Contacts of the strand formed by residues 155 - 165 (chain A) in PDB entry 1JSX
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 PRO 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A PRO* 4.2 1.6 - - - +
133A PHE 3.6 7.9 - - - +
136A VAL* 3.6 13.7 - - + -
151A CYS 3.1 12.1 - - - +
152A HIS 3.5 14.4 - - - +
153A HIS 4.7 2.9 - - - +
154A LEU* 1.3 93.0 - - + +
156A GLY* 1.3 72.2 + - - +
159A GLY 3.8 21.5 - - - +
160A ARG 4.1 2.7 - - - +
161A PHE* 3.2 35.0 - - + -
204A ALA* 6.5 0.9 - - + -
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Residues in contact with GLY 156 (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 PRO* 3.3 27.8 - - - +
133A PHE 3.1 14.3 + - - -
155A PRO* 1.3 82.1 - - - +
157A GLU* 1.3 67.2 + - - +
158A GLN 3.0 3.1 - - - -
159A GLY* 3.2 10.8 + - - +
204A ALA* 6.0 1.6 - - - +
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Residues in contact with GLU 157 (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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156A GLY* 1.3 72.2 - - - +
158A GLN* 1.3 64.9 + - + +
203A LYS* 3.6 6.9 + - - -
204A ALA* 4.9 5.2 + - - +
206A LYS* 3.0 37.7 + - + +
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Residues in contact with GLN 158 (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 ASP* 5.5 0.4 - - - -
156A GLY* 3.0 0.4 - - - -
157A GLU* 1.3 84.8 - - + +
159A GLY* 1.3 60.8 + - - +
160A ARG* 3.3 13.6 + - - +
203A LYS* 3.1 26.1 + - - +
206A LYS* 2.7 34.6 + - - +
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Residues in contact with GLY 159 (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 PHE 3.6 17.3 - - - -
134A ASP* 3.4 14.1 - - - -
155A PRO* 3.8 10.8 - - - +
156A GLY* 3.2 16.0 + - - +
157A GLU 4.8 0.2 - - - +
158A GLN* 1.3 78.3 - - - +
160A ARG* 1.3 58.9 + - - -
161A PHE* 5.4 0.7 - - - -
203A LYS* 3.0 23.4 + - - +
204A ALA 5.0 1.6 + - - -
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Residues in contact with ARG 160 (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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65A GLN* 3.9 37.6 + - - +
134A ASP* 3.0 12.7 + - - +
135A GLY* 3.3 1.6 - - - -
136A VAL* 2.8 35.9 + - - +
155A PRO* 4.1 1.9 - - - +
158A GLN* 3.3 14.1 + - - +
159A GLY* 1.3 75.9 - - - -
161A PHE* 1.3 59.3 + - - +
162A TYR* 3.2 33.6 - - + -
183A GLU* 2.6 38.6 + - - -
201A VAL* 3.6 12.1 - - + -
202A ILE 3.4 8.7 - - - +
203A LYS* 3.5 19.1 - - + +
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Residues in contact with PHE 161 (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 VAL* 3.6 11.9 - - + -
147A MET* 3.5 20.0 - - + -
148A VAL* 4.0 23.3 - - + -
151A CYS* 3.7 26.5 - - + -
152A HIS* 3.9 14.6 - - - -
155A PRO* 3.2 36.6 - - + -
159A GLY 5.5 0.2 - - - -
160A ARG* 1.3 73.6 - - - +
162A TYR* 1.3 60.7 + - - +
180A TYR* 4.0 23.1 - + - -
200A VAL 3.4 4.7 - - - +
201A VAL* 3.4 2.9 - - - +
202A ILE* 2.8 62.8 + - + +
203A LYS* 4.5 0.4 - - - -
204A ALA* 4.5 10.1 - - + -
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Residues in contact with TYR 162 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TYR* 3.4 22.0 + - + -
64A LEU* 3.5 33.7 - - + -
65A GLN* 3.2 23.8 + - - +
69A PHE* 4.7 0.4 - + - -
134A ASP 4.6 0.9 - - - -
135A GLY* 4.0 18.2 - - - -
136A VAL 2.8 20.4 + - - +
137A ILE* 3.8 29.3 - - + +
138A SER 4.0 1.7 + - - +
147A MET* 3.6 14.3 - - - +
160A ARG* 3.2 40.9 - - + -
161A PHE* 1.3 73.7 - - - +
163A ALA* 1.3 60.4 + - - +
199A LEU* 4.4 15.5 - - + -
200A VAL 3.5 1.3 - - - -
201A VAL* 3.7 30.5 - - + -
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Residues in contact with ALA 163 (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 ILE* 5.8 0.2 - - - -
138A SER 4.9 4.9 - - - +
144A LEU* 3.4 32.8 - - + -
147A MET* 3.9 16.8 - - + -
162A TYR* 1.3 75.9 - - - +
164A LEU* 1.3 64.0 + - - +
165A LYS* 3.7 4.8 + - + -
198A HIS 3.6 1.2 - - - +
199A LEU* 3.5 5.0 - - - +
200A VAL* 2.8 41.1 + - + +
202A ILE* 5.6 0.4 - - + -
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Residues in contact with LEU 164 (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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56A ASP* 3.6 38.8 - - + +
59A VAL* 5.4 0.4 - - + -
60A VAL* 4.0 26.9 - - + -
137A ILE* 6.3 1.9 - - + +
138A SER 5.4 2.4 + - - -
163A ALA* 1.3 73.8 - - - +
165A LYS* 1.3 66.0 + - - +
188A LEU* 4.6 3.6 - - + -
197A ARG* 3.4 31.4 - - + -
198A HIS 3.7 17.5 - - - +
199A LEU* 4.1 12.7 - - + +
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Residues in contact with LYS 165 (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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141A PHE 4.9 3.6 + - - -
142A ALA 3.7 14.1 + - - -
143A SER* 4.2 3.2 - - - +
144A LEU* 4.1 15.3 - - + +
163A ALA* 4.7 4.5 - - - +
164A LEU* 1.3 80.7 - - - +
166A GLY* 1.3 62.8 + - - +
167A GLN 4.0 12.3 - - - +
169A PRO* 3.9 24.7 - - + -
172A GLU* 2.9 43.3 + - - +
197A ARG* 3.5 13.1 - - - +
198A HIS* 2.7 33.2 + - + +
200A VAL* 4.6 6.7 - - + -
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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