Contacts of the strand formed by residues 177 - 186 (chain A) in PDB entry 1UB5
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 LEU 177 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A LYS 5.3 1.1 - - - +
120A THR* 4.1 19.5 - - + +
147A GLY* 3.6 37.0 - - - +
148A TYR 3.6 11.0 - - - +
149A PHE* 4.2 6.7 - - + -
173A LEU* 3.6 4.7 - - - +
174A GLN* 2.6 44.2 + - - +
175A SER* 4.7 4.5 - - - +
176A GLY* 1.3 90.5 - - - +
178A TYR* 1.3 59.0 + - - +
179A THR* 4.4 0.8 + - - +
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Residues in contact with TYR 178 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A GLY 3.1 14.6 + - - -
148A TYR* 2.8 55.7 + - + +
149A PHE* 3.7 24.0 - + - -
150A PRO 3.9 4.9 - - - -
151A GLU* 3.5 62.0 + - + +
171A ALA* 4.4 6.1 - - + -
172A LEU 3.4 4.5 - - - -
173A LEU* 3.5 45.9 - - + +
177A LEU* 1.3 69.6 - - - +
179A THR* 1.3 63.1 + - - +
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Residues in contact with THR 179 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144A LEU* 4.0 17.0 - - + -
145A VAL 3.2 13.2 - - - +
146A LYS* 3.3 35.8 + - + +
147A GLY 4.0 1.7 + - - -
148A TYR* 4.0 0.4 - - - -
170A PRO 4.4 0.7 - - - +
171A ALA* 3.3 1.4 - - - -
172A LEU* 2.8 43.7 + - - +
174A GLN* 3.7 12.4 + - - +
177A LEU* 4.4 3.8 + - - +
178A TYR* 1.3 77.7 + - - +
180A MET* 1.3 66.3 + - - +
165B LEU* 5.8 3.6 - - + -
183B THR* 5.7 7.2 - - + -
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Residues in contact with MET 180 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 3.9 3.5 - - - -
145A VAL* 2.7 52.9 + - + +
148A TYR* 3.3 17.9 - - + +
151A GLU* 5.2 1.6 - - + +
153A VAL* 3.5 31.9 - - + +
155A VAL* 4.4 14.4 - - - -
168A THR* 3.8 26.7 - - + -
169A PHE* 3.7 15.3 - - - +
170A PRO* 4.8 2.5 - - + -
171A ALA* 3.6 23.8 - - + +
179A THR* 1.3 76.7 - - - +
181A SER* 1.3 56.9 + - - +
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Residues in contact with SER 181 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
143A CYS 3.3 10.3 - - - -
144A LEU* 4.2 17.3 - - - -
145A VAL* 6.0 0.4 - - - -
155A VAL* 6.0 0.2 - - - -
168A THR* 3.9 2.3 - - - +
169A PHE* 3.2 35.4 + - - +
180A MET* 1.3 77.2 - - - +
182A SER* 1.3 62.4 + - - +
138B VAL* 4.6 6.9 - - - +
140B PHE* 3.3 30.4 - - - -
181B SER* 3.8 9.7 + - - -
183B THR* 5.1 2.5 + - - -
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Residues in contact with SER 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A GLY* 3.0 3.9 - - - -
143A CYS 2.9 35.0 + - - -
155A VAL* 3.8 25.9 - - - +
157A TRP* 3.2 23.2 + - - -
166A VAL* 5.0 0.5 - - - +
167A HIS 3.4 9.1 + - - -
168A THR* 3.0 24.7 + - - -
181A SER* 1.3 75.7 - - - +
183A SER* 1.3 60.1 + - - +
140B PHE* 4.4 2.9 - - - -
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Residues in contact with SER 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140A THR* 4.2 5.8 - - - -
141A LEU 3.2 7.4 - - - -
142A GLY* 4.1 0.4 - - - -
157A TRP* 4.7 0.7 - - - -
165A SER 3.8 0.7 - - - +
166A VAL* 3.3 4.5 - - - +
167A HIS* 2.8 46.8 + - - +
169A PHE* 3.9 2.1 - - - -
182A SER* 1.3 75.2 + - - +
184A VAL* 1.3 61.4 + - - +
185A THR* 5.7 0.2 + - - -
140B PHE* 3.3 35.3 - - - -
142B ASN* 3.2 20.3 + - - -
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Residues in contact with VAL 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A VAL 3.6 0.3 - - - +
140A THR* 3.5 3.6 - - - +
141A LEU* 2.7 50.1 + - + +
157A TRP* 3.5 48.0 - - + +
161A GLY* 5.7 2.7 - - - -
165A SER* 3.6 8.7 - - - +
166A VAL* 4.3 17.7 - - + -
183A SER* 1.3 75.0 - - - +
185A THR* 1.3 77.7 + - - +
186A VAL* 4.5 10.1 - - + -
196A VAL* 4.4 7.2 - - + -
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Residues in contact with THR 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A SER* 4.4 21.1 - - - +
139A VAL 3.4 10.8 - - - +
140A THR* 4.2 13.5 + - - +
165A SER* 3.0 38.3 + - - +
167A HIS* 5.6 3.5 - - - -
183A SER* 5.7 0.3 + - - -
184A VAL* 1.3 81.4 + - - +
186A VAL* 1.3 76.1 + - - +
142B ASN* 5.5 1.9 + - - -
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Residues in contact with VAL 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138A SER* 3.9 3.6 - - - -
139A VAL* 2.7 50.3 + - + +
141A LEU* 4.6 14.4 - - + -
184A VAL* 4.5 14.4 - - + -
185A THR* 1.3 89.4 - - - +
187A PRO* 1.3 75.4 - - + +
190A THR* 4.2 11.0 - - + +
191A TRP* 4.7 4.9 - - + -
196A VAL* 4.7 14.4 - - + -
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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