Contacts of the strand formed by residues 170 - 174 (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 170 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168E ASP 4.2 0.9 - - - -
169E SER* 1.3 75.7 - - - +
171E VAL* 1.3 63.9 + - - +
205E LEU* 4.3 8.1 - - + -
206E ILE* 3.4 17.0 - - - -
207E ARG* 3.4 36.9 + - + +
0G MSE 4.9 1.4 - - - +
135G PHE* 5.0 4.9 - + - -
140G GLU 4.7 2.6 + - - -
141G ALA* 3.7 34.8 + - - +
161G THR* 3.1 31.8 + - - +
164G LEU* 3.7 52.0 - - + -
165G ASN* 3.1 21.4 + - - +
168G TYR* 4.4 15.3 - - + -
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Residues in contact with VAL 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E PHE* 3.1 29.6 - - + +
41E PRO* 4.1 17.5 - - + -
169E SER* 4.5 4.5 - - - +
170E TYR* 1.3 79.9 - - - +
172E PHE* 1.3 69.0 + - - +
173E LEU* 3.8 2.1 + - + +
204E HIS 3.6 0.7 - - - +
205E LEU* 3.4 8.7 - - - +
206E ILE* 2.7 53.6 + - + +
208E TYR* 4.0 27.4 - - + +
211E ILE* 4.6 7.4 - - + -
0G MSE 4.8 4.3 - - + -
161G THR* 4.7 0.9 - - - -
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Residues in contact with PHE 172 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39E PHE* 3.6 29.3 - - + +
171E VAL* 1.3 73.2 - - - +
173E LEU* 1.3 60.9 + - - +
174E ARG 4.0 0.9 + - - -
203E GLN* 6.1 0.7 - - + -
204E HIS 3.3 6.5 - - - +
205E LEU* 3.4 28.7 - - + -
0G MSE 3.1 36.1 - - + +
145G LEU* 3.5 33.0 - - + -
153G ILE* 3.5 35.7 - - + -
157G GLY* 3.5 33.0 - - - -
160G LEU* 4.4 15.9 - - + -
161G THR* 4.3 3.8 - - - -
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Residues in contact with LEU 173 (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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36E ASN* 6.0 3.8 - - - +
171E VAL* 3.8 3.5 - - + -
172E PHE* 1.3 72.7 - - - +
174E ARG* 1.3 73.1 + - - +
175E VAL* 3.8 24.3 + - + -
179E GLN* 5.4 3.6 - - - +
198E LEU* 4.2 8.1 - - + -
202E SER 3.8 0.2 - - - +
203E GLN* 3.0 9.0 - - - +
204E HIS* 2.9 44.2 + - + +
206E ILE* 4.7 10.3 - - + -
211E ILE* 3.2 48.9 - - + -
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Residues in contact with ARG 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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35E MSE 4.8 16.2 - - + -
36E ASN* 5.5 3.5 + - - -
172E PHE 4.0 2.4 + - - -
173E LEU* 1.3 81.4 - - - +
175E VAL* 1.3 65.4 + - - +
176E ARG* 3.1 55.0 + - - +
201E GLY* 3.2 36.3 + - - -
202E SER 3.7 4.7 - - - +
203E GLN* 3.6 27.0 - - + +
90G PRO* 6.4 0.2 - - - +
150G LEU* 5.5 7.3 - - - +
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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