Contacts of the helix formed by residues 173 - 181 (chain E) 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 E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171E TRP 3.8 1.4 + - - -
172E GLY* 1.3 70.5 - - - +
174E ILE* 1.3 58.8 + - + +
176E ASP* 3.4 2.9 + - - +
177E VAL* 3.0 41.9 + - + +
196E THR* 3.4 46.4 - - + -
199E ARG* 3.7 33.8 - - + +
200E LEU* 3.9 7.2 - - + -
203E LEU* 4.0 14.8 - - + -
204E ARG 5.4 0.7 - - - -
206E TYR* 3.5 11.0 - - + -
258E VAL* 2.8 25.7 + - + +
259E LEU* 4.0 10.3 - - + +
299E LEU* 3.8 28.0 - - + -
1001E UUL 3.5 25.8 - - + -
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Residues in contact with ILE 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E ALA* 3.7 20.6 - - + -
171E TRP 5.1 0.7 - - - +
172E GLY 3.2 0.8 - - - -
173E PHE* 1.3 71.1 - - - +
175E ALA* 1.3 61.5 + - - +
177E VAL* 3.1 3.5 + - - +
178E ASP* 2.9 34.3 + - - +
259E LEU* 3.8 35.5 - - + +
260E VAL 5.1 0.9 - - - +
261E LEU* 4.2 22.9 - - + -
268E LEU* 4.5 7.4 - - + -
1001E UUL 3.5 70.2 - - + +
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Residues in contact with ALA 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170E ALA* 3.3 25.9 - - - +
172E GLY 3.0 13.4 + - - +
174E ILE* 1.3 78.1 - - - +
176E ASP* 1.3 61.9 + - - +
178E ASP* 3.4 2.8 + - - +
179E LEU* 3.2 22.9 + - - +
337E VAL* 3.4 28.0 - - + +
338E PHE 3.8 1.5 - - - +
339E ALA* 3.6 21.5 - - - +
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Residues in contact with ASP 176 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172E GLY* 2.7 21.4 + - - +
173E PHE 3.6 4.3 - - - +
175E ALA* 1.3 73.1 - - - +
177E VAL* 1.3 57.3 + - - +
179E LEU* 3.3 8.2 + - - +
180E GLU* 2.8 33.9 + - + +
199E ARG* 2.8 34.7 + - - +
204E ARG* 4.5 3.1 + - - -
206E TYR* 3.1 28.9 + - - +
337E VAL* 3.8 22.8 - - - +
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Residues in contact with VAL 177 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173E PHE* 3.0 36.5 + - + +
174E ILE 3.1 1.1 + - - +
176E ASP* 1.3 74.9 - - - +
178E ASP* 1.3 55.6 + - - +
180E GLU* 3.7 7.4 - - - +
181E SER* 2.6 43.1 + - - +
192E PHE* 4.1 7.4 - - - +
195E GLY* 3.6 42.0 - - - +
196E THR 3.9 1.3 - - - +
199E ARG* 3.7 16.6 - - + -
1001E UUL 3.6 28.0 - - + -
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Residues in contact with ASP 178 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170E ALA* 5.5 0.2 - - - +
174E ILE* 2.9 20.2 + - - +
175E ALA 3.7 4.5 - - - +
176E ASP 3.2 0.2 - - - -
177E VAL* 1.3 75.4 - - - +
179E LEU* 1.3 62.2 + - - +
181E SER* 3.3 20.4 + - - +
191E ARG* 3.9 7.7 + - - +
192E PHE* 3.4 17.8 - - - -
339E ALA* 3.6 24.9 - - + +
342E GLY* 3.9 20.6 - - - +
1001E UUL 2.8 29.1 + - - -
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Residues in contact with LEU 179 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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175E ALA 3.2 13.3 + - - +
176E ASP* 3.6 9.6 - - - +
178E ASP* 1.3 73.2 - - - +
180E GLU* 1.3 60.7 + - + +
181E SER 3.0 19.1 + - - +
182E GLU* 5.3 0.5 - - - +
337E VAL* 4.5 17.9 - - + -
344E LEU* 4.0 39.7 - - + -
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Residues in contact with GLU 180 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176E ASP* 2.8 22.3 + - + +
177E VAL* 3.8 13.0 - - - +
179E LEU* 1.3 73.8 - - + +
181E SER* 1.3 59.9 + - - +
182E GLU* 3.7 15.9 + - - +
183E LYS* 4.4 14.6 + - - -
195E GLY* 3.6 27.1 - - - +
198E LEU* 4.4 17.0 - - - +
199E ARG* 5.3 7.0 - - + -
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Residues in contact with SER 181 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177E VAL* 2.6 27.3 + - - +
178E ASP* 3.3 7.8 - - - +
179E LEU 3.0 10.7 - - - +
180E GLU* 1.3 75.9 + - - +
182E GLU* 1.3 63.9 + - - +
183E LYS* 4.5 4.0 - - - +
191E ARG* 3.2 58.3 + - - +
192E PHE* 4.5 2.3 - - - -
195E GLY* 4.8 2.1 - - - -
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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