Contacts of the strand formed by residues 179 - 184 (chain B) in PDB entry 6VSU
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 179 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B VAL* 4.4 10.3 - - + +
171B VAL* 4.6 11.2 - - + -
172B SER* 5.0 3.4 - - - -
175B LEU* 4.7 6.1 - - + -
177B GLY 4.4 5.8 - - - +
178B PRO* 1.3 77.7 - - - +
180B ASP* 1.3 67.1 + - - +
181B ILE* 3.9 15.5 - - + -
213B TYR 3.0 15.4 + - - +
214B ALA* 3.0 8.3 - - - -
215B ARG 2.6 29.9 + - - -
262B VAL* 4.2 2.7 - - - -
263B LYS* 4.7 0.9 - - + -
264B GLY 3.3 22.0 - - - +
265B VAL 4.4 0.7 - - - +
266B TYR* 4.0 13.0 - - + +
307B VAL* 4.1 21.5 - - + -
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Residues in contact with ASP 180 (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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179B VAL* 1.3 73.5 - - - +
181B ILE* 1.3 61.3 + - - +
215B ARG* 2.9 40.2 + - - +
216B ARG* 3.1 37.3 + - + +
258B LEU* 3.8 17.2 - - + +
259B GLY* 2.8 32.2 + - - +
262B VAL* 4.0 1.8 - - - +
264B GLY 3.0 7.0 + - - +
265B VAL* 3.1 8.0 - - + +
266B TYR 3.0 23.4 + - - +
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Residues in contact with ILE 181 (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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168B VAL* 3.9 30.7 - - + -
179B VAL* 3.9 9.6 - - + -
180B ASP* 1.3 78.5 - - - +
182B LEU* 1.3 66.9 + - - +
183B HIS* 4.3 0.9 - - + +
205B PHE* 4.1 17.3 - - + -
208B ILE* 3.9 9.9 - - + -
214B ALA* 3.6 27.6 - - + -
216B ARG 3.0 7.0 + - - +
217B LEU* 3.5 22.7 - - + -
218B LEU* 2.9 34.7 + - - +
258B LEU* 4.7 4.2 - - - +
266B TYR* 3.1 21.3 - - + +
268B SER 4.8 1.3 - - - +
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Residues in contact with LEU 182 (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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180B ASP 4.3 0.4 - - - -
181B ILE* 1.3 72.4 - - - +
183B HIS* 1.3 57.6 + - - +
184B LEU* 4.4 18.2 - - + -
218B LEU* 3.5 9.4 - - + +
220B VAL* 3.8 30.5 - - + -
256B LEU* 3.9 18.4 - - + -
258B LEU* 4.2 13.0 - - + +
265B VAL* 4.7 0.8 - - + +
266B TYR 3.0 8.8 + - - +
267B ILE* 3.3 18.6 - - + +
268B SER 2.8 32.6 + - - +
298B ILE* 4.0 23.8 - - + -
299B LEU* 4.4 4.0 - - + -
302B LEU* 4.2 20.4 - - + -
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Residues in contact with HIS 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B HIS* 3.4 14.1 - + - -
182B LEU* 1.3 71.6 - - - +
184B LEU* 1.3 56.0 + - - +
185B ASP* 2.9 31.0 + - + +
187B HIS 3.6 11.2 - - - -
188B PRO 3.4 7.9 - - - -
189B ASP* 4.3 0.9 - - - -
205B PHE* 3.4 39.0 - + + -
217B LEU* 3.8 14.8 - - + -
218B LEU 2.6 15.9 + - - +
219B GLN* 2.9 36.6 + - + +
220B VAL* 2.8 32.1 + - - +
268B SER* 3.4 7.4 - - - -
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Residues in contact with LEU 184 (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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182B LEU* 4.4 22.4 - - + -
183B HIS* 1.3 71.4 - - - +
185B ASP* 1.3 62.7 + - - +
220B VAL* 3.3 36.1 - - + +
267B ILE* 5.0 0.4 - - + -
268B SER 2.8 13.4 + - - +
269B ILE* 3.9 24.9 - - + -
270B ASP 3.0 26.5 + - - +
273B CYS* 3.5 15.7 - - - -
290B LEU* 4.0 15.5 - - + -
295B VAL* 4.0 23.1 - - + -
298B ILE* 4.4 13.5 - - + -
299B LEU* 4.4 6.5 - - + -
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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