Contacts of the strand formed by residues 154 - 161 (chain B) in PDB entry 3ESF
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 LEU 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129B VAL* 4.0 22.2 - - + -
130B GLN 3.4 4.9 - - - +
131B ASP* 4.3 12.8 - - + +
132B THR* 4.9 0.9 - - - -
138B LYS* 4.9 9.9 - - + +
140B PHE* 3.8 44.0 - - + -
148B PRO* 3.8 29.2 - - + +
149B LEU* 4.4 7.3 - - - +
151B GLU* 3.5 18.1 + - + +
152B ALA 3.5 3.5 + - - +
153B ASP* 1.3 94.7 - - - +
155B LYS* 1.3 60.3 + - - +
156B PRO* 3.9 7.1 - - - +
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Residues in contact with LYS 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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129B VAL* 3.3 2.2 - - - -
130B GLN* 2.8 61.5 + - - +
132B THR* 3.8 21.0 - - + +
153B ASP 4.1 0.2 + - - -
154B LEU* 1.3 73.3 - - - +
156B PRO* 1.4 77.4 - - + +
157B ILE* 3.9 9.1 - - - +
194B GLN* 3.3 21.1 + - + +
195B PHE 2.9 25.6 + - - -
197B ARG* 4.2 27.6 - - + +
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Residues in contact with PRO 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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74B PHE* 4.0 28.3 - - + -
78B PHE* 3.4 20.9 - - + -
127B TRP* 3.7 30.5 - - + -
128B LEU 3.9 4.9 - - - +
129B VAL* 4.1 5.1 - - + -
148B PRO* 4.2 7.9 - - + -
149B LEU* 3.8 21.5 - - + -
154B LEU 3.9 2.9 - - - +
155B LYS* 1.4 90.4 - - + +
157B ILE* 1.3 62.3 + - - +
194B GLN* 3.6 12.8 - - - +
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Residues in contact with ILE 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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78B PHE* 3.5 9.8 - - - -
95B LEU* 4.5 7.9 - - + -
128B LEU* 2.8 37.2 + - + +
129B VAL 4.1 2.9 - - - -
130B GLN* 4.0 16.4 - - + +
137B LEU* 4.5 5.2 - - + -
155B LYS* 3.9 20.9 - - - +
156B PRO* 1.3 82.4 - - - +
158B LEU* 1.3 63.8 + - + +
190B HIS* 3.6 15.8 - - - -
191B ALA* 3.5 35.5 - - + +
194B GLN* 3.9 5.1 - - - +
195B PHE* 3.6 35.9 - - + +
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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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78B PHE* 3.5 6.0 - - - -
82B SER* 3.5 18.2 - - - +
109B PHE* 5.0 3.6 - - + -
113B PHE* 3.5 35.7 - - + -
127B TRP* 3.2 7.3 - - - -
128B LEU* 3.0 43.7 + - + +
157B ILE* 1.3 79.7 - - - +
159B THR* 1.3 63.7 + - - +
182B PHE* 4.1 13.9 - - + -
183B TRP* 5.8 0.9 - - + -
186B VAL* 3.7 23.6 - - + -
187B ASN 5.4 0.7 - - - +
188B TRP* 3.7 24.2 - - + -
190B HIS* 5.2 0.7 - - + -
191B ALA* 4.1 13.5 - - + -
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Residues in contact with THR 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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75B ASN 3.8 10.8 - - - +
78B PHE* 3.9 8.3 - - + -
79B TYR* 3.6 36.5 - - + +
82B SER* 3.1 22.9 + - - -
113B PHE* 4.6 0.2 - - - -
125B TRP* 3.5 17.0 - - + +
126B ALA 2.9 17.0 + - - -
127B TRP* 3.4 32.3 - - + -
158B LEU* 1.3 77.6 - - - +
160B CYS* 1.3 57.2 + - - +
182B PHE* 3.5 12.2 - - - -
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Residues in contact with CYS 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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79B TYR* 4.0 1.1 - - - -
113B PHE* 3.8 18.6 - - + -
117B ALA* 5.0 0.9 - - - -
125B TRP* 3.6 1.0 - - - -
126B ALA* 2.9 33.7 + - + -
159B THR* 1.3 76.9 - - - +
161B ASP* 1.3 66.7 + - - +
162B VAL* 3.4 10.8 + - - +
178B TYR* 3.5 31.9 - - - -
179B VAL* 4.9 6.7 - - - -
182B PHE* 3.7 39.5 - - + -
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Residues in contact with ASP 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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28B HIS* 2.8 12.3 + - - -
76B HIS* 3.2 2.4 + - - -
79B TYR* 3.5 25.1 - - + -
124B GLY 3.7 0.5 - - - +
125B TRP* 3.5 27.9 - - + -
160B CYS* 1.3 69.7 - - - +
162B VAL* 1.3 62.0 + - - +
163B TRP* 3.2 28.3 + - - +
166B ALA* 3.7 14.2 - - + +
178B TYR* 2.6 32.2 + - - -
198B FE 2.0 30.4 - - - -
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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