Contacts of the helix formed by residues 98 - 113 (chain C) in PDB entry 6P7B
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 TYR 98 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96C GLY 3.9 0.4 + - - -
97C SER* 1.3 73.9 + - - +
99C ARG* 1.3 65.5 + - - +
101C ARG* 3.1 30.2 + - + +
102C LYS* 4.0 2.8 + - - +
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Residues in contact with ARG 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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97C SER* 3.3 10.0 + - - +
98C TYR* 1.3 78.6 - - - +
100C ASN* 1.3 64.1 + - - +
101C ARG 3.5 0.3 + - - -
102C LYS* 3.7 45.2 + - - +
103C LYS* 3.8 7.6 + - - +
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Residues in contact with ASN 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 GLY* 5.8 0.9 - - - -
97C SER* 3.4 30.6 + - - +
98C TYR 3.2 0.6 - - - -
99C ARG* 1.3 76.9 - - - +
101C ARG* 1.3 64.3 + - - +
102C LYS 3.2 2.7 - - - -
103C LYS* 3.4 31.8 - - + +
104C GLN* 3.1 35.0 + - + +
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Residues in contact with ARG 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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60C GLU* 4.3 3.8 + - - -
91C PRO* 3.7 29.7 - - - +
92C THR* 4.3 7.3 + - - +
93C PHE* 3.5 43.4 + - - -
95C GLY 5.5 2.0 - - - +
97C SER 3.1 12.9 + - - +
98C TYR* 3.1 34.8 + - + +
100C ASN* 1.3 77.7 - - - +
102C LYS* 1.3 52.7 + - - +
104C GLN* 3.9 9.0 - - - +
105C SER* 2.5 64.6 + - - -
135C ASN* 3.5 28.4 + - - +
138C ASN* 5.6 1.8 - - - +
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Residues in contact with LYS 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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98C TYR 4.0 2.7 + - - +
99C ARG* 3.7 47.6 + - - +
100C ASN 3.2 0.4 - - - -
101C ARG* 1.3 79.9 - - - +
103C LYS* 1.3 63.2 + - - +
105C SER* 3.4 4.0 + - - -
106C ILE* 2.9 63.3 + - + +
131C ASP* 3.4 37.7 - - + +
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Residues in contact with LYS 103 (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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99C ARG 3.8 4.1 + - - +
100C ASN* 3.1 37.4 + - - +
102C LYS* 1.3 84.3 - - - +
104C GLN* 1.3 60.8 + - - +
106C ILE* 3.2 14.5 - - + +
107C ASP* 2.9 37.8 + - + +
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Residues in contact with GLN 104 (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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93C PHE* 3.3 51.6 - - + +
95C GLY 4.3 14.8 + - - -
96C GLY* 5.7 1.8 - - - -
97C SER 5.4 0.2 + - - -
100C ASN* 3.1 21.3 + - - +
101C ARG* 3.9 8.3 - - - +
103C LYS* 1.3 80.9 - - - +
105C SER* 1.3 65.2 + - - +
107C ASP* 3.4 7.6 - - - +
108C VAL* 2.9 30.8 + - + +
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Residues in contact with SER 105 (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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93C PHE* 3.1 13.2 - - - -
101C ARG* 2.5 47.3 + - - -
102C LYS* 3.4 7.4 + - - -
103C LYS 3.2 0.2 - - - -
104C GLN* 1.3 81.3 - - - +
106C ILE* 1.3 60.5 + - - +
108C VAL* 3.3 1.1 + - - +
109C PHE* 2.9 22.9 + - - +
134C ALA* 5.4 2.5 - - - -
135C ASN* 5.6 2.7 - - - -
138C ASN* 3.0 31.4 + - - +
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Residues in contact with ILE 106 (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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102C LYS* 2.9 58.3 + - + +
103C LYS* 3.2 13.5 - - + +
105C SER* 1.3 74.5 - - - +
107C ASP* 1.3 57.3 + - - +
109C PHE* 3.3 9.5 - - + +
110C ILE* 2.9 32.1 + - - +
130C LEU* 4.6 17.3 - - + -
131C ASP* 4.6 10.5 - - - +
134C ALA* 4.0 19.7 - - + -
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Residues in contact with ASP 107 (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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103C LYS* 2.9 27.4 + - + +
104C GLN* 3.4 10.6 - - - +
105C SER 3.1 0.2 - - - -
106C ILE* 1.3 76.0 - - - +
108C VAL* 1.3 63.3 + - + +
110C ILE* 3.2 13.3 - - - +
111C GLN* 2.9 33.6 + - - +
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Residues in contact with VAL 108 (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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93C PHE* 4.1 19.5 - - + -
104C GLN* 2.9 22.0 + - + +
105C SER 3.8 3.1 - - - +
107C ASP* 1.3 75.2 - - + +
109C PHE* 1.3 65.8 + - - +
111C GLN* 3.2 15.7 + - - +
112C LYS* 3.0 49.3 + - - +
137C PHE* 5.0 0.3 - - - -
138C ASN* 4.2 11.7 - - + +
141C LEU* 5.4 3.6 - - + -
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Residues in contact with PHE 109 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32C ILE* 4.7 8.7 - - + -
105C SER 2.9 15.0 + - - +
106C ILE* 3.3 12.6 - - - +
108C VAL* 1.3 75.1 - - - +
110C ILE* 1.3 72.9 + - + +
112C LYS 2.9 20.8 + - - -
113C ILE* 2.9 45.0 + - + +
130C LEU* 3.6 32.5 - - + -
133C ILE* 4.4 17.0 - - + -
134C ALA* 3.8 24.9 - - + -
137C PHE* 3.5 36.1 - + + -
138C ASN* 3.7 8.2 + - - +
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Residues in contact with ILE 110 (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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106C ILE 2.9 18.6 + - - +
107C ASP* 3.2 24.7 - - - +
109C PHE* 1.3 75.6 - - + +
111C GLN* 1.3 60.6 + - - +
113C ILE* 3.5 28.5 - - + +
114C SER* 4.8 4.5 + - - -
130C LEU* 6.0 3.6 - - + -
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Residues in contact with GLN 111 (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 ASP* 2.9 22.6 + - - +
108C VAL* 3.4 19.9 - - - +
109C PHE 3.0 0.2 - - - -
110C ILE* 1.3 81.2 - - + +
112C LYS* 1.3 79.9 + - + +
113C ILE 3.6 0.2 - - - -
114C SER* 5.0 4.5 + - - -
115C GLU* 5.2 2.9 - - - +
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Residues in contact with LYS 112 (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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108C VAL* 3.0 37.3 + - - +
109C PHE 2.9 4.0 + - - +
111C GLN* 1.3 101.0 + - + +
113C ILE* 1.3 63.5 + - - +
114C SER 3.4 2.7 - - - -
115C GLU* 3.3 39.3 - - - +
116C TYR* 3.3 18.3 - - - +
137C PHE* 4.4 1.6 - - + -
141C LEU* 3.7 30.5 - - + -
145C GLU* 4.1 17.7 + - - +
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Residues in contact with ILE 113 (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 PHE* 2.9 65.2 + - + +
110C ILE* 3.5 35.2 - - + +
111C GLN 3.6 0.2 - - - -
112C LYS* 1.3 75.6 - - - +
114C SER* 1.3 70.0 + - - +
115C GLU 3.3 0.5 + - - -
116C TYR* 3.5 13.5 + - - +
117C THR* 4.1 13.4 - - + +
120C LYS* 3.6 32.2 - - - +
137C PHE* 4.2 14.5 - - + -
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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