Contacts of the strand formed by residues 191 - 203 (chain F) in PDB entry 3U8M
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 ALA 191 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146F HIS* 3.3 4.3 - - - +
147F SER* 2.8 37.5 + - - +
182F SER* 3.6 20.9 - - - +
183F VAL 3.4 9.4 - - - +
184F THR* 4.0 11.4 - - - +
189F PRO 4.1 0.2 + - - -
190F GLU* 1.3 79.0 + - - +
192F TYR* 1.3 61.3 + - - +
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Residues in contact with TYR 192 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F TYR* 4.7 8.3 - - - +
142F SER 4.5 4.9 - - - +
143F TRP 4.4 13.9 - - - -
144F THR* 3.6 19.7 + - - -
145F HIS 3.5 17.7 - - - +
146F HIS* 3.4 33.1 - - + +
182F SER* 3.8 0.8 - - - -
183F VAL* 2.7 37.4 + - - +
185F TYR* 4.1 27.6 + + + -
188F CYS* 3.7 33.4 - - + +
190F GLU* 3.5 24.7 - - + +
191F ALA* 1.3 77.2 - - - +
193F GLU* 1.3 66.5 + - - +
194F ASP* 4.0 1.6 + - - +
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Residues in contact with GLU 193 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F TYR* 5.0 1.7 + - - -
141F GLY* 3.5 15.8 - - - -
142F SER* 3.9 7.5 + - - +
145F HIS 5.3 2.0 + - - -
147F SER* 3.9 26.8 - - - +
150F ILE 4.4 8.0 + - - +
151F SER* 3.1 17.9 - - - -
152F VAL* 3.0 29.7 + - + +
180F LYS* 2.6 33.0 + - - +
181F ASN 3.3 9.4 - - - +
182F SER* 4.1 14.1 + - - +
192F TYR* 1.3 77.7 - - - +
194F ASP* 1.3 62.4 + - - +
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Residues in contact with ASP 194 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89F TYR* 4.8 3.1 - - + -
139F LYS* 3.3 37.6 - - + -
140F ILE 3.2 15.5 - - - +
141F GLY* 4.2 1.3 - - - -
152F VAL* 3.5 9.1 - - - +
180F LYS* 3.6 3.5 - - - +
181F ASN* 2.9 57.9 + - - +
183F VAL* 3.5 23.4 - - - +
185F TYR* 4.3 1.5 + - - +
192F TYR 4.4 0.5 - - - +
193F GLU* 1.3 76.8 - - - +
195F VAL* 1.3 62.0 + - - +
196F GLU* 3.9 10.8 - - - +
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Residues in contact with VAL 195 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F VAL* 4.9 14.4 - - + +
138F ILE 3.5 2.9 - - - +
139F LYS* 3.5 0.9 - - - -
140F ILE* 2.7 41.1 + - + +
152F VAL* 4.0 9.4 - - + +
153F ASP* 3.9 15.3 - - - +
154F PRO* 3.9 40.2 - - + -
178F GLN* 4.6 9.0 - - + +
179F LYS 3.5 8.7 - - - +
180F LYS* 4.6 1.1 - - + -
194F ASP* 1.3 79.3 - - - +
196F GLU* 1.3 64.4 + - - +
197F VAL* 3.9 21.3 + - + +
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Residues in contact with GLU 196 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F ARG* 3.8 32.8 + - + +
138F ILE 3.4 3.1 - - - +
139F LYS* 4.0 26.3 - - + +
177F THR 3.8 0.2 - - - +
178F GLN* 3.5 1.6 - - - -
179F LYS* 2.6 57.7 + - + +
181F ASN* 3.3 25.0 + - - +
194F ASP* 3.9 9.2 + - - +
195F VAL* 1.3 71.0 - - - +
197F VAL* 1.3 62.4 + - - +
198F SER* 3.7 3.7 + - - +
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Residues in contact with VAL 197 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31F VAL* 6.5 0.7 - - + -
32F SER* 6.1 0.4 - - - -
33F LEU* 3.9 28.7 - - + +
35F PHE* 4.0 20.4 - - + -
136F CYS 3.5 4.3 - - - +
137F ARG* 3.5 1.0 - - - -
138F ILE* 2.8 45.1 + - + +
140F ILE* 5.4 4.0 - - + -
176F VAL* 3.8 26.0 - - + -
177F THR 3.5 3.6 - - - +
178F GLN* 3.8 20.2 - - - +
195F VAL* 4.0 18.4 - - + +
196F GLU* 1.3 72.3 - - - +
198F SER* 1.3 62.1 + - - +
199F LEU* 3.6 0.7 + - - +
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Residues in contact with SER 198 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F THR* 4.2 16.9 - - - +
136F CYS 3.6 4.0 - - - -
137F ARG* 3.4 22.7 - - - +
175F ASP 3.8 0.2 - - - +
176F VAL* 3.3 7.1 - - - +
177F THR* 2.7 51.0 + - - -
179F LYS* 6.1 0.9 - - - +
196F GLU* 3.7 3.9 + - - +
197F VAL* 1.3 71.5 - - - +
199F LEU* 1.3 61.8 + - - +
200F ASN* 3.7 2.0 + - - +
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Residues in contact with LEU 199 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35F PHE* 3.9 41.1 - - + -
38F ILE* 3.9 24.2 - - + -
48F VAL* 6.3 0.2 - - + -
50F VAL* 4.7 9.9 - - + -
134F ALA 3.5 2.1 - - - +
135F THR* 3.2 2.4 - - - -
136F CYS* 2.7 52.5 + - + +
138F ILE* 5.6 2.0 - - + -
173F ILE* 4.1 22.9 - - + -
175F ASP 4.0 0.4 - - - -
176F VAL* 4.0 22.4 - - + +
197F VAL 3.6 1.4 + - - +
198F SER* 1.3 70.5 - - - +
200F ASN* 1.3 62.4 + - - +
201F PHE* 3.7 16.7 - - + -
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Residues in contact with ASN 200 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132F SER 3.3 24.4 + - - +
133F GLY 4.1 1.0 + - - -
134F ALA 2.8 24.8 + - - -
135F THR* 3.1 20.7 + - + +
173F ILE* 3.6 1.9 - - - +
174F LEU* 2.6 47.4 + - - +
175F ASP* 2.8 36.0 + - + +
198F SER 3.7 1.5 + - - +
199F LEU* 1.3 71.5 - - - +
201F PHE* 1.3 54.8 + - - +
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Residues in contact with PHE 201 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38F ILE* 3.6 31.6 - - + -
41F VAL* 3.5 26.0 - - + -
48F VAL* 4.0 21.5 - - + -
124F ASP 5.1 0.2 - - - -
125F VAL* 4.6 4.0 - - + -
128F VAL* 3.7 11.7 - - + -
133F GLY* 3.3 3.1 - - - -
134F ALA* 2.8 59.4 + - + +
136F CYS* 3.9 21.1 - - + -
171F PHE* 4.1 11.7 - + + -
172F GLU 3.3 16.2 - - - +
173F ILE* 4.3 2.7 - - - -
174F LEU* 4.1 4.3 - - - +
199F LEU* 3.7 19.1 - - + -
200F ASN* 1.3 74.1 - - - +
202F ARG* 1.3 64.0 + - - +
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Residues in contact with ARG 202 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F VAL* 3.0 16.6 - - - +
130F THR 3.4 15.3 - - - +
131F GLU* 2.6 57.9 + - - +
133F GLY* 3.7 4.9 - - - -
171F PHE* 3.6 7.0 - - - -
172F GLU* 2.8 52.1 + - + +
174F LEU* 3.3 28.6 - - + +
201F PHE* 1.3 78.0 - - - +
203F LYS* 1.3 73.8 + - - +
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Residues in contact with LYS 203 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128F VAL* 2.7 17.5 + - + +
129F ASP* 3.1 42.8 + - + +
130F THR 5.5 0.3 - - - +
170F ARG* 4.2 32.2 - - + +
171F PHE* 3.7 25.4 - - + -
172F GLU* 4.3 0.5 - - - +
202F ARG* 1.3 85.3 + - - +
204F LYS* 1.3 71.0 + - - +
206F ARG* 4.6 20.0 - - + +
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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