Contacts of the strand formed by residues 116 - 122 (chain X) in PDB entry 5A0Q
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 116 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17X ASN* 1.6 80.6 - - + +
111X LEU* 3.8 33.2 - - + -
112X ASP 3.4 5.2 + - - -
115X THR* 1.3 80.6 - - - +
117X LYS* 1.3 58.3 + - - +
118X PRO* 3.4 9.1 - - - +
190X GLU* 4.2 6.7 - - + -
191X LYS* 3.3 45.3 - - + +
192X ASP* 4.9 4.0 - - - -
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Residues in contact with LYS 117 (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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111X LEU* 4.2 1.1 - - - -
112X ASP* 2.6 55.3 + - + +
115X THR* 3.8 29.3 + - + +
116X PHE* 1.3 77.2 - - - +
118X PRO* 1.3 71.8 - - + +
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Residues in contact with PRO 118 (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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14X LYS* 3.5 34.9 - - + +
16X LYS 4.5 1.8 - - - +
17X ASN* 2.8 37.9 - - - +
19X VAL* 3.4 22.2 - - + -
110X GLY 3.9 2.5 - - - +
111X LEU* 4.1 1.6 - - + -
116X PHE 3.4 9.6 - - - +
117X LYS* 1.3 99.1 - - + +
119X PHE* 1.3 59.9 + - - +
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Residues in contact with PHE 119 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14X LYS* 4.9 1.6 - - - +
48X LEU* 4.5 0.5 - - - +
83X PRO* 3.4 42.8 - - + +
84X TYR* 4.2 30.7 - + + -
87X MET* 4.2 15.9 - - + -
108X ILE* 4.1 6.3 - - + +
109X ALA* 3.8 3.5 + - - -
110X GLY 3.0 26.0 + - - +
112X ASP* 5.5 1.6 - - + -
117X LYS 4.8 1.6 - - - +
118X PRO* 1.3 74.9 - - - +
120X ILE* 1.3 66.0 + - - +
121X CYS* 3.6 33.7 - - + -
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Residues in contact with ILE 120 (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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12X ALA* 4.9 4.0 - - + -
13X MET* 4.4 7.9 - - - +
14X LYS* 3.8 27.8 - - + +
19X VAL* 3.4 32.3 - - + -
108X ILE 3.3 8.3 - - - +
109X ALA* 3.7 11.7 - - + -
118X PRO 4.3 0.2 - - - -
119X PHE* 1.3 81.7 - - - +
121X CYS* 1.3 64.6 + - - +
134X ASP 3.4 37.7 - - - +
135X PHE* 3.6 16.2 - - - +
136X VAL* 4.1 11.7 - - + +
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Residues in contact with CYS 121 (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 MET* 3.6 28.9 - - + -
107X VAL* 3.2 8.2 - - - +
108X ILE* 3.1 49.6 + - - +
119X PHE* 3.6 20.4 - - + -
120X ILE* 1.3 76.3 - - - +
122X SER* 1.4 67.6 + - - +
123X LEU* 4.3 6.0 - - - +
136X VAL* 4.2 9.4 - - - +
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Residues in contact with SER 122 (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 MET* 5.3 0.9 - - - +
105X GLU* 5.4 0.7 - - - -
106X PRO 3.4 6.5 - - - -
107X VAL* 3.9 12.3 - - - +
121X CYS* 1.4 79.7 - - - +
123X LEU* 1.3 74.0 + - - +
136X VAL* 3.1 32.0 - - - +
138X SER* 4.9 6.5 - - - -
146X TYR* 5.3 0.6 + - - -
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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