Contacts of the strand formed by residues 157 - 164 (chain B) in PDB entry 6D6Q
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 CYS 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B ASN* 3.6 5.6 - - - +
142B THR* 6.0 0.2 - - - -
155B PHE* 3.3 30.4 + - - +
156B VAL* 1.3 74.2 - - - +
158B ALA* 1.3 60.0 + - - +
187B ALA* 3.4 0.6 - - - -
188B LEU* 2.9 39.7 + - - +
190B PRO* 4.5 4.0 - - + -
220B ALA* 3.8 21.1 - - + +
223B VAL* 4.8 3.6 - - + -
224B HIS* 3.7 30.7 - - + +
227B LEU* 4.4 15.3 - - - -
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Residues in contact with ALA 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B GLN* 5.0 0.5 + - - -
134B TYR* 5.3 2.2 - - + -
135B ALA* 3.8 14.8 - - + +
138B VAL* 3.8 24.7 - - + -
139B ASN* 3.3 23.4 + - - -
157B CYS* 1.3 73.6 - - - +
159B CYS* 1.3 66.8 + - - +
186B LEU 3.1 16.2 - - - +
187B ALA* 3.4 18.2 - - + +
220B ALA* 4.6 3.4 - - - -
223B VAL* 4.4 7.4 - - - +
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Residues in contact with CYS 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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21B LEU* 5.2 0.7 - - - -
42B GLN* 4.4 1.8 - - - +
135B ALA* 3.7 14.1 - - - +
158B ALA* 1.3 78.2 - - - +
160B SER* 1.3 87.3 + - - +
171B ASP* 3.2 34.1 - - - -
185B ALA* 3.6 1.5 - - - +
186B LEU* 2.9 38.8 + - - +
216B ALA* 4.7 1.8 - - - +
219B ALA* 3.9 17.3 - - + -
220B ALA* 4.3 20.5 - - + +
223B VAL* 4.5 8.3 - - + -
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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
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132B GLY* 4.5 16.4 - - - -
135B ALA* 4.9 2.7 - - - +
159B CYS* 1.3 83.2 - - - +
161B ALA* 1.3 60.0 + - - +
170B ALA* 3.6 1.7 - - - +
171B ASP* 2.6 35.0 + - - -
172B LEU* 3.5 24.1 + - - +
183B GLN* 5.9 5.2 - - - -
184B LEU 3.5 10.1 - - - -
185B ALA* 4.0 13.5 - - - +
216B ALA* 4.6 4.6 - - - +
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Residues in contact with ALA 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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160B SER* 1.3 75.2 - - - +
162B GLY* 1.3 59.9 + - - +
169B LEU 3.1 13.9 - - - +
170B ALA* 4.8 1.1 - - - -
172B LEU* 3.3 9.8 - - - +
183B GLN* 3.3 5.7 - - - +
184B LEU* 2.9 34.2 + - + +
212B VAL* 3.7 18.4 - - + +
215B ALA* 4.7 3.6 - - + -
216B ALA* 3.6 29.1 - - + +
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Residues in contact with GLY 162 (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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161B ALA* 1.3 76.8 - - - +
163B PHE* 1.3 61.4 + - - +
164B VAL* 5.3 0.2 - - - -
168B ALA* 3.2 7.1 - - - +
169B LEU* 2.9 32.1 + - - -
172B LEU* 3.3 15.6 - - - +
182B PRO 3.2 13.9 - - - -
184B LEU 5.0 0.2 - - - -
212B VAL* 3.7 9.3 - - - +
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Residues in contact with PHE 163 (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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162B GLY* 1.3 74.5 - - - -
164B VAL* 1.3 70.1 + - - +
165B ASP 5.1 1.3 - - - -
166B GLY* 3.4 38.4 - - - -
167B THR 3.2 17.0 - - - -
168B ALA* 5.2 0.2 - - + -
181B GLY* 4.8 3.3 - - - -
182B PRO* 3.4 42.4 + - + +
204B LEU* 4.8 11.2 - - + -
208B HIS* 3.2 44.4 - + + -
211B ARG* 4.5 8.1 - - + -
212B VAL* 3.9 21.1 - - + -
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Residues in contact with VAL 164 (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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5B LEU* 4.2 36.3 - - + -
6B LEU* 3.4 9.7 - - + +
163B PHE* 1.3 85.2 - - - +
165B ASP* 1.3 82.5 + - - +
166B GLY 3.2 1.8 - - - -
167B THR* 2.6 36.3 + - - -
169B LEU* 3.9 26.1 - - + +
176B GLU* 5.4 4.5 - - + +
181B GLY* 6.1 2.5 - - - -
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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