Contacts of the helix formed by residues 191 - 202 (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 ARG 191 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112E SER* 3.4 47.1 + - - +
178E ASP* 3.9 9.3 + - - +
181E SER* 3.2 42.0 + - - +
182E GLU 4.3 0.9 - - - +
183E LYS* 3.4 54.0 + - + +
184E TYR 4.9 0.4 - - - +
185E ARG 4.1 3.9 + - - +
190E MET* 1.3 83.6 - - - +
192E PHE* 1.3 88.7 + - + +
194E LEU* 4.3 2.4 - - - +
195E GLY* 3.0 25.5 + - - -
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Residues in contact with PHE 192 (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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112E SER* 4.5 6.5 - - - -
113E GLY* 4.1 26.0 - - - -
177E VAL* 4.1 4.5 - - + +
178E ASP* 3.4 28.0 - - - -
181E SER* 4.5 4.7 - - - -
190E MET* 3.2 15.6 - - + -
191E ARG* 1.3 118.7 - - + +
193E THR* 1.3 55.9 + - - +
195E GLY 4.0 0.3 - - - -
196E THR* 2.5 36.7 + - - -
268E LEU 5.9 1.1 - - - -
269E GLY* 5.9 3.1 - - - -
272E MET* 4.1 31.4 - - + -
303E PHE* 4.4 2.7 - - + -
1001E UUL 3.7 14.4 - + + -
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Residues in contact with THR 193 (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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190E MET* 3.3 21.6 + - - +
192E PHE* 1.3 77.1 - - - +
194E LEU* 1.3 68.0 + - - +
196E THR* 2.9 12.0 + - - -
197E PHE* 2.9 52.6 + - + -
303E PHE* 4.0 19.0 - - + -
304E LEU* 5.8 1.3 - - + -
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Residues in contact with LEU 194 (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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183E LYS* 3.8 34.1 - - + +
190E MET 3.2 14.0 + - - +
191E ARG* 4.3 3.4 - - - +
193E THR* 1.3 80.7 - - - +
195E GLY* 1.3 63.1 + - - +
197E PHE* 3.3 12.5 + - + +
198E LEU* 3.0 54.6 + - + +
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Residues in contact with GLY 195 (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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177E VAL* 3.6 16.8 - - - +
180E GLU* 3.6 23.6 - - - +
181E SER* 4.8 1.1 - - - -
183E LYS* 5.6 1.1 - - - +
191E ARG 3.0 21.2 + - - -
193E THR 3.2 0.2 - - - -
194E LEU* 1.3 76.4 - - - +
196E THR* 1.3 56.8 + - - +
198E LEU* 3.6 2.0 + - - +
199E ARG* 3.0 28.9 + - - +
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Residues in contact with THR 196 (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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173E PHE* 3.4 29.4 - - + -
177E VAL* 4.1 0.7 - - - -
192E PHE 2.5 21.8 + - - -
193E THR 2.9 5.2 + - - -
195E GLY* 1.3 74.5 - - - +
197E PHE* 1.3 68.0 + - + +
199E ARG 3.2 0.3 + - - -
200E LEU* 2.9 34.4 + - + +
300E LEU* 6.0 0.2 - - + -
303E PHE* 3.7 22.4 - - + -
1001E UUL 3.0 39.6 + - - +
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Residues in contact with PHE 197 (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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193E THR* 2.9 41.8 + - + -
194E LEU* 3.4 14.8 - - + +
196E THR* 1.3 80.4 - - + +
198E LEU* 1.3 65.4 + - + +
200E LEU* 3.2 21.2 - - - +
201E ALA* 3.3 8.8 + - - +
300E LEU* 3.9 28.7 - - + -
303E PHE* 4.4 6.1 - + - -
304E LEU* 4.3 19.3 - - + -
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Residues in contact with LEU 198 (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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180E GLU* 4.4 20.9 - - - +
183E LYS* 4.6 10.5 - - - +
194E LEU* 3.0 47.4 + - + +
195E GLY* 3.9 4.5 - - - +
197E PHE* 1.3 80.3 - - + +
199E ARG* 1.3 65.4 + - - +
200E LEU 3.1 1.9 + - - -
201E ALA* 3.3 16.1 + - - +
202E ALA* 3.7 9.0 + - - +
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Residues in contact with ARG 199 (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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173E PHE* 3.7 24.1 - - + +
176E ASP* 2.8 39.6 + - + +
177E VAL* 3.7 25.8 - - + +
180E GLU* 5.3 7.3 - - + -
195E GLY 3.0 17.9 + - - +
196E THR 3.2 0.2 + - - -
198E LEU* 1.3 76.3 - - - +
200E LEU* 1.3 57.0 + - - +
202E ALA* 3.2 30.0 + - - +
203E LEU* 3.1 22.3 + - - -
204E ARG* 4.0 21.3 - - - +
206E TYR* 3.6 14.4 + - - -
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Residues in contact with LEU 200 (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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173E PHE* 3.9 4.0 - - + -
196E THR* 2.9 22.6 + - + +
197E PHE* 3.2 15.9 - - - +
198E LEU 3.1 0.2 - - - -
199E ARG* 1.3 73.5 - - - +
201E ALA* 1.3 60.1 + - - +
202E ALA 3.1 2.0 - - - -
203E LEU* 2.9 26.6 + - + +
296E ARG* 3.1 48.4 + - + +
299E LEU* 3.6 31.6 - - + -
300E LEU* 3.7 45.1 - - + +
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Residues in contact with ALA 201 (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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197E PHE 3.3 8.0 + - - +
198E LEU* 3.3 13.2 + - - +
200E LEU* 1.3 77.7 - - - +
202E ALA* 1.3 57.5 + - + +
203E LEU 4.0 0.2 + - - -
296E ARG* 4.2 14.6 + - - +
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Residues in contact with ALA 202 (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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198E LEU 3.7 6.3 + - - +
199E ARG* 3.2 31.7 + - - +
200E LEU 3.1 0.2 - - - -
201E ALA* 1.3 77.7 - - + +
203E LEU* 1.3 66.8 + - - +
204E ARG* 3.0 7.1 + - - +
296E ARG* 5.5 0.2 - - - -
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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