Contacts of the strand formed by residues 173 - 182 (chain E) in PDB entry 1FSK
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 TYR 173 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105E GLU* 4.0 14.4 + - - +
138E ASN* 2.7 23.0 + - - -
139E PHE* 3.1 28.9 + - + -
140E TYR* 4.0 19.4 - + - -
141E PRO 5.0 0.2 - - - -
142E LYS* 3.5 42.9 - - + +
163E TRP* 5.2 3.6 - + + -
164E THR* 4.2 18.6 - - - +
165E ASP* 5.1 0.7 - - - -
166E GLN* 3.5 58.8 + - + +
171E SER 3.9 2.0 - - - -
172E THR* 1.3 81.9 - - - +
174E SER* 1.3 71.5 + - - +
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Residues in contact with SER 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E LEU 3.4 7.0 - - - -
137E ASN* 3.7 10.5 - - - -
138E ASN 3.1 3.8 + - - -
139E PHE* 3.4 3.6 - - - -
163E TRP* 3.1 6.2 - - - +
164E THR* 3.0 37.1 + - - -
172E THR* 4.8 0.2 + - - -
173E TYR* 1.3 85.6 + - - +
175E MET* 1.3 61.3 + - - +
169F HIS* 2.7 41.1 + - - -
171F PHE* 3.6 9.6 - - - -
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Residues in contact with MET 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135E PHE* 3.7 1.9 - - - -
136E LEU* 2.9 37.9 + - + +
139E PHE* 3.9 8.7 - - + -
144E ILE* 3.3 36.6 - - + +
145E ASN* 5.2 0.4 - - - -
146E VAL* 4.0 18.6 - - + -
161E ASN* 3.2 28.5 - - - +
162E SER 3.3 16.2 - - - +
163E TRP* 3.3 45.8 - - + -
174E SER* 1.3 75.6 - - - +
176E SER* 1.3 72.0 + - - +
171F PHE* 3.1 11.7 - - - -
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Residues in contact with SER 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E VAL* 5.9 0.6 - - - +
134E CYS 3.4 5.6 - - - -
135E PHE* 3.7 23.6 - - - -
160E LEU 3.4 1.9 - - - +
161E ASN* 3.2 20.2 - - - -
162E SER* 3.0 13.1 + - - -
175E MET* 1.3 78.6 - - - +
177E SER* 1.3 58.6 + - - +
178E THR* 4.0 10.9 - - - +
171F PHE* 3.5 22.8 - - - +
183F SER* 3.4 16.3 + - - -
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Residues in contact with SER 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134E CYS* 3.0 32.4 + - - +
136E LEU* 4.5 1.9 - - - +
146E VAL* 3.3 18.5 - - - +
148E TRP* 3.2 28.9 + - - -
159E VAL* 4.2 0.9 - - - -
160E LEU 3.0 5.6 - - - -
161E ASN* 3.2 31.9 - - - -
175E MET 4.3 0.2 - - - -
176E SER* 1.3 75.7 + - - +
178E THR* 1.3 62.0 + - - +
194E CYS* 4.5 0.2 - - - -
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Residues in contact with THR 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131E SER* 4.6 4.0 - - - -
132E VAL 3.3 4.9 + - - -
133E VAL* 3.8 25.1 - - + +
148E TRP* 4.5 1.1 - - - -
158E GLY 3.4 4.2 - - - +
159E VAL* 3.4 3.5 - - - -
160E LEU* 2.8 44.0 + - + +
176E SER* 4.0 14.6 - - - +
177E SER* 1.3 80.2 - - - +
179E LEU* 1.3 60.5 + - - +
180E THR* 3.6 14.4 + - - -
146F LEU* 5.0 5.2 - - + +
148F LYS* 5.8 0.3 + - - -
183F SER* 5.1 6.1 - - - +
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Residues in contact with LEU 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130E ALA 3.7 0.9 - - - +
131E SER* 3.1 1.7 - - - -
132E VAL* 2.5 53.8 + - + +
148E TRP* 3.9 39.0 - - + -
150E ILE* 5.7 5.6 - - + -
155E ARG* 4.0 16.6 - - + +
157E ASN 3.8 15.9 - - - +
158E GLY 3.7 0.4 - - - -
159E VAL* 3.7 24.5 - - + -
178E THR* 1.3 71.1 - - - +
180E THR* 1.3 69.8 + - - +
181E LEU* 3.6 31.9 - - + -
192E TYR* 6.0 2.7 - - + -
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Residues in contact with THR 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E GLN* 4.8 1.6 - - - +
130E ALA 3.3 5.8 - - - +
131E SER* 2.9 25.2 + - - +
155E ARG* 5.4 0.9 + - - -
158E GLY* 2.9 28.5 + - - +
160E LEU* 6.2 0.3 - - - +
178E THR* 3.6 12.6 + - - -
179E LEU* 1.3 79.8 + - - +
181E LEU* 1.3 74.3 + - - +
148F LYS* 3.9 26.1 + - - +
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Residues in contact with LEU 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E GLY* 4.0 1.4 - - - -
130E ALA* 2.7 45.9 + - + +
132E VAL* 5.7 3.1 - - + -
150E ILE* 5.2 6.5 - - + -
155E ARG* 4.5 20.0 - - - +
179E LEU* 3.6 23.3 - - + -
180E THR* 1.3 80.5 - - - +
182E THR* 1.3 61.5 + - - +
185E GLU* 4.2 23.1 - - + +
186E TYR* 3.5 44.0 - - + +
192E TYR* 4.7 12.1 - - + +
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Residues in contact with THR 182 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128E GLY 4.3 6.5 - - - +
130E ALA* 4.1 0.7 - - - -
181E LEU* 1.3 73.3 - - - +
183E LYS* 1.3 55.1 + - - +
184E ASP* 4.2 11.2 - - - +
185E GLU* 2.8 34.0 + - - +
186E TYR* 2.6 34.3 + - - +
188E ARG* 5.8 0.5 + - - -
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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