Contacts of the strand formed by residues 194 - 198 (chain E) in PDB entry 2EHO
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 TYR 194 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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182E ILE 3.9 0.2 - - - +
183E LEU* 4.1 5.4 - - - +
184E VAL* 2.6 67.5 + - + +
186E PRO* 4.3 8.7 - - + -
192E ARG* 3.9 16.2 - - - -
193E ASP* 1.3 76.3 - - - +
195E VAL* 1.3 56.7 + - - +
196E ILE* 3.5 26.9 - - + -
140G GLU* 5.3 6.5 + - - -
141G ALA 6.2 0.4 - - - -
142G HIS* 2.7 48.5 + + - +
143G ALA* 5.2 0.2 - - - -
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Residues in contact with VAL 195 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
181E ASN* 4.0 21.8 - - + +
182E ILE 3.2 25.6 - - - +
183E LEU* 4.2 14.3 - - + +
194E TYR* 1.3 74.7 - - - +
196E ILE* 1.3 70.2 + - - +
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Residues in contact with ILE 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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181E ASN 3.8 0.2 - - - -
182E ILE* 2.8 43.9 + - + +
184E VAL* 4.7 2.7 - - + -
194E TYR* 3.5 33.2 - - + -
195E VAL* 1.3 81.3 - - - +
197E ASP* 1.3 68.1 + - - +
198E LEU* 3.4 34.1 - - + -
204E HIS* 4.8 2.9 - - + -
206E ILE* 6.2 0.2 - - + -
142G HIS* 4.2 16.8 - - + +
144G LYS* 6.0 7.0 - - - +
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Residues in contact with ASP 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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178E ARG* 3.7 24.3 + - - +
179E GLN 4.0 2.0 - - - +
180E GLU* 3.3 9.8 - - - +
181E ASN* 2.6 43.5 + - - -
196E ILE* 1.3 81.1 - - - +
198E LEU* 1.3 61.0 + - - +
199E GLU* 3.4 18.4 + - - +
204E HIS* 5.0 2.8 + - - -
144G LYS* 5.4 5.5 + - - -
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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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173E LEU* 4.2 14.1 - - + -
175E VAL* 3.7 11.5 - - + +
178E ARG* 3.4 3.0 - - - -
179E GLN* 2.8 50.4 + - + +
182E ILE* 3.7 28.3 - - + -
196E ILE* 3.4 21.8 - - + -
197E ASP* 1.3 68.5 - - - +
199E GLU* 1.3 66.7 + - - +
204E HIS* 3.1 36.8 - - + +
206E ILE* 5.1 5.2 - - + -
211E ILE* 4.0 23.1 - - + -
142G HIS* 4.7 2.2 - - + -
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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