Contacts of the strand formed by residues 148 - 157 (chain C) in PDB entry 5J13
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 148 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C PRO* 5.0 12.8 - - + -
147C THR* 1.3 78.5 - - - +
149C ALA* 1.3 65.5 + - - +
195C THR* 3.9 4.0 - - - +
196C VAL* 2.8 38.2 + - + +
197C PRO 4.3 7.1 + - - +
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Residues in contact with ALA 149 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B THR* 5.3 8.7 - - + +
123B PHE* 3.5 25.8 - - + -
138C PRO* 3.6 13.8 - - - +
148C ALA* 1.3 78.0 - - - +
150C LEU* 1.3 63.5 + - - +
193C VAL* 4.8 9.2 - - + -
194C VAL 3.3 17.9 - - - +
195C THR* 4.5 4.3 - - + +
196C VAL* 4.4 4.3 - - - -
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Residues in contact with LEU 150 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B PHE* 4.3 2.0 - - - -
136C LEU 3.2 15.5 - - - +
137C ALA* 4.6 5.2 - - + -
138C PRO* 5.0 2.0 - - + -
149C ALA* 1.3 74.8 - - - +
151C GLY* 1.3 57.7 + - - +
166C TRP* 4.2 3.6 - - + -
193C VAL* 3.2 7.7 - - - +
194C VAL* 2.7 56.2 + - + +
196C VAL* 4.3 17.0 - - + -
206C TYR* 3.8 37.9 - - + -
223C VAL* 4.0 23.8 - - + +
224C GLU 4.5 13.7 - - - +
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Residues in contact with GLY 151 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C LEU* 2.6 41.1 + - - +
150C LEU* 1.3 77.7 - - - +
152C CYS* 1.3 56.7 + - - -
166C TRP* 3.5 16.8 - - - -
192C SER 3.0 14.4 - - - -
193C VAL* 4.0 2.5 - - - -
223C VAL* 3.5 12.6 - - - +
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Residues in contact with CYS 152 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C VAL* 3.7 12.6 - - + -
134C PHE 3.1 12.3 - - - +
135C PRO* 4.7 1.3 - - + -
136C LEU* 3.6 6.1 - - - +
151C GLY* 1.3 74.6 - - - +
153C LEU* 1.3 60.7 + - - +
154C VAL* 3.7 6.4 + - - +
164C VAL* 4.4 10.1 - - - -
166C TRP* 3.6 7.9 - - + -
192C SER* 3.0 30.1 + - - +
208C CYS* 2.0 54.1 - - - -
210C VAL* 4.9 3.1 - - - -
221C LYS* 5.5 0.9 - - + -
223C VAL* 4.7 2.2 - - + -
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Residues in contact with LEU 153 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLU* 4.7 5.4 - - - +
136B THR* 4.1 22.0 - - + +
138B VAL* 4.1 16.4 - - + -
182B TYR* 3.5 30.7 - - + -
132C SER 3.2 7.6 - - - +
133C VAL* 3.3 1.5 - - - -
134C PHE* 2.6 45.9 + - + +
136C LEU* 3.7 18.7 - - + +
152C CYS* 1.3 69.6 - - - +
154C VAL* 1.3 62.7 + - - +
155C LYS* 4.2 23.6 - - + -
189C SER* 5.0 2.2 - - - -
190C LEU 3.5 15.7 - - - +
191C SER* 3.6 5.4 - - - +
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Residues in contact with VAL 154 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C PRO* 3.3 32.1 - - + -
132C SER 3.7 2.5 - - - -
133C VAL* 4.7 5.2 - - + +
152C CYS* 4.4 10.8 - - - +
153C LEU* 1.3 71.4 - - - +
155C LYS* 1.3 58.7 + - - +
157C TYR* 3.7 13.3 - - + -
162C VAL* 4.4 6.5 - - + -
164C VAL* 4.1 7.6 - - + -
189C SER* 3.3 4.6 - - - -
190C LEU* 2.9 54.6 + - + +
192C SER 5.7 0.2 - - - +
210C VAL* 3.9 32.3 - - + -
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Residues in contact with LYS 155 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129B GLU* 3.6 23.1 + - - -
134B LYS* 3.8 27.5 - - - +
136B THR* 3.8 18.7 + - + +
182B TYR* 6.2 0.4 - - + -
302B SO4 5.0 1.0 + - - -
131C PRO* 3.4 2.0 - - - +
132C SER* 2.8 47.3 + - - +
134C PHE* 3.8 20.3 - - + -
153C LEU* 4.2 21.3 - - + +
154C VAL* 1.3 74.5 - - - +
156C ASP* 1.3 93.5 + - - +
157C TYR* 3.7 1.6 - - - -
183C GLN* 5.1 2.0 - - - +
189C SER* 3.4 13.7 - - - +
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Residues in contact with ASP 156 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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134B LYS* 4.6 10.7 + - - -
302B SO4 5.1 1.7 + - - -
129C LYS* 2.8 39.1 + - - +
130C GLY 3.4 2.6 - - - +
132C SER* 5.4 3.1 + - - +
155C LYS* 1.3 102.0 + - - +
157C TYR* 1.3 56.0 + - - +
183C GLN* 3.1 25.1 + - - +
185C SER* 5.3 0.5 + - - -
187C LEU* 4.0 23.7 - - + +
188C TYR 3.0 6.9 + - - -
189C SER* 2.9 13.3 + - - -
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Residues in contact with TYR 157 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129C LYS* 3.3 13.9 - - - +
131C PRO* 3.7 20.6 - - + -
154C VAL* 3.7 30.5 - - + -
156C ASP* 1.3 73.8 - - - +
158C PHE* 1.3 66.4 + - - +
159C PRO 3.8 15.3 - - - -
160C GLU* 3.0 28.7 + - - -
162C VAL* 3.6 33.4 - - + -
180C ALA* 3.4 10.6 - - - +
187C LEU* 3.8 2.9 - - - -
188C TYR* 2.9 60.4 + + + +
189C SER* 3.8 2.7 - - - -
190C LEU* 3.4 21.5 - - + +
212C HIS* 3.8 2.0 - - - +
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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