Contacts of the strand formed by residues 168 - 172 (chain B) in PDB entry 3VZC
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 SER 168 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153B LEU* 5.5 0.7 - - - -
165B SER* 3.4 8.7 + - - -
167B LEU* 1.3 90.6 - - - +
169B LEU* 1.3 61.4 + - - +
170B ALA* 4.2 2.6 + - - +
261B LEU* 4.1 11.7 - - - -
262B ALA 3.1 12.8 - - - -
263B LEU* 4.0 14.1 - - - -
264B LEU* 4.8 1.6 - - - -
268B LEU* 4.7 6.8 - - - +
339B ALA 4.2 1.3 + - - -
340B VAL* 3.3 4.0 - - - +
341B ASP* 2.8 45.7 + - - +
342B GLY 4.6 3.3 + - - -
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Residues in contact with LEU 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153B LEU* 4.6 8.9 - - + +
155B LEU* 3.9 16.4 - - + -
168B SER* 1.3 73.6 - - - +
170B ALA* 1.3 63.1 - - - +
260B VAL* 4.0 3.3 - - + +
261B LEU* 3.7 2.1 - - - -
262B ALA* 2.8 46.0 + - + +
327B PHE* 3.4 34.8 - - + -
329B LEU* 4.8 7.4 - - + -
338B PHE* 4.4 27.4 - - + -
339B ALA 3.3 4.9 - - - +
340B VAL* 3.6 27.8 - - + -
345B MET* 4.8 0.7 - - + -
350B VAL* 4.5 12.6 - - + -
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Residues in contact with ALA 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168B SER* 4.2 3.6 - - - +
169B LEU* 1.3 77.4 - - - +
171B TRP* 1.3 62.1 + - - +
174B ILE* 3.6 35.0 - - + -
175B ALA* 4.3 2.0 - - - +
260B VAL 3.5 5.2 - - - +
261B LEU* 4.1 13.0 - - + -
268B LEU* 6.2 0.2 - - + -
338B PHE* 3.3 10.2 - - - +
339B ALA* 2.8 42.3 + - + +
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Residues in contact with TRP 171 (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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170B ALA* 1.3 76.1 - - - +
172B GLY* 1.3 73.1 + - - +
174B ILE 4.4 1.0 + - - -
175B ALA* 4.1 6.1 - - - -
206B TYR* 3.8 28.3 - + + +
207B ARG 3.5 17.0 - - - -
208B GLY* 3.6 26.9 - - - -
257B PHE* 3.8 23.8 - + + -
259B LEU* 3.3 7.2 - - - +
260B VAL* 2.9 43.3 + - + +
329B LEU* 3.5 39.7 - - + -
331B PRO* 3.7 20.3 - - + +
336B GLY* 4.5 6.5 - - - -
337B VAL* 3.4 22.4 - - + +
338B PHE* 3.7 24.7 - + + -
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Residues in contact with GLY 172 (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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171B TRP* 1.3 85.3 - - - +
173B PHE* 1.3 66.2 + - - -
174B ILE 3.1 1.0 + - - -
175B ALA* 3.3 3.8 + - - +
176B ASP* 3.0 24.6 + - - +
206B TYR* 3.7 36.1 - - - -
258B VAL 3.7 2.2 - - - -
259B LEU* 4.3 1.8 - - - -
337B VAL* 4.3 0.8 + - - +
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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
------------------------------------------------------------
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