Contacts of the strand formed by residues 152 - 161 (chain B) in PDB entry 3JSP
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 GLU 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B ARG* 3.6 3.9 - - - +
149B ILE* 3.0 36.0 + - + +
150B ASP 3.0 4.8 + - - +
151B ASP* 1.3 76.9 - - - +
153B VAL* 1.3 70.0 - - - +
154B THR* 3.4 15.4 + - - +
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Residues in contact with VAL 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82B VAL* 4.0 32.9 - - + +
89B LEU* 4.5 13.7 - - + -
113B LEU* 3.9 25.4 - - + -
146B VAL* 3.7 25.4 - - + -
147B ALA 3.4 5.2 - - - -
148B ARG* 3.8 25.1 - - + -
151B ASP 3.8 1.0 + - - -
152B GLU* 1.3 75.2 - - - +
154B THR* 1.3 64.5 + - - +
189B GLU* 5.0 0.4 - - + -
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Residues in contact with THR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B VAL* 3.3 7.6 - - - +
147B ALA* 2.6 43.9 + - - +
149B ILE* 4.5 14.8 - - + +
152B GLU* 3.4 18.5 + - - +
153B VAL* 1.3 79.6 + - - +
155B VAL* 1.3 72.3 + - - +
156B ALA* 4.3 6.7 - - + -
167B LEU* 5.1 8.1 - - + -
177B ILE* 4.7 20.1 - - + +
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Residues in contact with VAL 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B LEU* 5.0 9.2 - - + -
115B VAL* 4.5 23.8 - - + -
116B SER 5.5 3.1 - - - +
119B SER* 4.0 12.1 + - - +
120B MET* 3.8 20.3 - - + +
125B ILE* 5.4 4.5 - - + -
131B LEU* 3.8 33.0 - - + -
144B VAL* 4.6 13.5 - - + -
145B VAL 3.3 11.2 - - - +
146B VAL* 4.5 4.5 - - + -
154B THR* 1.3 80.8 - - - +
156B ALA* 1.3 67.4 + - - +
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Residues in contact with ALA 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B SER* 6.5 0.7 - - - -
120B MET* 4.0 16.2 - - - -
144B VAL* 4.4 0.7 - - - -
145B VAL* 2.9 38.2 + - - +
154B THR* 4.3 8.2 - - + -
155B VAL* 1.3 76.0 - - - +
157B ARG* 1.3 63.2 + - - +
167B LEU* 3.9 26.2 - - + +
168B LEU 3.4 15.5 - - - +
169B PRO* 4.8 1.6 - - + -
177B ILE* 6.2 2.2 - - + -
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Residues in contact with ARG 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B MET* 4.1 6.7 - - + +
123B ILE* 4.1 14.1 - - - +
142B GLY* 2.7 39.8 + - - +
143B GLN 3.3 11.2 - - - +
144B VAL* 3.7 24.6 - - - +
156B ALA* 1.3 70.9 - - - +
158B LEU* 1.3 66.6 + - - +
166B GLU 3.6 0.3 - - - +
167B LEU* 3.4 4.4 - - - -
168B LEU* 2.8 60.7 + - + +
170B GLU* 3.0 37.5 + - + +
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Residues in contact with LEU 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL* 3.7 30.5 - - + +
140B ARG 3.6 26.7 - - - +
141B ASN* 4.6 0.9 - - - +
142B GLY* 2.9 26.0 + - - -
143B GLN* 2.9 13.8 + - + +
145B VAL* 3.9 16.4 - - + -
156B ALA 3.7 2.6 + - - -
157B ARG* 1.3 74.8 - - - +
159B LYS* 1.3 68.7 - - - +
160B LYS* 4.4 20.2 - - + +
165B VAL* 4.0 24.5 - - + -
166B GLU 3.9 1.8 - - - -
167B LEU* 4.0 13.2 - - + -
168B LEU* 4.8 0.3 - - - +
186B PHE* 4.7 1.6 - - + -
188B ILE* 4.6 11.2 - - + -
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Residues in contact with LYS 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ASN* 3.5 17.5 - - + +
142B GLY 5.2 0.7 - - - +
158B LEU* 1.3 78.3 - - - +
160B LYS* 1.3 61.6 + - - +
161B GLN* 3.7 24.2 + - + +
164B LYS 4.2 0.7 - - - +
166B GLU* 2.9 53.9 + - + +
168B LEU* 3.7 24.5 - - + +
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Residues in contact with LYS 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B VAL 4.2 20.1 + - - -
140B ARG* 5.4 1.6 - - - +
141B ASN* 3.0 37.3 + - - +
158B LEU* 4.4 13.4 - - + +
159B LYS* 1.3 74.3 - - - +
161B GLN* 1.3 66.4 + - - +
162B GLY 4.0 7.2 - - - +
164B LYS 3.7 4.0 - - - -
165B VAL* 3.9 26.2 - - + +
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Residues in contact with GLN 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ASN* 5.4 1.1 - - - +
159B LYS* 3.7 38.1 + - - +
160B LYS* 1.3 77.2 - - - +
162B GLY* 1.3 59.3 + - - +
163B ASN 3.0 9.2 + - - -
164B LYS* 2.7 49.3 + - + +
166B GLU* 4.2 10.3 + - - +
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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