Contacts of the helix formed by residues 127 - 135 (chain C) in PDB entry 3IN7
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 SER 127 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A LYS* 3.9 13.0 - - - +
87A GLU* 3.4 28.5 - - - -
88A SER 6.1 0.2 - - - -
118C TYR* 3.7 9.8 - - - -
125C PHE* 3.3 9.8 - - - +
126C ASN* 1.3 82.5 - - - +
128C LEU* 1.3 61.6 + - - +
129C ASN* 3.5 5.9 + - - +
130C GLU* 2.9 37.4 + - - +
131C LEU* 3.2 17.8 + - - +
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Residues in contact with LEU 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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61A PHE* 4.2 13.9 - - + -
87A GLU* 2.8 16.4 + - - +
95A PHE* 4.0 10.3 - - + -
60C TRP* 4.1 12.1 - - + -
61C PHE* 4.5 0.9 - - + -
85C ILE* 4.4 15.9 - - + -
95C PHE* 3.9 44.2 - - + -
110C VAL* 3.9 19.1 - - + -
118C TYR* 3.8 32.6 - - + -
127C SER* 1.3 69.4 - - - +
129C ASN* 1.3 60.1 + - - +
131C LEU* 3.2 8.6 + - + +
132C VAL* 2.9 34.9 + - + +
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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
----------------------------------------------------------
62A PHE 4.3 0.3 - - - +
63A GLY* 4.3 1.3 - - - -
64A LYS* 3.0 30.0 + - + +
65A ILE* 5.8 0.2 - - - +
87A GLU* 3.0 16.4 + - - +
58C HIS* 2.9 36.8 + - - -
60C TRP* 3.8 14.1 - - - -
127C SER* 3.6 6.3 - - - +
128C LEU* 1.3 76.8 - - - +
130C GLU* 1.3 57.6 + - + +
132C VAL* 3.4 0.7 + - - +
133C ASP* 3.0 57.1 + - - -
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Residues in contact with GLU 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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64A LYS* 2.8 41.4 + - + -
125C PHE* 3.8 17.5 - - + -
126C ASN* 3.5 18.3 + - - +
127C SER* 2.9 31.1 + - - +
129C ASN* 1.3 76.3 - - + +
131C LEU* 1.3 62.9 + - - +
133C ASP* 4.3 4.6 - - - +
134C TYR* 3.2 25.8 + - - +
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Residues in contact with LEU 131 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85C ILE* 5.1 8.5 - - + -
97C LEU* 4.7 9.9 - - + -
110C VAL* 4.0 19.7 - - + -
118C TYR* 4.1 4.5 - - + -
119C PHE* 4.0 22.9 - - - +
120C LEU* 4.1 26.7 - - + -
125C PHE* 3.8 34.3 - - + -
127C SER 3.2 10.6 + - - +
128C LEU* 3.2 11.3 + - + +
130C GLU* 1.3 76.1 - - - +
132C VAL* 1.3 73.1 + - + +
134C TYR* 3.5 0.5 + - - +
135C HIS* 3.1 39.6 + - + +
148C LEU* 5.4 0.9 - - + -
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Residues in contact with VAL 132 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60C TRP* 3.6 37.7 - - + +
83C PHE* 3.5 41.1 - - + -
85C ILE* 4.1 14.4 - - + -
128C LEU 2.9 19.6 + - - +
129C ASN 3.7 2.9 - - - +
131C LEU* 1.3 79.3 - - + +
133C ASP* 1.3 66.2 + - - +
135C HIS* 3.2 12.1 + - - +
136C ARG* 3.4 24.9 + - - +
148C LEU* 3.9 11.5 - - + +
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Residues in contact with ASP 133 (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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58C HIS* 5.6 1.6 - - - -
60C TRP* 5.3 0.2 + - - -
129C ASN* 3.0 39.8 + - - +
130C GLU* 4.3 4.0 - - - +
132C VAL* 1.3 74.9 - - - +
134C TYR* 1.3 63.0 + - - +
136C ARG* 3.1 47.4 + - - +
137C SER* 4.3 3.5 + - - -
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Residues in contact with TYR 134 (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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123C VAL* 3.7 31.2 - - + +
125C PHE* 3.5 31.4 - + + -
130C GLU 3.2 19.6 + - - +
131C LEU 3.8 1.1 - - - +
133C ASP* 1.3 76.2 - - - +
135C HIS* 1.3 75.6 + + - +
136C ARG 3.2 1.4 + - - -
137C SER* 3.2 11.9 + - - -
138C THR* 3.2 53.7 + - + +
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Residues in contact with HIS 135 (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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120C LEU* 3.7 25.4 - - + +
121C TRP* 4.9 8.3 - + - -
125C PHE* 4.3 7.9 - + - -
131C LEU* 3.1 32.7 + - + +
132C VAL 3.2 7.2 + - - +
133C ASP 3.2 0.6 - - - -
134C TYR* 1.3 102.5 - + - +
136C ARG* 1.3 57.7 + - - +
137C SER 3.4 0.7 - - - -
138C THR* 3.0 29.3 + - + +
139C SER 3.4 19.1 + - - -
140C VAL* 3.4 26.9 - - + +
146C ILE 4.6 0.7 - - - +
147C PHE* 3.8 2.1 - - - -
148C LEU* 3.0 29.7 + - + +
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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