - - - +
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Residues in contact with LEU 182 (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 TYR* 4.4 1.1 - - - -
170B MET* 3.2 27.9 + - + +
172B MET* 3.2 39.5 - - + -
180B VAL* 3.7 21.5 - - + +
181B PRO* 1.3 79.1 - - - +
183B PRO* 1.3 59.5 - - + +
184B ARG 3.1 1.6 - - - +
185B PHE* 2.7 50.3 + - + +
186B SER* 2.8 14.3 + - - -
284B LEU* 4.2 7.4 - - + -
288B GLU* 4.1 32.1 - - + +
291B LEU* 6.2 0.2 - - + -
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Residues in contact with PRO 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
152B TYR* 3.5 21.9 - - - +
181B PRO 3.4 10.5 - - - +
182B LEU* 1.3 84.5 - - + +
184B ARG* 1.3 61.4 + - - +
186B SER* 3.3 17.3 + - - +
192B PRO* 5.7 1.7 - - - +
193B VAL* 3.7 10.3 + - + +
194B SER* 5.2 3.8 + - - -
202B LEU* 3.8 27.1 - - + -
206B VAL* 4.0 22.2 - - + -
288B GLU* 6.1 0.4 - - + +
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Residues in contact with ARG 184 (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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182B LEU 3.1 0.8 - - - -
183B PRO* 1.3 80.8 - - - +
185B PHE* 1.3 80.5 + - + +
186B SER 3.4 4.8 + - - +
187B THR* 5.4 2.9 - - - +
192B PRO* 5.7 3.5 - - - +
283B PRO* 3.0 27.3 + - - +
285B ASN* 3.3 24.4 - - - +
288B GLU* 2.7 47.2 + - - +
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Residues in contact with PHE 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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169B ALA* 3.5 1.2 - - - -
170B MET* 2.9 36.8 + - + +
182B LEU* 2.7 35.8 + - + +
184B ARG* 1.3 112.6 - - + +
186B SER* 1.3 55.1 + - - +
187B THR* 5.3 1.6 - - - -
282B LEU* 4.1 28.7 - - + -
283B PRO* 4.4 14.4 - - + -
284B LEU* 3.6 26.9 - - + -
288B GLU* 3.8 7.6 - - - -
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Residues in contact with SER 186 (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 TYR* 3.1 26.3 + - - -
168B GLN 3.4 6.1 - - - -
169B ALA* 3.3 11.1 - - - +
170B MET 4.5 0.2 + - - -
182B LEU 2.8 20.4 + - - -
183B PRO 3.3 12.9 + - - +
184B ARG 3.4 2.4 + - - +
185B PHE* 1.3 74.3 - - - +
187B THR* 1.3 70.6 + - - +
192B PRO* 3.5 2.8 - - - +
193B VAL* 3.1 37.4 + - - -
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Residues in contact with THR 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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166B ASP 3.8 0.2 - - - +
167B VAL* 3.7 2.1 - - - +
168B GLN* 2.9 59.1 + - - +
184B ARG 5.4 0.4 - - - +
185B PHE 5.3 0.9 - - - -
186B SER* 1.3 83.4 - - - +
188B ILE* 1.3 67.5 + - - +
189B SER 4.0 0.4 - - - -
190B GLY* 3.6 28.7 + - - +
191B ILE 3.0 16.6 - - - +
192B PRO* 3.9 1.8 - - + -
193B VAL* 3.9 2.6 - - - +
1312B NA 3.8 20.0 - - - -
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Residues in contact with ILE 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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156B ILE* 3.2 35.0 - - + -
160B ALA* 4.2 1.3 - - + -
162B VAL* 4.2 25.1 - - + -
166B ASP* 3.0 19.1 - - + +
167B VAL* 4.0 5.6 - - + -
187B THR* 1.3 77.4 - - - +
189B SER* 1.3 72.9 + - - +
191B ILE* 2.7 26.4 + - + +
193B VAL* 4.0 6.1 - - + -
196B PHE* 3.5 51.1 - - + -
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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