Contacts of the strand formed by residues 124 - 130 (chain C) in PDB entry 2XN9
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 GLU 124 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111C GLY* 3.4 0.2 - - - -
112C ALA* 2.8 45.2 + - + +
114C VAL* 4.0 20.9 - - + -
122C GLU* 4.1 7.1 - - - +
123C THR* 1.3 79.7 - - - +
125C LEU* 1.3 71.7 + - - +
142C ILE* 5.6 1.8 - - + -
145C ILE* 3.5 40.2 - - + +
146C LEU* 5.6 1.3 - - + -
149C LYS* 2.9 40.0 + - - +
150C TYR* 4.8 4.3 + - + -
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Residues in contact with LEU 125 (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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109C VAL* 4.0 23.6 - - + -
110C ILE 3.7 1.8 - - - -
111C GLY* 4.0 14.1 - - - -
112C ALA* 6.1 0.2 - - - -
123C THR* 4.9 7.6 - - + +
124C GLU* 1.3 91.2 + - - +
126C ILE* 1.3 71.6 + - - +
127C ARG* 4.7 11.8 + - - +
145C ILE* 3.6 10.4 - - - +
66E ASP* 3.6 43.1 - - + +
69E GLU* 4.1 10.8 - - + +
70E GLN* 4.3 22.2 - - + +
73E ALA* 5.1 2.2 - - + -
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Residues in contact with ILE 126 (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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109C VAL* 3.5 6.4 - - - +
110C ILE* 2.9 51.1 + - + +
125C LEU* 1.3 80.4 - - - +
127C ARG* 1.3 66.7 + - - +
138C LEU* 3.9 35.4 - - + +
141C LYS* 3.9 23.1 - - + +
142C ILE* 3.7 23.1 - - + -
145C ILE* 3.8 13.2 - - + -
207C ILE* 3.7 28.7 - - + -
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Residues in contact with ARG 127 (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 GLU* 3.4 42.7 + - + +
108C ARG 3.3 8.1 - - - +
109C VAL* 4.3 10.1 - - + +
110C ILE* 5.7 0.9 - - - -
125C LEU* 4.7 10.7 + - - +
126C ILE* 1.3 83.1 - - - +
128C THR* 1.3 59.8 + - - +
138C LEU* 5.0 1.9 - - - +
141C LYS* 2.8 35.3 + - - +
65E LYS* 3.9 15.1 - - - +
66E ASP* 3.7 10.9 + - - -
69E GLU* 2.6 45.3 + - - -
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Residues in contact with THR 128 (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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104C LEU* 3.7 2.4 - - - +
107C GLU* 4.3 4.3 - - - -
108C ARG* 2.9 41.0 + - + +
110C ILE* 4.8 8.1 - - + -
127C ARG* 1.3 79.6 - - - +
129C ASN* 1.3 61.9 + - - +
130C LYS* 3.1 26.8 + - - +
133C VAL* 3.9 22.1 - - + +
137C GLU* 3.9 6.9 + - - -
138C LEU* 4.7 7.9 - - + -
141C LYS* 4.6 1.8 - - - +
201C SER* 3.7 23.6 - - - +
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Residues in contact with ASN 129 (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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28C GLU* 4.3 16.8 + - - +
103C LYS* 3.4 27.2 - - + +
104C LEU* 2.9 35.2 + - + +
106C GLN 5.8 0.2 - - - -
107C GLU* 4.7 15.7 - - + +
128C THR* 1.3 73.4 + - - +
130C LYS* 1.3 67.8 + - - +
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Residues in contact with LYS 130 (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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26C ILE* 6.4 0.2 - - - +
28C GLU* 4.2 14.6 + - - +
72C ASP* 3.9 26.5 + - - +
73C ILE 5.5 1.0 + - - -
74C TYR* 4.8 12.4 - - - +
96C GLY 6.0 0.9 - - - -
98C THR* 3.4 28.0 - - - +
99C LEU 5.9 0.4 - - - +
102C GLU 3.9 6.7 - - - +
103C LYS* 4.3 8.5 - - - +
104C LEU* 3.7 4.6 - - - +
128C THR* 3.1 15.3 + - - +
129C ASN* 1.3 86.9 + - - +
131C LYS* 1.3 54.8 + - - +
132C ASN 3.2 17.7 - - - +
133C VAL* 4.3 5.2 - - + +
134C THR 5.7 0.4 - - - +
137C GLU* 3.0 30.1 + - - +
201C SER* 2.5 31.9 + - - -
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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