Contacts of the strand formed by residues 166 - 174 (chain B) in PDB entry 5U1R
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 PHE 166 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ILE* 6.5 0.9 - - + -
112B GLN* 6.0 7.9 - - + -
113B ASN 5.8 4.0 - - - -
136B ASP* 4.1 14.4 - - + -
159B LEU* 3.8 0.7 - - + +
160B ASP* 3.4 6.5 + - - +
161B MET* 2.9 63.3 + - + +
164B MET* 4.3 11.4 - - + +
165B ASP* 1.3 78.0 - - - +
167B LYS* 1.3 71.4 + - - +
168B SER* 3.5 32.8 - - - -
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Residues in contact with LYS 167 (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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14B GLU* 3.1 37.2 + - - +
80B MET* 3.7 27.1 - - + +
109B PRO* 4.3 12.1 - - + -
110B ASP 5.6 3.6 - - - +
111B ILE* 3.9 20.8 - - + +
112B GLN* 5.8 5.1 - - - +
158B VAL* 4.4 7.9 - - + -
159B LEU 3.5 5.4 - - - +
160B ASP* 3.3 34.3 + - + +
162B ARG* 4.1 19.4 - - - +
165B ASP* 5.1 7.9 + - - -
166B PHE* 1.3 82.1 - - - +
168B SER* 1.3 62.2 + - - +
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Residues in contact with SER 168 (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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111B ILE* 4.9 4.7 - - - -
135B THR* 4.7 1.9 + - - -
136B ASP* 3.3 29.7 + - - +
157B CYS 3.7 0.3 - - - +
158B VAL* 3.5 5.7 - - - +
159B LEU* 3.2 52.5 + - - +
166B PHE* 3.5 15.1 - - - -
167B LYS* 1.3 76.4 - - - +
169B ASN* 1.3 66.9 + - - +
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Residues in contact with ASN 169 (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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109B PRO* 3.4 8.9 - - - +
111B ILE* 3.3 19.6 - - - +
135B THR* 3.2 3.1 + - - -
136B ASP 3.1 23.3 + - - +
137B PHE* 3.3 51.5 + - + +
138B ASP 4.0 0.8 - - - -
139B SER* 3.6 20.4 + - - +
156B LYS* 4.7 10.4 - - + +
157B CYS 3.4 4.9 - - - +
158B VAL* 3.2 26.3 - - - +
168B SER* 1.3 74.1 - - - +
170B SER* 1.3 65.1 + - - +
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Residues in contact with SER 170 (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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133B LEU* 4.2 15.0 - - - -
134B PHE 3.2 12.8 - - - -
135B THR* 4.1 7.9 - - - -
137B PHE* 4.0 4.0 - - - -
155B ASP 4.2 1.2 - - - +
156B LYS* 3.3 2.6 - - - -
157B CYS* 2.9 41.4 + - - +
159B LEU* 4.2 20.0 + - - +
169B ASN* 1.3 80.4 - - - +
171B ALA* 1.3 59.4 + - - +
172B VAL* 5.5 1.8 - - - -
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Residues in contact with ALA 171 (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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132B CYS 4.1 0.2 - - - +
133B LEU* 3.7 3.6 - - - +
134B PHE* 2.8 42.5 + - + +
137B PHE* 4.3 1.0 - - + -
143B VAL* 3.9 30.7 - - + -
153B ILE* 5.2 1.6 - - + -
154B THR* 3.7 21.5 - - - +
156B LYS* 4.2 4.7 - - + +
170B SER* 1.3 75.5 - - - +
172B VAL* 1.3 64.4 + - - +
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Residues in contact with VAL 172 (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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131B VAL* 3.5 28.0 - - + -
132B CYS 3.6 3.1 - - - +
133B LEU* 3.9 18.2 - - + -
152B TYR 3.5 1.0 - - - +
153B ILE* 3.4 3.8 - - - +
154B THR* 2.9 45.6 + - + +
170B SER* 5.5 1.3 - - - -
171B ALA* 1.3 80.5 - - - +
173B ALA* 1.3 63.7 + - - +
174B TRP* 4.0 17.9 - - + -
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Residues in contact with ALA 173 (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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131B VAL* 3.8 1.6 - - - +
132B CYS* 2.8 44.0 + - + +
151B VAL* 5.1 0.4 - - + -
152B TYR 3.1 8.3 - - - +
153B ILE* 4.2 19.3 - - + -
171B ALA 4.3 0.2 + - - -
172B VAL* 1.3 75.9 - - - +
174B TRP* 1.3 63.2 + - - +
180B PHE* 4.1 17.3 - - + -
185B ALA* 4.4 13.2 - - + +
186B PHE* 6.3 0.2 - - - -
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Residues in contact with TRP 174 (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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130B SER 4.0 16.6 - - - +
131B VAL* 4.0 13.0 - - + -
151B VAL* 3.4 0.9 - - - +
152B TYR* 2.7 83.4 + + + -
154B THR* 3.7 29.6 - - + -
172B VAL* 4.0 18.6 - - + -
173B ALA* 1.3 76.9 - - - +
175B SER* 1.3 68.3 + - - +
180B PHE* 4.0 10.7 - - - -
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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