Contacts of the strand formed by residues 170 - 174 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169I SER* 1.3 76.1 + - - +
171I VAL* 1.3 58.7 + - - +
205I LEU* 4.4 11.2 - - + -
206I ILE* 3.4 20.9 - - - -
207I ARG* 3.6 35.9 + - + +
135K PHE* 5.2 3.8 - + - -
140K GLU 4.9 1.9 + - - -
141K ALA* 3.4 36.4 + - - +
161K THR* 2.6 38.8 - - + +
164K LEU* 3.3 52.7 - - + -
165K ASN* 2.9 20.5 + - - +
168K TYR* 4.1 13.7 - - + -
171K ARG* 5.1 7.4 + - - -
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Residues in contact with VAL 171 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39I PHE* 3.2 30.1 - - + +
41I PRO* 4.0 9.2 - - + -
169I SER* 3.4 10.5 + - - +
170I TYR* 1.3 78.1 - - - +
172I PHE* 1.3 79.9 + - - +
173I LEU* 3.7 8.9 + - + +
204I HIS 3.5 2.1 - - - +
205I LEU* 3.4 10.0 - - - +
206I ILE* 2.7 35.2 + - - +
208I TYR* 4.0 23.6 - - + +
211I ILE* 5.2 5.4 - - + -
0K MSE 4.9 3.4 - - + -
161K THR* 4.5 2.0 - - - -
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Residues in contact with PHE 172 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35I MSE 5.9 0.7 - - + -
39I PHE* 3.4 31.8 - + - +
171I VAL* 1.3 81.3 - - - +
173I LEU* 1.3 62.5 + - - +
174I ARG* 3.9 19.3 - - + -
203I GLN* 3.7 19.1 - - + -
204I HIS 3.5 7.6 - - - -
205I LEU* 4.7 4.9 - - + +
1003I SO4 3.2 23.4 + - - -
0K MSE 3.5 24.7 - - + +
145K LEU* 4.4 7.0 - - + -
150K LEU* 3.6 30.1 - - + -
153K ILE* 3.2 45.5 - - + -
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Residues in contact with LEU 173 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171I VAL* 3.7 4.9 + - + -
172I PHE* 1.3 78.8 - - - +
174I ARG* 1.3 72.2 + - - +
175I VAL* 3.9 15.5 - - + +
179I GLN* 4.3 11.4 - - - +
198I LEU* 3.9 22.7 - - + -
202I SER 3.5 1.0 - - - +
203I GLN* 3.1 4.4 - - - +
204I HIS* 2.7 51.1 + - + +
206I ILE* 4.7 7.0 - - + -
211I ILE* 3.4 40.4 - - + -
1003I SO4 3.5 13.9 - - - +
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Residues in contact with ARG 174 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35I MSE 6.1 2.0 - - - +
172I PHE* 3.9 14.7 - - + -
173I LEU* 1.3 72.8 - - - +
175I VAL* 1.3 72.2 + - - +
176I ARG* 3.0 17.2 + - - +
201I GLY* 4.3 13.8 + - - +
202I SER 3.2 5.6 - - - +
203I GLN* 2.6 35.4 + - + +
1003I SO4 2.9 35.5 + - - +
90K PRO* 6.2 2.6 - - - +
91K TYR* 5.2 3.8 + - - -
149K THR* 6.1 0.4 - - - +
150K LEU* 3.1 41.3 - - - +
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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