Contacts of the strand formed by residues 306 - 312 (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 306 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153B ARG* 3.0 21.6 + - - -
265B VAL* 3.2 9.0 - - + +
267B ILE* 3.9 31.4 - - + -
304B ALA* 3.5 22.8 + - + +
305B ASP* 1.3 72.1 + - - +
307B VAL* 1.3 57.8 + - - +
308B GLY 3.4 23.6 - - - +
309B ALA* 4.8 0.7 - - + -
339B LYS* 4.2 21.9 + - + +
340B ILE* 3.6 37.0 - - + +
342B LYS* 4.9 2.0 + - - +
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Residues in contact with VAL 307 (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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147B MET* 5.0 4.2 - - + +
153B ARG* 3.9 29.7 - - - +
154B PRO* 3.7 18.5 - - - +
171B VAL* 3.7 26.0 - - + +
175B LEU* 3.7 20.9 - - + -
179B VAL* 4.1 8.7 - - + -
263B LYS 3.6 21.1 - - - +
264B GLY* 4.0 0.4 - - - -
265B VAL 2.8 26.8 + - - +
266B TYR* 4.6 2.0 - - + +
305B ASP* 3.9 12.1 - - - +
306B VAL* 1.3 74.8 - - - +
308B GLY* 1.3 57.6 + - - +
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Residues in contact with GLY 308 (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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153B ARG* 5.4 0.2 - - - -
154B PRO* 3.2 17.5 - - - -
171B VAL* 5.1 1.6 - - - -
266B TYR* 3.3 23.2 - - - -
267B ILE 3.2 18.7 + - - -
306B VAL* 3.4 9.9 - - - +
307B VAL* 1.3 81.0 - - - +
309B ALA* 1.3 63.7 + - - +
340B ILE* 4.4 3.7 - - - +
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Residues in contact with ALA 309 (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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154B PRO 3.1 7.2 + - - +
155B LEU* 3.3 5.6 - - + -
156B VAL* 2.7 31.0 + - - +
266B TYR* 3.6 11.5 + - - -
267B ILE* 3.1 20.9 - - + +
306B VAL* 4.8 0.4 - - + -
308B GLY* 1.3 77.0 - - - +
310B ASP* 1.3 57.6 + - - +
336B LEU* 4.0 22.0 - - + -
340B ILE* 3.8 19.0 - - + +
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Residues in contact with ASP 310 (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 LEU* 4.8 0.7 - - - -
156B VAL* 3.1 21.3 - - + +
163B ILE* 5.3 1.6 - - + -
164B SER* 2.5 29.8 + - - -
167B VAL* 5.1 0.2 - - - +
266B TYR* 2.6 28.0 + - - +
267B ILE 2.9 8.6 + - - +
268B SER* 2.6 21.7 + - - -
269B ILE* 2.9 32.1 + - - +
309B ALA* 1.3 76.1 - - - +
311B VAL* 1.3 63.8 + - - +
312B VAL* 3.5 19.1 - - + +
336B LEU* 4.5 0.9 - - - +
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Residues in contact with VAL 311 (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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89B ILE* 4.7 5.9 - - + +
155B LEU* 4.5 2.5 - - + -
156B VAL 3.0 8.2 + - - +
157B LEU* 3.8 4.3 - - + -
158B GLY* 2.9 25.1 + - - +
269B ILE* 3.3 8.1 - - + +
271B VAL* 4.1 23.1 - - + -
310B ASP* 1.3 77.2 - - - +
312B VAL* 1.3 64.6 + - - +
314B PHE* 5.8 1.0 - - + +
329B ALA* 4.2 23.8 - - + +
332B LEU* 4.3 13.7 - - + -
333B VAL* 3.8 24.2 - - + -
336B LEU* 3.7 23.6 - - + -
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Residues in contact with VAL 312 (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 GLY* 4.1 1.6 - - - -
159B GLY 3.5 10.5 - - - +
160B ASP 4.3 0.7 - - - +
161B HIS* 3.5 42.6 - - + +
163B ILE* 3.8 31.6 - - + -
164B SER* 4.5 2.2 - - - +
269B ILE 2.8 16.8 + - - +
270B ASP* 3.8 4.0 - - - -
271B VAL* 3.1 28.5 + - - +
310B ASP* 3.5 21.1 - - + +
311B VAL* 1.3 78.2 - - - +
313B GLU* 1.3 62.4 + - + +
314B PHE* 3.2 9.4 + - - -
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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