Contacts of the helix formed by residues 122 - 134 (chain I) in PDB entry 5AN9
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 ASP 122 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99I GLU* 5.7 1.5 - - - +
101I PHE* 3.1 39.1 - - - +
120I ASP 4.5 2.8 - - - +
121I ILE* 1.3 80.0 - - - +
123I ARG* 1.3 63.9 + - - +
124I GLU* 4.5 5.2 - - + +
125I THR* 2.6 33.9 + - + +
126I GLU* 3.2 11.6 + - - +
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Residues in contact with ARG 123 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I ILE 3.9 0.2 + - - -
122I ASP* 1.3 73.1 - - - +
124I GLU* 1.3 62.0 + - - +
126I GLU* 3.1 27.5 + - - +
127I GLU* 2.9 60.0 + - - +
139I ARG* 3.7 25.0 - - - +
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Residues in contact with GLU 124 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122I ASP* 3.4 3.3 - - + +
123I ARG* 1.3 78.6 - - - +
125I THR* 1.3 61.4 + - + +
127I GLU* 3.2 16.3 + - - +
128I ILE* 2.9 50.7 + - + +
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Residues in contact with THR 125 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97I ILE* 4.8 4.1 - - + +
98I GLU* 4.2 8.3 - - + +
99I GLU* 3.6 45.7 - - + +
101I PHE* 6.0 1.1 - - + -
121I ILE* 3.3 11.1 - - - +
122I ASP* 2.6 40.6 + - + +
124I GLU* 1.3 80.9 - - + +
126I GLU* 1.3 56.4 + - - +
128I ILE* 3.2 13.9 + - + +
129I ILE* 2.9 36.0 + - - +
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Residues in contact with GLU 126 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I VAL* 4.6 0.6 - - + +
121I ILE* 4.3 13.5 - - + -
122I ASP 3.5 8.5 - - - +
123I ARG* 3.1 35.6 + - - +
125I THR* 1.3 82.1 + - - +
127I GLU* 1.3 57.2 + - - +
129I ILE* 3.2 13.9 + - - +
130I ALA* 2.9 28.3 + - + +
137I VAL* 3.8 41.5 - - + +
138I PHE* 4.6 0.3 - - - -
139I ARG* 3.4 40.1 + - - +
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Residues in contact with GLU 127 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123I ARG* 2.9 48.2 + - - +
124I GLU* 3.4 17.3 + - + +
126I GLU* 1.3 76.6 - - + +
128I ILE* 1.3 58.9 + - + +
130I ALA* 3.2 7.8 + - - +
131I ASP* 2.9 40.2 + - - +
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Residues in contact with ILE 128 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95I GLN* 5.0 5.4 - - + -
97I ILE* 4.2 28.9 - - + -
98I GLU* 5.5 14.6 - - + -
124I GLU* 2.9 42.4 + - + +
125I THR* 3.2 14.3 + - + +
127I GLU* 1.3 75.5 - - + +
129I ILE* 1.3 58.0 + - - +
131I ASP* 3.2 12.2 + - - +
132I VAL* 2.9 40.5 + - + +
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Residues in contact with ILE 129 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71I LEU* 3.7 38.1 - - + -
97I ILE* 4.5 10.5 - - + -
99I GLU* 3.5 24.2 - - - +
104I LEU* 4.6 2.2 - - + -
108I ILE* 3.9 18.6 - - + -
117I VAL* 5.6 1.8 - - + -
121I ILE* 3.7 17.0 - - + -
125I THR* 2.9 20.4 + - - +
126I GLU* 3.4 7.4 - - - +
128I ILE* 1.3 76.9 - - - +
130I ALA* 1.3 57.4 + - - +
132I VAL* 3.2 1.4 + - - +
133I LEU* 2.9 44.1 + - + +
137I VAL* 4.4 13.5 - - + -
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Residues in contact with ALA 130 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I GLU* 2.9 13.0 + - + +
127I GLU* 3.3 12.3 - - - +
129I ILE* 1.3 76.5 - - - +
131I ASP* 1.3 60.6 + - - +
133I LEU* 5.3 0.7 - - - -
134I GLY* 2.9 31.0 + - - -
135I VAL 3.7 12.1 + - - +
137I VAL* 4.0 23.5 - - + +
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Residues in contact with ASP 131 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127I GLU* 2.9 26.5 + - - +
128I ILE* 3.2 12.2 + - - +
130I ALA* 1.3 79.8 - - - +
132I VAL* 1.3 66.4 + - + +
134I GLY* 3.8 6.2 + - - -
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Residues in contact with VAL 132 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I ASN* 3.0 23.9 - - - +
69I GLY* 3.6 19.3 - - - -
70I LEU 3.8 13.5 - - - +
71I LEU* 3.9 11.9 - - + -
93I VAL* 3.8 25.2 - - + +
95I GLN* 3.9 26.7 - - + +
97I ILE* 4.4 3.4 - - + -
128I ILE* 2.9 28.3 + - + +
129I ILE 3.6 3.4 - - - +
131I ASP* 1.3 79.0 - - + +
133I LEU* 1.3 63.2 + - - +
134I GLY* 4.5 0.3 - - - -
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Residues in contact with LEU 133 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65I GLY* 3.8 16.6 - - - -
66I ASN* 4.0 11.5 + - - +
68I ASN* 3.5 21.5 + - - +
69I GLY* 3.4 31.6 + - - +
71I LEU* 4.1 20.6 - - + -
108I ILE* 5.1 1.8 - - + -
110I THR* 3.9 27.1 - - + +
115I ALA* 4.9 4.0 - - + -
129I ILE* 2.9 40.5 + - + +
132I VAL* 1.3 72.1 - - - +
134I GLY* 1.3 62.4 + - - +
135I VAL* 3.6 25.5 - - + +
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Residues in contact with GLY 134 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68I ASN* 5.3 4.7 + - - -
112I ASP 4.5 2.9 - - - +
113I TYR* 5.5 0.3 - - - -
130I ALA 2.9 13.4 + - - -
131I ASP 4.2 5.4 - - - -
132I VAL 3.2 3.2 - - - -
133I LEU* 1.3 78.6 - - - +
135I VAL* 1.3 61.9 + - - +
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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