Contacts of the strand formed by residues 173 - 182 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105H GLU* 4.0 14.2 + - - +
138H ASN* 2.7 23.0 + - - -
139H PHE* 3.1 28.9 + - + -
140H TYR* 4.0 19.1 - + - -
141H PRO 5.0 0.2 - - - -
142H LYS* 3.5 43.6 - - + +
163H TRP* 5.2 3.6 - + + -
164H THR* 4.2 17.0 - - - +
165H ASP* 5.1 0.7 - - - -
166H GLN* 3.5 58.4 + - + +
171H SER 3.9 2.2 - - - -
172H THR* 1.3 82.6 - - - +
174H SER* 1.3 72.2 + - - +
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Residues in contact with SER 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136H LEU 3.4 8.1 - - - -
137H ASN* 3.7 11.0 - - - -
138H ASN 3.1 4.3 + - - -
139H PHE* 3.4 3.4 - - - -
163H TRP* 3.1 6.2 - - - +
164H THR* 3.0 35.9 + - - -
172H THR* 4.8 0.2 + - - -
173H TYR* 1.3 85.2 + - - +
175H MET* 1.3 61.5 + - - +
169I HIS* 2.7 41.7 + - - -
171I PHE* 3.7 9.2 - - - -
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Residues in contact with MET 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135H PHE* 3.7 1.9 - - - -
136H LEU* 2.9 37.6 + - + +
137H ASN* 3.8 0.7 - - - +
139H PHE* 3.9 8.5 - - + -
144H ILE* 3.3 36.6 - - + +
145H ASN* 5.2 0.4 - - - -
146H VAL* 4.0 17.9 - - + +
161H ASN* 3.2 28.7 - - - +
162H SER 3.3 17.5 - - - +
163H TRP* 3.3 45.8 - - + -
174H SER* 1.3 76.2 - - - +
176H SER* 1.3 72.0 + - - +
171I PHE* 3.2 8.3 - - - -
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Residues in contact with SER 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
133H VAL* 5.9 0.3 - - - +
134H CYS 3.4 5.8 - - - -
135H PHE* 3.7 23.6 - - - -
160H LEU 3.4 2.3 - - - +
161H ASN* 3.2 20.7 - - - -
162H SER* 3.0 13.6 + - - -
175H MET* 1.3 78.4 - - - +
177H SER* 1.3 60.4 + - - +
178H THR* 4.0 10.7 - - - +
171I PHE* 3.5 21.9 - - - +
183I SER* 3.6 15.6 + - - -
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Residues in contact with SER 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133H VAL* 4.3 0.2 - - - +
134H CYS* 3.0 33.0 + - - +
136H LEU* 4.5 2.1 - - - +
146H VAL* 3.3 18.0 - - - +
148H TRP* 3.2 28.9 + - - -
159H VAL* 4.2 0.7 - - - -
160H LEU 3.0 4.9 - - - -
161H ASN* 3.2 32.7 - - - +
175H MET 4.3 0.2 - - - -
176H SER* 1.3 76.8 + - - +
178H THR* 1.3 62.4 + - - +
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Residues in contact with THR 178 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131H SER* 4.6 2.9 - - - -
132H VAL 3.2 5.5 + - - -
133H VAL* 3.8 24.6 - - + +
148H TRP* 4.3 1.1 - - - -
158H GLY 3.4 3.5 - - - +
159H VAL* 3.4 3.9 - - - -
160H LEU* 2.8 43.9 + - + +
176H SER* 4.0 14.6 - - - +
177H SER* 1.3 80.2 - - - +
179H LEU* 1.3 59.8 + - - +
180H THR* 3.6 14.6 + - - -
146I LEU* 5.3 4.6 - - + +
183I SER* 5.2 6.3 - - - +
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Residues in contact with LEU 179 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130H ALA 3.7 0.9 - - - +
131H SER* 3.1 2.3 - - - -
132H VAL* 2.5 53.3 + - + +
148H TRP* 3.9 37.9 - - + -
150H ILE* 5.7 5.8 - - + -
155H ARG* 4.0 17.7 - - + +
157H ASN 3.8 16.2 - - - +
158H GLY 3.7 0.7 - - - -
159H VAL* 3.7 24.5 - - + -
178H THR* 1.3 70.8 - - - +
180H THR* 1.3 69.6 + - - +
181H LEU* 3.6 32.1 - - + -
192H TYR* 6.0 2.5 - - + -
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Residues in contact with THR 180 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124H GLN* 4.8 1.6 - - - +
130H ALA 3.3 6.7 - - - +
131H SER* 2.9 24.9 + - - +
155H ARG* 5.4 1.0 + - - -
158H GLY* 2.9 28.3 + - - +
160H LEU* 6.2 0.5 - - - +
178H THR* 3.6 13.0 + - - -
179H LEU* 1.3 80.3 - - - +
181H LEU* 1.3 72.1 + - - +
148I LYS* 4.3 23.1 + - - +
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Residues in contact with LEU 181 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129H GLY* 4.0 1.6 - - - -
130H ALA* 2.7 45.6 + - + +
132H VAL* 5.7 3.1 - - + -
150H ILE* 5.2 6.5 - - + -
155H ARG* 4.5 19.3 - - - +
179H LEU* 3.6 23.3 - - + +
180H THR* 1.3 81.6 - - - +
182H THR* 1.3 61.2 + - - +
185H GLU* 4.2 23.1 - - + +
186H TYR* 3.5 44.2 - - + +
192H TYR* 4.7 11.9 - - + +
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Residues in contact with THR 182 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128H GLY 4.3 6.3 - - - +
130H ALA* 4.1 0.4 - - - -
181H LEU* 1.3 73.7 - - - +
183H LYS* 1.3 56.3 + - - +
184H ASP* 4.2 11.8 - - - +
185H GLU* 2.8 33.4 + - - +
186H TYR* 2.6 34.5 + - - +
188H ARG* 5.8 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