Contacts of the helix formed by residues 95 - 102 (chain C) in PDB entry 4J1R
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 ASN 95 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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87C VAL* 4.4 14.5 - - - +
89C GLN* 3.4 27.9 + - + +
93C PHE 3.9 1.2 + - - -
94C LYS* 1.3 74.3 - - - +
96C ARG* 1.3 63.1 - - - +
97C GLU* 2.9 17.8 + - - +
98C LEU* 2.7 35.0 + - + +
99C GLN* 3.1 28.9 + - - +
128C LEU* 3.6 29.2 - - + +
130C LEU* 6.2 0.2 - - - +
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Residues in contact with ARG 96 (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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94C LYS 3.7 4.2 + - - +
95C ASN* 1.3 71.0 + - - +
97C GLU* 1.3 67.0 + - - +
99C GLN* 3.2 7.4 + - - +
100C ILE* 3.0 33.1 + - + +
180C ARG* 4.0 10.7 - - - +
204C ALA 4.1 19.0 + - - +
205C LYS* 3.6 36.1 - - + +
501C PO4 2.7 31.5 + - - -
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Residues in contact with GLU 97 (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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85C LYS* 3.0 37.3 + - - +
87C VAL* 5.0 3.1 - - - +
95C ASN* 2.9 11.9 + - - +
96C ARG* 1.3 79.6 - - - +
98C LEU* 1.3 57.2 + - - +
100C ILE* 3.3 5.7 + - - +
101C MET* 2.9 41.5 + - + +
130C LEU* 3.6 26.5 - - + +
132C LEU* 5.1 6.2 - - - +
200C ASP* 4.7 1.4 - - - -
201C PHE* 3.4 46.0 + - + +
202C GLY* 3.6 7.4 - - - +
502C I5R 5.9 0.2 - - - -
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Residues in contact with LEU 98 (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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95C ASN* 2.7 27.0 + - + +
97C GLU* 1.3 73.2 - - - +
99C GLN* 1.3 73.8 + - - +
100C ILE 3.3 0.3 + - - -
101C MET* 4.1 2.0 - - - +
102C ARG* 3.1 40.0 + - + +
112C LEU* 4.0 13.5 - - + -
115C PHE* 3.8 47.3 - - + -
117C TYR* 4.0 9.9 - - - +
128C LEU* 3.9 21.8 - - + -
130C LEU* 3.9 18.1 - - + +
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Residues in contact with GLN 99 (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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94C LYS* 4.0 30.2 - - + +
95C ASN 3.1 22.5 + - - +
96C ARG* 3.2 9.2 + - - +
98C LEU* 1.3 91.3 - - - +
100C ILE* 1.3 62.8 - - + +
102C ARG* 3.9 13.5 + - - +
103C LYS* 3.7 25.6 + - - +
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Residues in contact with ILE 100 (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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96C ARG* 3.0 23.2 + - + +
97C GLU* 3.8 6.1 - - - +
99C GLN* 1.3 76.5 - - + +
101C MET* 1.3 61.0 + - + +
102C ARG 3.1 4.7 - - - -
103C LYS* 3.1 21.3 + - + +
104C LEU* 3.3 27.8 + - + +
177C ILE* 3.6 36.1 - - + -
201C PHE* 4.6 10.5 - - + -
204C ALA* 3.9 36.3 - - + +
205C LYS* 4.0 9.9 - - - +
206C GLN* 4.4 6.3 - - + +
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Residues in contact with MET 101 (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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45C GLY 4.6 0.3 - - - +
46C GLN* 4.1 3.5 - - - +
97C GLU* 2.9 43.5 + - + +
98C LEU* 3.5 3.1 + - + +
100C ILE* 1.3 71.1 - - - +
102C ARG* 1.3 59.4 + - - +
103C LYS 3.4 0.2 - - - -
104C LEU* 3.8 24.8 - - + +
109C ILE* 5.3 0.9 - - + -
110C VAL* 3.5 28.9 - - + +
112C LEU* 3.7 41.7 + - + +
130C LEU* 5.0 5.8 - - + -
132C LEU* 3.7 26.7 - - + -
201C PHE* 3.7 35.0 - - + -
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Residues in contact with ARG 102 (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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43C THR* 4.0 12.5 - - - +
44C PRO 4.0 6.7 + - - -
45C GLY 3.7 18.6 + - - +
46C GLN* 3.4 17.8 + - - +
47C GLY 4.6 5.3 + - - -
49C ASP* 3.6 39.4 + - - +
98C LEU* 3.1 34.4 + - + +
99C GLN* 4.2 11.7 - - - +
100C ILE 3.1 0.8 - - - -
101C MET* 1.3 78.9 - - - +
103C LYS* 1.3 64.7 + - + +
112C LEU* 4.4 4.9 - - + -
115C PHE* 3.7 27.0 - - - -
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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