Contacts of the strand formed by residues 141 - 147 (chain B) in PDB entry 6DBV
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 THR 141 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ALA* 4.6 2.9 - - - +
77B ILE 6.0 0.2 - - - +
139B GLY 4.3 0.5 + - - -
140B HIS* 1.3 82.2 + - - +
142B LEU* 1.3 68.2 + - - +
143B SER* 4.9 1.3 - - - +
154B VAL 4.1 0.5 - - - +
155B LEU* 3.3 2.8 - - - +
156B PHE* 2.9 36.4 + - - +
206B PHE 4.9 0.3 - - - -
207B HIS* 2.5 33.9 + - - +
208B VAL* 4.7 1.8 - - - -
209B ALA* 3.7 39.9 - - + +
218B PHE* 4.5 5.3 - - - -
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Residues in contact with LEU 142 (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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76B ALA* 4.2 19.5 - - + +
77B ILE 2.7 23.8 + - - +
78B ALA* 4.1 18.8 - - + -
91B LEU* 4.8 15.7 - - + +
93B HIS* 5.2 14.6 - - + +
106B LEU* 6.1 4.9 - - + -
141B THR* 1.3 79.9 - - - +
143B SER* 1.3 80.0 + - - +
153B CYS* 3.9 13.9 - - + -
154B VAL 3.1 37.5 - - - +
155B LEU* 3.8 21.1 - - + +
185B ILE* 5.6 6.3 - - + -
218B PHE* 6.1 0.9 - - - -
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Residues in contact with SER 143 (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 ALA* 4.4 5.8 - - - +
141B THR* 4.9 3.5 - - - +
142B LEU* 1.3 82.8 + - - +
144B VAL* 1.3 68.7 + - - +
153B CYS* 3.2 5.0 - - - -
154B VAL* 2.9 41.3 + - - -
209B ALA* 4.6 16.0 + - - +
210B LEU* 5.0 0.2 - - - -
211B ALA* 4.0 23.3 + - - +
216B VAL* 5.0 5.4 - - - -
218B PHE* 6.3 1.7 - - - -
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Residues in contact with VAL 144 (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 ALA* 3.9 22.0 - - + -
79B HIS 5.0 4.2 - - - +
80B PHE* 4.0 26.2 - - + +
81B GLU* 5.4 1.6 - - + +
91B LEU* 4.3 6.5 - - + -
143B SER* 1.3 80.9 - - - +
145B ILE* 1.3 74.0 + - - +
146B ASN* 4.9 1.3 - - - +
151B THR* 3.7 22.0 - - + -
152B ALA 3.4 12.1 - - - +
153B CYS* 3.7 19.7 - - - +
211B ALA* 3.3 11.1 - - - +
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Residues in contact with ILE 145 (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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144B VAL* 1.3 81.0 - - - +
146B ASN* 1.3 68.7 + - - +
147B SER* 4.5 17.0 - - - +
151B THR* 3.4 1.0 - - - +
152B ALA* 2.9 53.8 + - + +
154B VAL* 4.8 9.6 - - + -
211B ALA* 3.6 19.3 - - + -
212B ARG 4.5 2.0 - - - +
213B GLN 6.1 0.2 - - - +
214B ASP* 3.6 26.9 - - + +
215B CYS 4.3 1.1 - - - +
216B VAL* 3.9 16.2 - - + -
238B VAL* 3.8 27.6 - - + -
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Residues in contact with ASN 146 (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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81B GLU* 5.1 9.3 + - - +
83B GLN* 4.9 11.3 + - - +
144B VAL* 4.9 1.7 - - - +
145B ILE* 1.3 81.3 + - - +
147B SER* 1.3 59.9 + - - +
148B ARG 3.9 1.8 + - - -
149B GLY* 3.5 18.5 + - - +
150B LYS 3.4 4.3 - - - -
151B THR* 3.3 21.3 + - - +
213B GLN* 4.4 7.6 + - - +
214B ASP* 2.9 27.9 + - - +
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Residues in contact with SER 147 (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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145B ILE* 4.1 10.2 - - - +
146B ASN* 1.3 70.1 - - - +
148B ARG* 1.3 71.6 + - - +
149B GLY* 3.3 2.0 - - - -
150B LYS* 2.9 30.1 + - - +
152B ALA* 5.5 0.7 - - - +
214B ASP* 3.8 9.6 - - - -
238B VAL 3.7 20.2 - - - -
239B GLU* 3.8 3.8 - - - -
240B LEU* 2.9 40.5 + - - +
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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