Contacts of the strand formed by residues 193 - 203 (chain A) in PDB entry 3AFF
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 ASN 193 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ARG* 5.1 1.6 + - - +
140A ASN 3.9 0.2 - - - -
141A TRP 3.6 2.8 + - - -
142A SER* 3.0 32.2 + - - -
145A CYS* 3.8 7.6 - - - -
146A ASP* 3.3 21.1 - - - +
178A ILE* 3.7 16.8 - - + -
179A LYS 3.3 6.7 - - - +
180A ASP* 3.4 17.8 + - - +
181A VAL* 2.8 31.1 - - - +
182A TRP* 3.0 23.0 - - - +
191A GLY* 2.7 17.1 + - - +
192A SER* 1.3 72.0 - - - +
194A THR* 1.3 62.1 + - - +
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Residues in contact with THR 194 (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* 3.6 23.1 - - - +
139A TRP 3.3 10.5 - - - +
140A ASN* 3.3 23.7 - - + +
141A TRP 4.4 0.2 + - - -
177A GLU 3.3 2.9 - - - +
178A ILE* 3.3 3.3 - - - -
179A LYS* 2.8 48.2 + - + +
181A VAL* 3.7 17.8 - - - +
193A ASN* 1.3 76.1 - - - +
195A LEU* 1.3 66.1 + - - +
196A VAL* 3.9 8.2 + - + -
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Residues in contact with LEU 195 (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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119A SER* 4.2 10.5 - - - -
138A SER* 3.4 3.1 - - - -
139A TRP* 2.7 44.8 + - + +
142A SER* 3.6 24.0 - - - +
145A CYS* 4.0 25.6 - - + -
151A THR* 3.3 33.2 - - + +
153A VAL* 4.1 11.7 - - + -
176A TYR* 3.9 31.6 - - + -
177A GLU 3.4 3.4 - - - -
178A ILE* 4.1 7.4 - - + -
194A THR* 1.3 76.0 - - - +
196A VAL* 1.3 62.8 + - - +
197A VAL* 4.5 6.1 - - + -
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Residues in contact with VAL 196 (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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137A GLY 3.8 7.2 - - - +
138A SER* 4.1 17.3 - - - +
175A GLU 4.6 0.2 - - - +
176A TYR* 3.3 6.2 - - - +
177A GLU* 2.9 49.1 + - + +
179A LYS* 4.6 15.7 - - + -
194A THR* 4.3 11.2 - - + +
195A LEU* 1.3 75.4 - - - +
197A VAL* 1.3 62.0 + - - +
198A LYS* 3.6 35.0 + - + +
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Residues in contact with VAL 197 (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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135A VAL* 3.7 27.4 - - + +
136A ASN* 3.5 2.8 - - - +
137A GLY 3.0 27.3 + - - +
139A TRP* 3.8 29.4 - - + -
151A THR* 5.7 0.2 - - + -
153A VAL* 4.6 7.2 - - + -
171A ILE* 3.9 15.0 - - + -
175A GLU 4.6 4.9 - - - +
176A TYR* 3.9 16.8 - - + -
195A LEU* 4.3 4.5 - - + +
196A VAL* 1.3 79.3 - - - +
198A LYS* 1.3 63.6 + - - +
199A ASP 4.2 0.2 - - - -
200A VAL* 3.7 25.1 - - + -
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Residues in contact with LYS 198 (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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136A ASN* 3.2 6.7 - - - +
175A GLU 4.9 1.0 + - - -
177A GLU* 3.9 21.7 + - - +
196A VAL* 3.6 26.8 + - + +
197A VAL* 1.3 78.9 - - - +
199A ASP* 1.3 75.1 + - + +
200A VAL* 3.2 11.4 + - - +
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Residues in contact with ASP 199 (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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134A LEU* 3.5 33.2 - - + +
135A VAL 3.2 5.1 + - - -
136A ASN* 2.7 33.3 + - - +
198A LYS* 1.3 75.2 - - + +
200A VAL* 1.3 58.2 + - - +
201A PHE 3.8 1.4 + - - -
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Residues in contact with VAL 200 (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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133A TYR 3.4 2.6 - - - +
134A LEU* 3.9 2.6 - - - +
135A VAL* 2.8 34.1 + - - +
171A ILE* 4.1 12.1 - - + -
175A GLU* 3.2 59.9 - - + +
197A VAL* 3.7 22.7 - - + -
198A LYS 3.5 14.4 - - - +
199A ASP* 1.3 74.9 - - - +
201A PHE* 1.3 69.8 + - - +
202A VAL* 3.5 7.5 + - + +
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Residues in contact with PHE 201 (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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129A VAL* 3.7 18.2 - - + -
130A ASP 3.4 22.0 - - - -
131A GLY* 3.4 25.1 - - - -
132A GLY* 3.8 10.1 - - - -
133A TYR 3.4 10.3 - - - -
134A LEU* 4.1 7.9 - - + +
175A GLU* 4.3 7.4 - - - +
199A ASP 3.8 3.6 + - - -
200A VAL* 1.3 76.6 - - - +
202A VAL* 1.3 60.7 - - - +
203A PRO* 4.0 27.2 - - + +
206A ARG* 4.8 2.9 + - - -
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Residues in contact with VAL 202 (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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132A GLY* 3.3 0.5 - - - -
133A TYR* 2.8 38.4 + - + +
135A VAL* 3.8 23.6 - - + -
169A PHE* 4.4 12.6 - - + -
170A LEU 3.9 7.6 - - - +
171A ILE* 3.7 28.7 - - + -
200A VAL* 3.9 6.3 - - + +
201A PHE* 1.3 78.6 - - - +
203A PRO* 1.3 75.7 - - + +
206A ARG* 3.5 36.3 - - + +
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Residues in contact with PRO 203 (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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131A GLY 3.6 13.0 - - - +
133A TYR* 4.4 1.3 - - - -
201A PHE* 4.0 18.1 - - + +
202A VAL* 1.3 91.0 - - + +
204A ARG* 1.3 60.9 + - - +
205A HIS* 3.2 35.2 - - + +
206A ARG* 2.8 60.6 + - + +
207A PHE 3.9 0.3 + - - -
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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