Contacts of the strand formed by residues 129 - 139 (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 GLY 129 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124E GLN* 3.1 32.4 + - - +
125E LEU* 3.4 17.8 - - - +
127E SER* 3.2 5.2 + - - -
128E GLY* 1.3 80.7 - - - +
130E ALA* 1.3 63.0 + - - +
181E LEU 4.4 1.6 - - - -
183E LYS* 4.5 1.1 - - - +
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Residues in contact with ALA 130 (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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120E PRO* 3.9 8.7 - - + -
124E GLN* 3.3 7.6 - - - +
125E LEU* 4.4 2.7 - - + -
129E GLY* 1.3 75.1 - - - +
131E SER* 1.3 59.8 + - - +
132E VAL* 5.2 0.3 - - - +
179E LEU 3.7 1.0 - - - +
180E THR* 3.3 3.4 - - - +
181E LEU* 2.7 53.4 + - + +
183E LYS* 4.0 6.7 - - - +
186E TYR* 3.7 34.1 - - + -
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Residues in contact with SER 131 (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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118E PHE 4.0 1.2 - - - +
119E PRO 4.0 0.2 - - - -
120E PRO* 3.2 25.7 - - - +
124E GLN* 2.7 34.1 + - - +
130E ALA* 1.3 72.7 - - - +
132E VAL* 1.3 60.8 + - - +
133E VAL* 4.0 4.5 + - - +
178E THR* 4.6 4.0 - - - -
179E LEU 3.1 2.7 - - - -
180E THR* 2.9 30.5 + - - +
129F LEU* 5.5 4.0 - - - +
146F LEU* 4.3 21.0 - - - +
148F LYS* 4.1 7.4 + - - +
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Residues in contact with VAL 132 (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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117E ILE* 3.9 4.0 - - + -
118E PHE 3.1 16.6 - - - +
120E PRO* 3.5 22.2 - - + -
130E ALA 5.2 1.6 - - - +
131E SER* 1.3 72.8 - - - +
133E VAL* 1.3 59.0 + - - +
148E TRP* 3.5 29.7 - - + -
178E THR* 3.3 0.5 - - - -
179E LEU* 2.5 52.9 + - + +
181E LEU* 5.7 2.7 - - + -
186E TYR* 4.4 13.7 - - + -
192E TYR* 4.7 11.4 - - + -
209E PHE* 3.7 23.3 - - + -
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Residues in contact with VAL 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117E ILE* 3.5 4.2 - - - +
118E PHE* 2.8 51.4 + - + +
131E SER 4.6 5.2 - - - +
132E VAL* 1.3 79.5 - - - +
134E CYS* 1.3 65.8 + - - +
135E PHE* 4.3 13.7 - - + -
148E TRP* 3.9 1.1 - - - -
176E SER* 5.9 0.7 - - - +
177E SER 3.7 5.6 - - - +
178E THR* 3.8 21.8 - - + +
129F LEU* 3.3 36.6 - - + -
146F LEU* 4.2 20.0 - - + -
183F SER* 5.6 3.4 - - - -
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Residues in contact with CYS 134 (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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115E VAL* 3.1 31.2 - - - -
116E SER 3.0 14.8 - - - -
117E ILE* 4.1 1.6 - - - -
133E VAL* 1.3 81.2 - - - +
135E PHE* 1.3 62.5 + - - +
136E LEU* 3.5 6.2 - - - +
148E TRP* 3.7 9.9 - - + -
176E SER* 3.4 4.7 - - - -
177E SER* 3.0 29.8 + - - +
194E CYS* 2.7 43.5 - - + -
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Residues in contact with PHE 135 (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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114E THR 3.0 3.6 - - - +
115E VAL* 3.0 24.9 - - - -
116E SER* 2.9 17.6 + - - +
118E PHE* 3.8 26.5 - + - -
133E VAL* 4.3 18.6 - - + -
134E CYS* 1.3 74.5 - - - +
136E LEU* 1.3 61.4 + - - +
137E ASN* 3.4 20.6 - - - +
175E MET 3.7 2.0 - - - -
176E SER* 3.7 25.4 - - - -
129F LEU* 4.3 11.2 - - + -
142F THR* 5.0 2.9 - - - -
143F LEU 3.7 13.5 - - - -
144F GLY* 4.7 0.7 - - - -
171F PHE* 4.3 10.3 - + - -
183F SER* 4.2 17.0 - - - -
184F SER 4.3 6.5 - - - -
185F SER* 3.2 36.1 - - - -
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Residues in contact with LEU 136 (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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113E PRO* 3.8 16.8 - - + -
114E THR 3.9 4.0 - - - -
115E VAL* 4.4 11.0 - - + +
134E CYS* 3.5 18.6 - - - +
135E PHE* 1.3 76.1 - - - +
137E ASN* 1.3 61.8 + - - +
139E PHE* 3.0 15.6 - - + -
144E ILE* 3.7 21.3 - - + -
146E VAL* 3.1 36.3 - - + -
175E MET* 2.9 48.6 + - + +
176E SER* 4.5 0.9 - - - -
177E SER* 4.5 2.5 - - - +
194E CYS* 5.8 0.7 - - - -
195E GLU 5.6 0.2 - - - -
196E ALA* 3.9 15.5 - - + -
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Residues in contact with ASN 137 (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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113E PRO* 3.6 0.2 - - - +
114E THR* 3.0 39.2 + - - +
116E SER* 6.0 0.2 + - - -
135E PHE* 3.4 23.5 - - - +
136E LEU* 1.3 81.3 + - - +
138E ASN* 1.3 88.6 + - - +
139E PHE* 3.6 2.0 - - - -
174E SER* 3.7 11.3 - - - +
142F THR* 5.8 4.4 + - - +
169F HIS* 3.8 13.6 + - - +
171F PHE* 3.8 6.8 - - - -
185F SER* 3.4 25.1 + - - -
187F THR* 5.1 7.1 + - - -
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Residues in contact with ASN 138 (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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111E ALA* 3.9 10.4 - - - +
112E ALA 3.7 10.1 - - - +
114E THR* 5.0 6.2 + - - +
137E ASN* 1.3 95.7 + - - +
139E PHE* 1.3 60.7 + - - +
167E ASP* 5.3 1.6 - - - +
170E ASP* 3.6 11.0 - - - +
172E THR* 3.3 24.4 + - + +
173E TYR 2.7 19.1 + - - -
174E SER* 3.1 0.8 + - - -
169F HIS* 3.3 24.2 + - - -
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Residues in contact with PHE 139 (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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111E ALA* 3.4 18.2 - - - +
113E PRO* 3.7 23.8 - - + -
136E LEU* 3.0 34.8 - - + -
138E ASN* 1.3 75.5 - - - +
140E TYR* 1.3 66.4 + - - +
141E PRO 3.1 20.9 - - - -
142E LYS* 3.3 26.2 - - - -
144E ILE* 3.5 24.5 - - + -
163E TRP* 4.0 8.1 - + - -
172E THR* 3.1 20.4 - - - +
173E TYR* 3.1 15.6 + - + -
174E SER* 3.4 16.4 - - - -
175E MET* 3.6 15.5 - - + -
198E HIS* 3.7 10.1 - + - +
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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