Contacts of the helix formed by residues 173 - 180 (chain D) 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 PHE 173 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171D TRP 3.8 1.2 + - - -
172D GLY* 1.3 68.1 - - - -
174D ILE* 1.3 66.4 + - + +
176D ASP* 3.1 3.9 + - - +
177D VAL* 3.0 40.3 + - + +
196D THR* 3.5 30.7 - - + -
199D ARG* 3.8 31.2 - - + -
200D LEU* 4.0 16.2 - - + -
203D LEU* 5.4 9.4 - - + -
204D ARG 5.5 4.5 - - - -
206D TYR* 3.4 12.8 - - + -
258D VAL* 2.7 32.2 + - + +
259D LEU* 4.1 9.4 - - + -
299D LEU* 4.6 6.1 - - + -
1001D UUL 3.3 44.4 - - - -
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Residues in contact with ILE 174 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170D ALA* 3.7 20.0 - - + -
171D TRP 5.2 0.9 - - - +
172D GLY 3.4 0.8 - - - -
173D PHE* 1.3 75.1 - - - +
175D ALA* 1.3 59.2 + - - +
177D VAL 3.6 0.2 + - - -
178D ASP* 3.0 31.0 + - - +
259D LEU* 3.6 39.8 - - + +
260D VAL 5.2 0.2 - - - +
261D LEU* 4.2 19.3 - - + -
268D LEU* 4.3 14.4 - - + -
1001D UUL 3.5 65.9 - - + +
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Residues in contact with ALA 175 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170D ALA* 3.6 25.2 - - - +
172D GLY 3.1 12.9 + - - +
174D ILE* 1.3 76.6 - - - +
176D ASP* 1.3 67.3 + - - +
178D ASP* 3.3 7.9 + - - +
179D LEU* 3.0 23.6 + - - +
337D VAL* 3.6 25.6 - - + +
338D PHE 4.0 1.6 - - - -
339D ALA* 3.8 15.9 - - - +
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Residues in contact with ASP 176 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172D GLY 2.8 14.2 + - - +
173D PHE* 3.1 5.1 + - - +
175D ALA* 1.3 76.7 - - - +
177D VAL* 1.3 56.4 + - - +
179D LEU* 3.2 7.3 + - - +
180D GLU* 2.9 25.3 + - - +
199D ARG* 3.4 33.1 + - - +
204D ARG* 3.7 17.9 + - - -
206D TYR* 2.3 39.4 + - - +
337D VAL* 3.6 25.8 - - - +
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Residues in contact with VAL 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173D PHE* 3.0 37.6 + - + +
176D ASP* 1.3 71.3 - - - +
178D ASP* 1.3 60.0 + - - +
179D LEU 3.3 0.3 + - - -
180D GLU* 3.5 6.9 - - - +
181D SER* 2.6 29.2 + - - +
192D PHE* 3.8 12.6 - - + +
195D GLY* 3.6 26.5 - - - +
196D THR 3.6 19.1 - - - +
199D ARG* 4.0 16.6 - - + +
1001D UUL 3.7 25.8 - - + -
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Residues in contact with ASP 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174D ILE* 3.0 24.6 + - - +
175D ALA* 3.3 9.4 + - - +
177D VAL* 1.3 77.8 - - - +
179D LEU* 1.3 61.6 + - - +
181D SER* 3.7 13.2 - - - +
191D ARG* 4.3 4.9 + - - -
192D PHE* 3.6 15.6 - - - -
339D ALA* 3.9 14.7 - - + +
342D GLY* 3.9 28.2 - - - +
1001D UUL 2.6 31.3 + - - -
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Residues in contact with LEU 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175D ALA 3.0 12.4 + - - +
176D ASP* 3.5 9.4 - - - +
178D ASP* 1.3 75.5 - - - +
180D GLU* 1.3 58.9 + - + +
181D SER 2.5 26.1 + - - +
199D ARG* 5.5 4.3 - - - +
337D VAL* 4.8 11.9 - - + -
344D LEU* 4.5 35.0 - - + -
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Residues in contact with GLU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ASP 2.9 10.6 + - - +
177D VAL* 3.5 3.7 - - - +
179D LEU* 1.3 73.2 - - + +
181D SER* 1.3 66.8 + - - +
182D GLU* 5.3 4.5 - - - +
183D LYS* 5.2 5.2 - - - -
195D GLY* 4.8 8.5 - - - -
198D LEU* 3.3 28.7 - - + +
199D ARG* 2.9 50.5 + - - +
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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