Contacts of the strand formed by residues 119 - 124 (chain c) in PDB entry 5GJQ
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 PRO 119 (chain c).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15c LYS* 3.2 37.4 + - + -
16c GLY 4.6 2.2 - - - +
17c LYS 3.7 24.2 - - - +
18c ASN* 4.2 6.7 - - - +
19c CYS 3.6 21.5 - - - +
20c VAL* 4.1 4.3 - - + -
111c GLY 3.7 0.2 - - - +
112c LEU* 3.5 15.7 - - + -
117c PHE 3.3 8.0 - - - +
118c LYS* 1.3 108.8 + - + +
120c PHE* 1.3 60.3 + - - +
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Residues in contact with PHE 120 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15c LYS* 4.3 3.4 - - - +
20c VAL* 4.2 1.0 - - - +
84c PRO* 3.5 34.3 - - + -
85c TYR* 3.4 48.9 - + - -
88c MET* 4.0 12.8 - - - -
109c ILE* 4.7 7.0 - - + -
110c ALA* 3.5 0.2 - - - -
111c GLY 2.9 40.4 + - - +
118c LYS 4.6 2.9 - - - +
119c PRO* 1.3 76.7 - - - +
121c ILE* 1.3 67.7 + - - +
122c CYS* 3.6 24.5 - - + -
132c VAL* 3.5 30.1 - - + -
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Residues in contact with ILE 121 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13c ALA* 4.0 20.4 - - + +
14c MET 4.2 3.4 - - - +
15c LYS* 4.1 11.2 - - + +
20c VAL* 3.6 24.0 - - + -
109c ILE 3.2 8.1 - - - +
110c ALA* 4.1 1.8 - - + -
120c PHE* 1.3 83.9 - - - +
122c CYS* 1.3 66.5 + - - +
132c VAL* 3.7 6.8 - - - +
133c THR* 3.3 51.4 + - - +
135c ASP 3.5 12.3 - - - +
136c PHE* 3.5 27.6 - - - +
137c VAL* 4.1 6.3 - - + +
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Residues in contact with CYS 122 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88c MET* 3.5 33.4 - - - -
108c VAL* 3.2 7.1 - - - +
109c ILE* 2.9 50.9 + - - +
120c PHE* 3.6 13.5 - - + -
121c ILE* 1.3 78.4 - - - +
123c SER* 1.3 65.5 + - - +
124c LEU* 4.6 1.6 - - - -
131c MET 3.3 14.6 - - - +
132c VAL* 3.6 15.5 - - + -
137c VAL* 4.1 8.2 - - - +
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Residues in contact with SER 123 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107c PRO 3.2 14.4 - - - -
108c VAL* 3.9 13.9 - - - -
122c CYS* 1.3 77.5 - - - +
124c LEU* 1.3 70.8 + - - +
129c CYS 3.6 0.9 - - - +
131c MET* 3.0 58.3 + - - +
137c VAL* 3.9 7.6 - - - +
138c VAL 4.5 3.9 + - - -
139c SER* 4.4 7.6 - - - -
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Residues in contact with LEU 124 (chain c).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88c MET* 3.8 17.7 - - + +
91c VAL* 4.2 10.8 - - + -
92c ALA* 3.6 42.2 - - + +
95c LEU* 4.4 0.2 - - + -
106c GLU* 3.5 22.7 - - - +
107c PRO* 3.1 33.2 + - + +
109c ILE* 4.7 5.6 - - + -
122c CYS* 4.6 4.9 - - - -
123c SER* 1.3 86.5 - - - +
125c ASP* 1.3 73.2 + - - +
128c GLY* 4.0 12.1 - - - +
129c CYS 3.2 5.8 - - - +
130c PRO* 4.1 13.2 - - + -
139c SER* 4.9 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