Contacts of the strand formed by residues 149 - 152 (chain E) in PDB entry 3HN3
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 PHE 149 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27E MET* 4.3 7.0 - - - -
122E ARG* 3.6 3.2 - - - -
123E ILE* 2.8 70.1 + - + +
125E SER 4.2 0.9 - - - -
126E ALA* 3.8 23.3 - - + -
130E ALA* 3.7 24.5 - - + -
132E VAL* 4.1 10.3 - - + -
140E LEU* 3.6 34.1 - - + -
141E GLU 4.8 0.4 - - - +
142E HIS* 3.3 52.5 - + + -
147E LEU 3.7 4.0 - - - -
148E PRO* 1.3 78.8 - - - +
150E GLU* 1.3 62.2 + - - +
170E ILE* 5.7 0.7 - - + -
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Residues in contact with GLU 150 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26E GLY 4.8 6.2 - - - +
27E MET* 4.3 16.1 - - + +
118E ARG* 4.2 11.6 + - - -
120E VAL* 3.7 11.9 - - + +
121E LEU 3.0 14.8 - - - +
122E ARG* 2.9 30.8 + - - +
140E LEU* 3.4 18.2 - - - +
149E PHE* 1.3 76.8 - - - +
151E ALA* 1.3 63.3 + - - +
221E TYR* 2.7 32.1 + - - -
229E ASP* 5.5 2.8 - - - +
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Residues in contact with ALA 151 (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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120E VAL* 3.5 5.5 - - - -
121E LEU* 2.9 32.3 + - + +
139E THR* 3.8 24.0 - - - +
140E LEU* 3.8 15.9 - - + +
150E GLU* 1.3 76.4 - - - +
152E ASP* 1.3 65.1 + - - +
153E ILE* 3.4 14.5 + - + +
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Residues in contact with ASP 152 (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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118E ARG* 3.2 41.4 + - - +
119E VAL 3.4 5.1 - - - +
120E VAL* 4.4 4.4 - - - +
151E ALA* 1.3 71.5 - - - +
153E ILE* 1.3 59.2 + - - +
154E SER* 2.6 33.9 + - - -
155E ASN* 4.3 6.9 + - - +
156E LEU* 5.6 0.7 - - - +
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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