Contacts of the helix formed by residues 171 - 176 (chain E) in PDB entry 4YC6
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 171 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169E TYR 4.0 1.2 + - - -
170E ARG* 1.3 73.5 - - - +
172E PRO* 1.3 71.1 - - - +
173E GLU* 3.4 25.9 + - - -
174E VAL* 3.1 28.1 + - - +
175E LEU* 3.1 21.2 + - - +
185E VAL* 3.6 11.6 - - - +
188E TRP* 3.7 21.5 - - - -
189E SER* 5.2 0.8 + - - -
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Residues in contact with PRO 172 (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 ARG 3.9 0.4 - - - -
171E SER* 1.3 86.7 - - - +
173E GLU* 1.3 66.1 + - - +
175E LEU* 3.7 11.7 - - + -
176E LEU* 2.8 36.0 + - + +
188E TRP* 3.6 41.5 - - + -
213E LEU* 4.6 11.4 - - + -
216E ILE* 4.9 6.7 - - + -
217E PHE* 5.4 0.9 - - + -
228E TRP* 3.9 16.4 - - + -
270E TYR* 4.0 20.9 - - + +
275E ARG* 4.4 2.9 - - - +
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Residues in contact with GLU 173 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E SER* 3.4 12.1 - - - +
172E PRO* 1.3 82.0 - - - +
174E VAL* 1.3 65.9 - - + +
176E LEU* 3.4 4.2 + - - +
178E SER* 3.0 41.8 + - - +
180E ARG 5.3 1.3 - - - +
181E TYR* 4.7 9.2 - - + +
182E SER 5.2 0.7 + - - -
184E PRO* 4.3 1.4 - - - +
185E VAL* 3.2 28.2 + - - +
228E TRP* 3.7 15.8 - - + -
272E PRO* 3.4 29.7 - - + +
275E ARG* 2.5 42.3 + - - -
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Residues in contact with VAL 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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39C SER* 5.8 9.3 - - - +
170E ARG* 4.2 25.6 - - + +
171E SER* 3.1 23.6 + - - +
173E GLU* 1.3 79.8 - - - +
175E LEU* 1.3 66.1 + - + +
177E GLY* 3.1 14.7 + - - -
178E SER* 4.9 2.9 - - - +
181E TYR* 4.5 18.6 - - + -
185E VAL* 4.0 17.0 - - + -
209E GLU* 5.1 0.7 - - - +
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Residues in contact with LEU 175 (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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167E LEU* 4.9 3.6 - - + -
170E ARG* 3.7 45.8 - - + +
171E SER 3.1 10.7 + - - +
172E PRO* 3.8 2.7 - - + +
173E GLU 3.3 0.2 - - - -
174E VAL* 1.3 80.0 - - + +
176E LEU* 1.3 58.8 + - - +
177E GLY 3.2 4.7 + - - -
209E GLU* 3.5 46.4 - - + +
212E GLN* 3.8 25.6 - - + -
213E LEU* 3.5 33.1 - - + +
216E ILE* 4.0 8.7 - - + -
236E ASP* 4.0 7.1 - - - +
60F HIS* 4.3 8.0 - - - -
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Residues in contact with LEU 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 PRO* 2.8 25.9 + - + +
173E GLU 4.2 0.4 - - - +
175E LEU* 1.3 71.6 - - - +
177E GLY* 1.3 60.5 + - - +
178E SER 3.4 1.1 - - - -
213E LEU* 4.0 23.8 - - + -
217E PHE* 4.6 10.1 - - + -
223E PRO* 5.0 2.9 - - + -
228E TRP* 3.8 24.7 - - + -
231E VAL* 4.4 7.9 - - + -
234E LEU* 3.6 27.2 - - + +
235E GLN 3.8 0.2 + - - -
236E ASP* 3.2 53.4 + - + +
237E TYR* 3.9 6.3 - - + -
241E PHE* 3.8 22.0 - - + -
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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