Contacts of the strand formed by residues 149 - 155 (chain X) in PDB entry 3AOI
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 X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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982D PHE* 5.5 12.3 - + - -
91X LEU* 3.5 42.3 - - + +
92X GLU 3.6 5.4 - - - -
93X ASP* 3.5 35.0 - - + -
94X PRO* 4.1 1.6 - - - -
98X GLU* 4.7 4.0 - - + -
100X LEU* 5.2 8.7 - - + -
136X ASP 3.8 0.9 - - - +
137X VAL* 3.6 6.4 - - - -
138X LEU* 3.4 29.4 + - - +
147X ARG* 2.9 69.8 - - + -
148X GLU* 1.3 72.8 - - - +
150X ARG* 1.3 59.8 - - - +
151X VAL* 4.0 1.6 + - - +
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Residues in contact with ARG 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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90X GLU 3.8 0.3 - - - +
91X LEU* 3.9 2.4 - - - -
92X GLU* 3.4 49.4 + - + +
94X PRO* 4.7 8.2 - - + +
134X VAL* 5.6 3.8 - - - +
135X GLY* 3.8 20.6 + - - +
136X ASP 3.3 13.5 - - - +
137X VAL* 4.7 10.1 - - + +
149X PHE* 1.3 74.1 - - - +
151X VAL* 1.3 58.3 + - - +
152X VAL* 2.6 53.1 + - - +
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Residues in contact with VAL 151 (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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83X ILE* 3.7 24.2 - - + -
89X VAL* 3.6 21.3 - - + -
90X GLU 3.9 3.6 - - - -
91X LEU* 4.1 12.3 - - + +
129X LEU* 5.2 4.0 - - + -
132X HIS* 4.7 3.4 - - + -
133X ARG 3.6 19.5 - - - +
134X VAL* 3.7 5.5 - - - +
135X GLY* 3.2 18.7 + - - +
136X ASP* 3.2 21.1 + - + +
138X LEU* 5.3 4.7 - - + -
149X PHE 4.0 1.9 + - - +
150X ARG* 1.3 68.6 + - - +
152X VAL* 1.3 69.2 + - - +
153X ALA 4.0 3.4 - - - +
154X ILE* 3.9 22.0 - - + -
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Residues in contact with VAL 152 (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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90X GLU* 2.6 42.7 + - + +
91X LEU 4.3 1.1 - - - -
92X GLU* 3.3 39.3 - - + +
99X ARG* 4.4 19.7 - - - +
134X VAL* 3.7 9.6 - - - +
150X ARG* 2.6 30.0 + - - +
151X VAL* 1.3 74.9 - - - +
153X ALA* 1.3 64.3 + - + +
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Residues in contact with ALA 153 (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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89X VAL* 4.2 1.0 - - - -
90X GLU* 3.6 22.2 + - - +
134X VAL* 3.7 13.0 - - + -
151X VAL* 3.4 6.2 - - - +
152X VAL* 1.3 86.4 - - + +
154X ILE* 1.3 64.1 + - - +
155X HIS* 3.3 33.9 + - + +
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Residues in contact with ILE 154 (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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80X GLY 5.4 2.0 - - - +
81X GLU* 2.5 58.9 - - - +
82X VAL 4.9 0.2 - - - +
83X ILE* 3.7 23.6 - - + -
87X SER* 4.6 17.5 - - - +
88X VAL 4.5 2.5 - - - +
89X VAL* 5.0 3.8 - - + +
133X ARG* 3.5 11.2 - - - -
134X VAL* 3.1 33.5 - - + +
151X VAL* 3.9 7.0 - - + -
153X ALA* 1.3 74.9 - - - +
155X HIS* 1.3 69.1 + - - +
156X GLY 4.3 0.6 + - - -
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Residues in contact with HIS 155 (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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87X SER* 4.7 0.5 - - - -
88X VAL* 3.5 33.8 + - + +
90X GLU* 2.8 45.5 + - + -
153X ALA* 3.3 27.9 - - + +
154X ILE* 1.3 80.0 + - - +
156X GLY* 1.3 72.6 + - - +
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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