Contacts of the strand formed by residues 170 - 177 (chain B) in PDB entry 5UWS
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 GLU 170 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160B CYS 4.2 0.3 - - - +
161B THR 3.8 5.6 + - - -
162B ALA* 3.6 2.8 + - - +
163B ASP 3.0 26.9 + - - +
166B GLU* 5.8 3.1 - - - +
168B GLU 4.0 6.6 - - - +
169B ALA* 1.3 78.2 - - - +
171B ALA* 1.3 72.2 + - - +
172B PHE* 3.2 40.9 + - + -
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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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197A TYR* 3.7 33.7 - - + +
160B CYS 3.2 11.0 - - - +
161B THR* 3.9 10.5 + - - +
170B GLU* 1.3 84.2 - - - +
172B PHE* 1.3 70.7 + - - +
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Residues in contact with PHE 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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95B ARG* 4.2 32.8 - - + -
96B PHE 5.9 1.8 - - - -
106B ARG* 3.3 30.7 - - - -
159B ALA* 3.4 2.8 - - - +
160B CYS* 2.6 43.1 + - + +
163B ASP* 4.0 11.4 - - + -
166B GLU* 5.4 4.7 - - + -
170B GLU* 3.2 50.0 - - + -
171B ALA* 1.3 78.0 - - - +
173B THR* 1.3 60.6 + - - +
174B PHE* 3.5 36.8 - + + -
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Residues in contact with THR 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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197A TYR* 5.5 1.4 + - - -
200A ASP* 4.5 19.4 - - - +
201A LEU* 4.0 24.0 + - + +
204A ALA* 3.5 31.6 - - + -
95B ARG* 3.6 1.6 - - - -
96B PHE* 3.1 39.4 + - - +
103B TRP* 3.4 6.1 - - + -
157B VAL* 4.2 5.6 - - + -
158B TYR 3.8 3.8 - - - +
159B ALA* 4.2 7.8 - - - +
172B PHE* 1.3 72.8 + - - +
174B PHE* 1.3 61.6 + - - +
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Residues in contact with PHE 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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93B LEU* 4.0 20.9 - - + -
94B PHE 3.4 14.4 - - - +
95B ARG* 4.2 3.8 - - + -
103B TRP* 3.8 1.1 - - - -
106B ARG* 3.2 42.0 - - - -
135B CYS 5.0 0.2 - - - -
136B ALA* 5.4 0.2 - - + -
138B HIS* 3.8 27.6 - + - -
156B TRP 3.9 0.4 - - - +
157B VAL* 3.3 8.7 - - - +
158B TYR* 2.9 52.7 + + + +
160B CYS* 3.8 31.6 - - + -
163B ASP* 4.0 5.6 - - + -
172B PHE* 3.5 30.3 - + + -
173B THR* 1.3 74.9 - - - +
175B ALA* 1.3 58.9 + - - +
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Residues in contact with ALA 175 (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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209A LEU* 3.5 29.2 - - + -
93B LEU* 3.5 4.3 - - - +
94B PHE* 2.7 41.9 + - + +
103B TRP* 3.4 27.3 - - + -
156B TRP 3.2 9.6 - - - +
157B VAL* 4.0 7.2 - - + -
174B PHE* 1.3 72.3 - - - +
176B ILE* 1.3 60.1 + - - +
177B ARG 4.3 0.2 - - - -
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Residues in contact with ILE 176 (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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209A LEU* 5.5 0.2 - - - -
91B ALA* 3.5 28.9 - - + -
92B LYS 3.4 7.2 - - - +
93B LEU* 4.4 10.5 - - + -
111B CYS* 4.1 15.7 - - + -
124B ILE* 6.2 0.7 - - + -
126B MET* 4.7 7.2 - - - -
155B SER* 3.2 5.3 - - - -
156B TRP* 3.0 40.9 + - + +
158B TYR* 4.7 11.2 - - + -
175B ALA* 1.3 73.4 - - - +
177B ARG* 1.3 61.9 + - - +
178B PHE* 3.6 27.8 - - + -
187B PHE* 3.9 24.2 - - + -
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Residues in contact with ARG 177 (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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209A LEU* 3.8 11.7 - - + +
210A PRO 2.9 24.4 + - - -
211A ASP* 3.0 27.0 + - - +
212A GLU* 2.8 37.6 + - - +
214A ASP* 4.6 1.6 - - - +
216A LEU* 2.6 30.8 + - - +
91B ALA* 3.1 7.6 - - - +
92B LYS* 2.8 42.2 + - + +
94B PHE* 3.6 26.8 - - + -
154B ARG* 3.5 31.1 - - + +
155B SER* 3.0 21.5 - - - +
175B ALA 4.3 0.2 - - - -
176B ILE* 1.3 72.7 - - - +
178B PHE* 1.3 66.3 + - - +
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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