Contacts of the strand formed by residues 152 - 159 (chain B) in PDB entry 3G65
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 VAL 152 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147B PHE* 4.2 6.3 - - + -
148B CYS 3.4 21.1 - - - +
149B SER* 3.3 20.1 + - - +
150B THR 3.5 1.8 + - - -
151B ASN* 1.3 76.3 - - - +
153B ILE* 1.3 66.8 + - - +
154B ASN 3.4 25.4 - - - +
155B LYS* 4.6 5.8 - - + -
216B ASN* 5.2 3.3 + - - -
244B ARG* 3.5 32.3 - - + -
245B THR 3.5 7.9 - - - +
246B ASP* 4.0 0.7 - - + +
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Residues in contact with ILE 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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151B ASN 4.8 0.7 - - - +
152B VAL* 1.3 77.3 - - - +
154B ASN* 1.3 77.7 + - - +
214B HIS 4.0 1.6 - - - +
216B ASN* 3.6 25.9 + - + +
217B GLN* 3.8 30.5 - - + +
219B GLN* 3.2 35.4 - - + +
245B THR* 3.0 10.5 + - + +
246B ASP 3.7 22.9 - - - +
247B ASN* 3.9 17.9 - - + +
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Residues in contact with ASN 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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152B VAL* 3.4 7.2 - - - +
153B ILE* 1.3 85.0 - - - +
155B LYS* 1.3 63.5 + - - +
181B MET* 3.4 40.2 + - + +
214B HIS 3.6 4.5 - - - +
215B CYS* 3.9 8.5 - - - -
216B ASN 2.9 25.8 + - - -
217B GLN 2.9 26.9 + - - +
219B GLN* 3.6 17.4 - - - +
244B ARG* 3.8 0.5 - - - -
245B THR* 3.2 33.9 + - + +
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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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152B VAL* 4.6 5.4 - - + -
154B ASN* 1.3 77.4 - - - +
156B ILE* 1.3 69.5 + - - +
157B ILE* 3.7 30.0 - - + +
181B MET* 3.8 0.9 - - - +
213B PHE* 3.9 0.5 - - - -
214B HIS* 2.9 55.6 + - + +
242B SER* 4.8 9.6 - - - -
243B ILE 3.6 10.1 - - - +
244B ARG* 4.5 24.0 - - + +
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Residues in contact with ILE 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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155B LYS* 1.3 77.4 - - - +
157B ILE* 1.3 68.1 + - - +
158B LEU* 4.1 18.1 + - + -
181B MET* 3.4 24.8 - - + +
187B TYR 4.2 0.4 - - - +
188B PHE* 3.9 28.0 - - + -
210B MET* 3.5 22.0 - - + -
212B ALA 3.8 4.5 - - - +
213B PHE* 3.6 36.8 - - + -
215B CYS* 3.8 5.2 - - - -
241B VAL 3.8 0.5 - - - +
242B SER 3.5 1.7 - - - -
243B ILE* 2.9 43.1 + - + +
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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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155B LYS* 3.7 27.1 - - + +
156B ILE* 1.3 79.7 - - - +
158B LEU* 1.3 61.6 + - - +
211B GLU* 2.9 53.1 + - - +
212B ALA* 3.0 32.7 + - + -
240B LYS* 4.7 10.1 - - + -
241B VAL 3.6 9.6 - - - +
242B SER* 3.6 26.7 - - - +
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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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156B ILE* 4.1 13.0 - - + -
157B ILE* 1.3 76.5 - - - +
159B GLN* 1.3 70.5 + - - +
163B LEU* 3.4 32.1 - - + -
188B PHE* 3.9 30.3 - - + -
203B TYR* 4.0 26.0 - - + -
209B LEU* 3.2 20.4 - - + +
210B MET* 4.4 10.3 - - + -
211B GLU* 4.3 2.5 - - - +
240B LYS* 4.2 2.6 - - - -
241B VAL* 3.3 30.8 + - + +
243B ILE* 4.0 7.6 - - + -
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Residues in contact with GLN 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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158B LEU* 1.3 91.6 - - - +
160B SER* 1.3 64.2 + - - +
161B GLU* 3.4 16.8 + - + +
162B GLY* 3.9 6.3 + - - -
163B LEU* 4.1 5.7 + - - +
208B ASP 3.4 20.2 + - - -
209B LEU* 3.1 34.2 + - + +
211B GLU* 5.8 6.5 - - + +
239B CYS 4.0 9.0 - - - +
240B LYS* 5.0 4.3 - - + +
241B VAL* 4.4 0.2 - - - -
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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