Contacts of the helix formed by residues 98 - 111 (chain C) in PDB entry 5MSF
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 98 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33A ILE* 6.0 1.7 - - - +
35A SER* 3.2 33.1 + - - +
36A ASN* 3.7 17.6 + - - +
97C THR* 1.3 75.6 - - - +
99C SER* 1.3 58.7 + - - +
101C CYS* 3.2 9.5 + - - +
102C GLU* 2.9 41.4 + - - +
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Residues in contact with SER 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 THR* 3.1 10.8 + - - -
98C ASN* 1.3 76.1 + - - +
100C ASP* 1.3 66.6 + - - +
102C GLU* 3.1 15.8 + - - +
103C LEU* 3.1 22.0 + - - +
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Residues in contact with ASP 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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95C PHE 3.9 2.6 - - - +
96C ALA* 3.5 16.7 - - + -
97C THR* 3.0 39.1 + - - +
99C SER* 1.3 79.7 - - - +
101C CYS* 1.3 60.6 + - - +
103C LEU* 3.3 13.4 - - - +
104C ILE* 3.2 27.7 + - + +
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Residues in contact with CYS 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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56C ARG* 6.1 3.1 - - - -
92C ILE* 4.3 21.1 - - + -
96C ALA* 4.0 19.5 - - - -
97C THR 3.0 17.3 + - - +
98C ASN* 3.5 12.1 - - - +
99C SER 3.1 0.2 - - - -
100C ASP* 1.3 73.6 - - - +
102C GLU* 1.3 65.0 + - + +
103C LEU 3.1 1.3 - - - -
104C ILE* 3.2 10.2 + - - +
105C VAL* 3.0 28.4 + - + +
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Residues in contact with GLU 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 ASN* 2.9 28.6 + - - +
99C SER* 3.1 15.3 + - - +
101C CYS* 1.3 77.1 - - - +
103C LEU* 1.3 57.1 + - - +
105C VAL* 3.3 8.9 + - - +
106C LYS* 3.0 38.6 + - + +
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Residues in contact with LEU 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 SER 3.1 10.8 + - - +
100C ASP* 3.3 16.2 - - - +
101C CYS 3.1 0.2 - - - -
102C GLU* 1.3 75.2 - - - +
104C ILE* 1.3 67.2 + - + +
106C LYS* 2.9 17.5 + - + +
107C ALA* 2.9 22.7 + - + +
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Residues in contact with ILE 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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90C LEU* 4.0 22.0 - - + -
91C THR 5.8 0.2 - - - +
92C ILE* 3.9 37.9 - - + -
93C PRO* 6.1 0.9 - - + -
96C ALA* 5.1 2.5 - - + -
100C ASP* 3.2 18.3 + - + +
101C CYS* 3.4 12.1 - - - +
103C LEU* 1.3 80.0 - - + +
105C VAL* 1.3 62.8 + - + +
107C ALA* 3.2 10.8 + - + +
108C MET* 3.1 40.8 + - + +
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Residues in contact with VAL 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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101C CYS* 3.0 19.7 + - + +
102C GLU* 3.5 9.9 - - - +
104C ILE* 1.3 74.8 - - + +
106C LYS* 1.3 66.4 + - + +
108C MET* 3.0 21.5 + - + +
109C GLN* 2.9 46.3 + - + +
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Residues in contact with LYS 106 (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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102C GLU* 3.0 25.1 + - - +
103C LEU* 2.9 17.1 + - + +
105C VAL* 1.3 76.2 - - + +
107C ALA* 1.3 53.7 + - - +
109C GLN* 3.2 17.3 + - - +
110C GLY* 2.8 32.7 + - - -
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Residues in contact with ALA 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 LEU* 2.9 11.6 + - + +
104C ILE* 3.3 13.5 - - + +
105C VAL 3.1 0.2 - - - -
106C LYS* 1.3 78.4 - - - +
108C MET* 1.3 57.1 + - + +
110C GLY* 3.3 1.1 + - - -
111C LEU* 2.9 30.1 + - - +
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Residues in contact with MET 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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88C MET* 4.0 27.1 - - + -
90C LEU* 3.5 24.7 - - + -
104C ILE* 3.1 42.3 + - + +
105C VAL* 3.0 27.0 + - + +
107C ALA* 1.3 76.9 - - + +
109C GLN* 1.3 64.9 + - + +
111C LEU* 3.4 20.1 + - + +
112C LEU* 3.4 22.5 + - + +
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Residues in contact with GLN 109 (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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105C VAL* 2.9 35.3 + - + +
106C LYS* 3.6 22.0 + - - +
108C MET* 1.3 77.4 - - + +
110C GLY* 1.3 63.5 + - - +
112C LEU* 3.3 6.2 + - - +
113C LYS* 3.0 21.7 + - - +
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Residues in contact with GLY 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 LYS 2.8 16.9 + - - -
107C ALA* 3.7 1.8 - - - -
109C GLN* 1.3 75.2 - - - +
111C LEU* 1.3 60.9 + - - +
112C LEU 3.1 0.9 + - - -
113C LYS* 3.1 11.9 + - - -
116C ASN* 2.7 31.7 + - - -
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Residues in contact with LEU 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 ALA 2.9 17.2 + - - +
108C MET* 3.6 12.3 - - + +
109C GLN 3.3 0.2 - - - -
110C GLY* 1.3 75.7 - - - +
112C LEU* 1.3 75.8 + - + +
116C ASN* 4.3 3.7 - - - +
118C ILE* 3.9 31.9 + - + +
119C PRO* 3.3 21.0 - - - +
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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