Contacts of the helix formed by residues 79 - 87 (chain C) in PDB entry 2JIF
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 LEU 79 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75C GLN 3.5 22.0 - - - +
76C ILE 2.8 11.8 + - - +
78C PRO* 1.3 81.5 - - + +
80C VAL* 1.3 66.3 + - - +
81C SER 3.3 2.8 + - - -
82C THR* 3.3 20.2 + - + +
83C MET* 3.0 37.0 + - + +
90C GLU* 4.1 16.6 - - + -
92C SER* 3.6 22.7 - - - +
93C VAL* 3.8 10.3 - - + -
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Residues in contact with VAL 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C ILE* 3.2 17.2 + - + +
77C ALA* 3.5 13.2 + - - +
79C LEU* 1.3 76.0 - - - +
81C SER* 1.3 62.9 + - - +
83C MET* 3.9 7.7 - - - +
84C ASP* 3.1 23.2 + - - +
131C VAL* 3.8 35.2 - - + +
132C ASP* 3.8 12.4 - - + +
402C LYS* 3.4 36.9 - - + +
1435C EDO 4.3 11.2 - - - +
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Residues in contact with SER 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77C ALA 5.1 0.8 + - - -
78C PRO 5.1 2.6 + - - -
79C LEU 3.3 1.0 - - - -
80C VAL* 1.3 79.1 - - - +
82C THR* 1.3 57.8 + - - +
84C ASP* 3.3 7.6 + - - +
85C GLU* 2.9 30.0 + - - +
396C LYS 4.5 11.7 + - - -
402C LYS* 5.5 2.2 - - - -
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Residues in contact with THR 82 (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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78C PRO 5.4 1.1 + - - +
79C LEU* 3.3 32.0 + - + +
81C SER* 1.3 75.3 - - - +
83C MET* 1.3 72.0 + - + +
85C GLU* 4.4 5.2 - - - -
86C ASN* 3.1 40.4 + - - +
88C LYS* 5.8 0.2 - - - +
90C GLU* 5.2 7.9 - - - +
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Residues in contact with MET 83 (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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76C ILE* 4.3 9.6 - - + -
79C LEU* 3.0 34.7 + - + +
80C VAL* 3.9 3.4 - - - +
82C THR* 1.3 77.9 - - + +
84C ASP* 1.3 56.6 + - - +
87C SER* 3.0 24.9 + - - -
88C LYS 3.1 29.4 + - - +
89C MET* 3.8 8.7 - - + -
90C GLU* 3.4 38.4 - - + +
93C VAL* 4.1 14.6 - - + -
132C ASP* 3.4 23.3 - - - +
135C VAL* 4.2 14.4 - - + -
257C ALA* 3.9 15.0 - - + +
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Residues in contact with ASP 84 (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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80C VAL 3.1 18.0 + - - +
81C SER* 3.5 6.8 - - - +
83C MET* 1.3 73.6 - - - +
85C GLU* 1.3 65.3 + - - +
86C ASN 3.2 0.5 + - - -
87C SER 3.3 5.2 + - - -
256C ARG* 2.8 51.7 + - - +
257C ALA* 4.8 3.3 - - - +
396C LYS* 4.9 4.7 + - - +
401C GLU* 4.7 0.3 - - - +
402C LYS* 3.6 27.3 - - + +
405C ARG* 2.9 43.9 + - - -
406C ASP* 4.8 1.6 - - - +
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Residues in contact with GLU 85 (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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81C SER 2.9 20.5 + - - +
82C THR* 3.9 3.8 - - - +
84C ASP* 1.3 76.3 - - - +
86C ASN* 1.3 74.5 + - - +
256C ARG* 3.2 19.9 + - - +
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Residues in contact with ASN 86 (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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82C THR* 3.1 34.6 + - - +
85C GLU* 1.3 85.7 + - - +
87C SER* 1.3 71.4 + - - +
88C LYS* 3.2 15.4 + - + +
256C ARG* 4.9 0.4 - - - -
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Residues in contact with SER 87 (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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83C MET 3.0 8.4 + - - -
84C ASP 3.3 3.2 + - - -
86C ASN* 1.3 78.5 - - - +
88C LYS* 1.3 57.3 + - - +
212C GLU* 5.0 6.4 - - - +
249C PRO* 5.6 8.2 - - - +
250C GLU 4.9 10.7 + - - -
251C ASN* 4.8 2.4 + - - -
252C LYS* 5.2 0.5 + - - -
256C ARG* 3.2 62.7 + - - +
257C ALA* 4.2 1.4 - - - +
259C SER* 6.1 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