Contacts of the strand formed by residues 146 - 150 (chain X) in PDB entry 2AE0
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 ILE 146 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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112X ARG* 5.0 1.3 - - - +
119X PRO* 3.9 17.5 - - + -
120X ILE 3.6 3.4 - - - +
121X TYR* 3.5 25.6 - - + +
122X ARG* 5.7 0.6 + - - -
143X ASP* 3.1 40.4 + - - +
144X LYS 3.4 3.7 - - - +
145X TYR* 1.3 76.4 - - - +
147X LEU* 1.3 63.0 + - - +
148X ALA* 3.5 24.0 - - - +
149X TYR* 3.2 47.6 - - + +
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Residues in contact with LEU 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110X HIS* 4.8 5.7 - - - -
120X ILE* 2.7 20.5 + - + +
121X TYR 3.7 15.5 - - - +
122X ARG* 3.7 30.3 - - + +
145X TYR 3.5 0.2 + - - -
146X ILE* 1.3 74.4 - - - +
148X ALA* 1.3 62.7 + - + +
167X ILE* 6.1 0.4 - - + -
169X PHE* 3.9 12.3 - - - -
178X PHE* 3.9 40.1 - - + -
236X PHE* 3.6 29.8 - - + +
237X LYS 4.4 0.2 - - - +
238X PRO* 4.6 13.9 - - + -
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Residues in contact with ALA 148 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X ALA* 3.8 13.2 - - + -
109X ARG 3.7 6.1 - - - -
110X HIS* 5.3 0.7 - - - +
118X TYR 3.9 0.3 - - - +
119X PRO* 3.2 5.0 - - - +
120X ILE* 2.8 31.8 + - + +
146X ILE* 3.5 4.9 - - - +
147X LEU* 1.3 83.3 - - + +
149X TYR* 1.3 67.3 + - - +
150X SER 4.0 0.9 - - - -
167X ILE* 4.1 15.5 - - + -
169X PHE* 3.6 24.5 - - + -
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Residues in contact with TYR 149 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108X ALA* 3.2 3.3 - - - -
109X ARG 2.9 32.5 + - - +
110X HIS 3.5 23.3 - - - -
111X THR* 3.5 24.0 - - - +
112X ARG* 3.7 49.9 + - + +
116X PHE* 3.4 21.7 - - + +
117X GLN 4.6 2.7 - - - -
118X TYR 3.6 3.6 - - - +
119X PRO* 3.9 15.5 - - + -
143X ASP* 4.2 13.0 + - - +
146X ILE* 3.2 40.2 - - + +
148X ALA* 1.3 74.1 - - - +
150X SER* 1.3 63.4 + - - +
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Residues in contact with SER 150 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106X ILE* 3.6 23.3 - - - -
107X GLN 3.4 7.0 - - - -
108X ALA* 3.9 1.8 - - - +
116X PHE* 3.9 2.0 - - - -
117X GLN 3.1 23.7 + - - -
118X TYR* 2.8 18.3 + - - +
120X ILE* 4.2 6.2 - - - +
148X ALA 4.0 1.2 - - - -
149X TYR* 1.3 75.1 - - - +
151X ASN* 1.3 60.9 + - - +
152X SER 3.1 16.9 + - - -
156X ASN* 2.7 33.0 + - - -
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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
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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