Contacts of the strand formed by residues 156 - 161 (chain B) in PDB entry 3SN6
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 GLN 156 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152B LEU* 3.4 40.7 + - + +
153B ASP* 3.0 31.2 + - - +
155B ASN* 1.3 83.6 - - + +
157B ILE* 1.3 58.7 + - - +
168B LEU* 3.6 20.2 - - + +
169B TRP 2.9 19.7 - - - +
170B ASP* 4.0 5.8 - - + +
171B ILE* 4.8 0.2 - - - -
177B THR* 4.8 8.1 + - - +
213B VAL* 5.7 1.2 - - - +
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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
----------------------------------------------------------
113B ALA* 3.6 17.0 - - + -
121B CYS* 3.9 11.4 - - - -
123B ILE* 3.6 23.8 - - + -
139B LEU* 3.8 21.1 - - + -
149B CYS* 4.4 8.3 - - + -
150B ARG 3.1 22.7 - - - +
151B PHE* 3.9 16.6 - - + +
152B LEU 4.6 0.2 - - - +
156B GLN* 1.3 75.7 - - - +
158B VAL* 1.3 63.0 + - - +
159B THR* 4.6 0.9 - - + -
168B LEU* 3.6 4.7 - - - -
169B TRP* 2.9 37.7 + - + -
171B ILE* 3.7 20.6 - - + -
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149B CYS* 3.0 4.3 - - - +
150B ARG* 2.7 55.8 + - + +
152B LEU* 4.9 5.3 - - + +
157B ILE* 1.3 72.4 - - - +
159B THR* 1.3 66.6 + - - +
167B ALA 3.3 14.1 - - - +
168B LEU* 3.8 14.0 - - + +
180B PHE* 4.8 0.7 - - + -
190B LEU* 4.3 8.5 - - + -
192B LEU* 3.7 28.3 - - + -
199B PHE* 3.7 38.6 - - + -
213B VAL* 6.2 1.3 - - + -
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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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121B CYS* 3.8 23.6 - - + -
142B HIS* 3.1 21.4 + - - -
146B LEU* 3.5 16.6 - - + -
148B CYS 3.3 6.7 - - - -
149B CYS* 3.4 16.2 - - + +
157B ILE* 4.4 4.7 - - + +
158B VAL* 1.3 78.8 - - - +
160B SER* 1.3 58.9 + - - +
166B CYS* 3.3 5.7 - - - +
167B ALA 2.9 32.8 + - - -
169B TRP* 3.3 24.9 + - + +
190B LEU* 3.6 4.7 - - - +
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Residues in contact with SER 160 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B LEU* 3.4 6.9 - - - +
147B SER* 2.8 41.4 + - - -
148B CYS* 2.7 31.5 + - - +
159B THR* 1.3 73.2 - - - +
161B SER* 1.3 62.8 + - - +
165B THR 4.1 1.6 - - - -
166B CYS* 3.4 25.8 - - - -
187B VAL* 3.7 12.6 + - - -
189B SER 4.1 2.6 - - - -
190B LEU* 3.5 10.0 - - - +
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Residues in contact with SER 161 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142B HIS* 3.3 23.2 + - - -
144B GLY 2.9 15.2 + - - -
145B TYR 2.5 23.4 + - - -
146B LEU* 4.1 0.7 - - - -
147B SER* 3.6 2.6 + - - -
160B SER* 1.3 77.4 - - - +
162B GLY* 1.3 58.3 + - - +
163B ASP* 2.8 29.3 + - - +
164B THR 3.1 10.0 + - - -
165B THR 3.4 5.3 + - - -
187B VAL* 3.2 22.8 + - - +
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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
------------------------------------------------------------
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