Contacts of the helix formed by residues 89 - 107 (chain C) in PDB entry 3ENM
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 89 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B GLU* 3.5 19.3 + - - +
123B GLY 4.5 5.8 - - - +
3C SO4 2.7 28.1 + - - +
87C THR 3.5 3.4 + - - -
88C VAL* 1.3 77.0 - - - +
90C SER* 1.3 58.8 + - - +
91C GLN* 2.4 37.0 + - - +
92C GLU* 2.7 30.3 + - - +
93C GLN* 3.0 19.8 + - - +
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Residues in contact with SER 90 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120B PHE* 3.2 31.5 - - - +
121B ARG* 2.8 35.4 + - - -
123B GLY* 3.2 12.6 + - - +
124B ASP 4.3 0.9 + - - -
3C SO4 2.6 12.2 + - - -
89C ASN* 1.3 70.3 - - - +
91C GLN* 1.3 55.8 + - - -
93C GLN* 3.0 13.1 + - - +
94C LYS* 2.9 33.8 + - - +
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Residues in contact with GLN 91 (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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3C SO4 2.5 27.0 + - - +
89C ASN* 2.4 42.6 + - - +
90C SER* 1.3 68.8 - - - +
92C GLU* 1.3 104.5 + - - +
93C GLN 2.7 4.9 - - - -
94C LYS* 2.9 18.4 + - - +
95C ARG* 2.9 20.5 + - - +
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Residues in contact with GLU 92 (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 ARG* 3.8 19.3 + - - -
87C THR 4.2 2.4 - - - +
88C VAL* 3.2 15.7 - - + -
89C ASN* 2.7 39.4 + - - +
91C GLN* 1.3 100.8 - - - +
93C GLN* 1.3 58.7 + - - +
95C ARG* 4.6 4.3 - - - -
96C LEU* 3.0 28.6 + - - +
203C TYR* 3.4 24.6 - - + +
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Residues in contact with GLN 93 (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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120B PHE* 6.4 0.6 - - - -
123B GLY* 4.8 8.8 - - - -
84C ILE* 4.6 10.3 - - + -
88C VAL* 3.6 33.6 - - + +
89C ASN 3.0 12.3 + - - +
90C SER* 3.0 17.6 + - - +
91C GLN 2.7 0.8 - - - -
92C GLU* 1.3 82.4 - - - +
94C LYS* 1.3 55.6 + - - +
96C LEU* 3.3 10.1 - - + +
97C LEU* 2.9 47.3 + - + +
120C PHE* 5.3 3.0 - - - -
125C VAL* 4.1 25.1 - - + +
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Residues in contact with LYS 94 (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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51B ASP* 5.9 1.0 + - - -
120B PHE* 4.2 37.5 + - - +
90C SER* 2.9 14.4 + - - +
91C GLN* 2.9 11.6 + - - +
93C GLN* 1.3 74.2 - - - +
95C ARG* 1.3 54.4 + - - +
97C LEU* 2.8 14.9 + - + +
98C MSE 2.5 37.5 + - + +
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Residues in contact with ARG 95 (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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91C GLN* 2.9 18.9 + - - +
92C GLU* 4.2 4.7 - - - +
94C LYS* 1.3 72.2 - - - +
96C LEU* 1.3 67.2 + - - +
98C MSE 3.0 49.6 + - - +
99C ASP* 2.8 41.5 + - - +
178C ARG* 6.1 3.0 - - - +
203C TYR* 3.4 19.1 - - - +
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Residues in contact with LEU 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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84C ILE* 3.4 38.1 - - + -
92C GLU 3.0 21.0 + - - +
93C GLN* 3.3 13.7 - - + +
95C ARG* 1.3 77.3 - - - +
97C LEU* 1.3 71.8 + - + +
99C ASP* 3.3 4.4 + - - +
100C LEU* 2.9 30.1 + - + +
127C ILE* 4.3 7.4 - - + -
198C PHE* 3.7 17.9 - - + -
200C ILE* 3.9 15.0 - - + -
203C TYR* 3.6 38.1 - - + -
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Residues in contact with LEU 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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93C GLN* 2.9 39.0 + - + +
94C LYS* 2.8 15.5 + - + +
96C LEU* 1.3 85.7 - - + +
98C MSE 1.3 65.4 + - - +
100C LEU* 3.7 12.7 - - + +
101C ASP* 3.0 23.2 + - - +
118C ALA* 4.1 26.0 - - + -
120C PHE* 5.1 13.0 - - + -
125C VAL* 5.0 9.0 - - + -
127C ILE* 5.1 0.2 - - + -
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Residues in contact with MSE 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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94C LYS* 2.5 21.7 + - + +
95C ARG* 3.0 51.6 - - - +
97C LEU* 1.3 68.5 - - - +
99C ASP* 1.3 64.8 + - - +
101C ASP* 3.0 7.5 + - - +
102C ILE* 2.8 57.3 + - + +
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Residues in contact with ASP 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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95C ARG* 2.8 39.6 + - - +
96C LEU* 3.8 1.7 - - - +
98C MSE 1.3 97.3 - - - +
100C LEU* 1.3 57.9 + - - +
102C ILE* 3.8 10.6 - - - +
103C SER* 2.8 29.3 + - - -
197C ASP* 5.1 0.3 - - - +
198C PHE* 3.6 45.1 - - + +
203C TYR* 5.1 1.7 + - - -
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Residues in contact with LEU 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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49C LYS* 5.6 0.9 - - - +
96C LEU* 2.9 18.9 + - + +
97C LEU* 3.7 14.4 - - + +
99C ASP* 1.3 76.5 - - - +
101C ASP* 1.3 60.6 + - - +
103C SER* 3.3 3.6 + - - -
104C MSE 2.8 52.3 + - + +
115C PHE* 3.6 40.2 - - + -
117C GLY* 4.4 8.1 - - - -
118C ALA* 4.4 15.9 - - + +
127C ILE* 4.0 31.6 - - + -
198C PHE* 3.8 15.2 - - + -
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Residues in contact with ASP 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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49C LYS* 5.9 0.5 + - - -
97C LEU 3.0 13.9 + - - +
98C MSE 3.0 9.5 + - - +
100C LEU* 1.3 74.2 - - - +
102C ILE* 1.3 67.8 + - + +
104C MSE 3.3 13.1 + - + +
105C ARG* 3.0 54.8 + - - +
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Residues in contact with ILE 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 MSE 2.8 57.1 + - + +
99C ASP* 3.8 10.3 - - - +
101C ASP* 1.3 77.4 - - + +
103C SER* 1.3 61.2 + - - +
105C ARG* 3.2 8.1 + - - +
106C THR* 2.7 38.1 + - + +
107C VAL* 6.2 0.4 - - + -
175C VAL* 5.4 14.8 - - + -
197C ASP* 5.7 2.2 - - - +
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Residues in contact with SER 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 ASP 2.8 23.2 + - - -
100C LEU* 3.4 8.5 - - - -
101C ASP 3.2 0.2 - - - -
102C ILE* 1.3 73.9 - - - +
104C MSE 1.3 62.4 + - - +
107C VAL* 3.1 37.6 + - - +
113C VAL 4.8 2.3 + - - -
115C PHE* 3.6 18.8 + - - +
197C ASP* 3.0 31.6 + - - -
198C PHE* 4.3 5.2 - - - -
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Residues in contact with MSE 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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48C VAL* 4.6 13.5 - - + -
49C LYS* 4.0 19.5 - - - +
100C LEU* 2.8 64.1 + - + +
101C ASP* 3.3 12.8 + - + +
103C SER* 1.3 74.7 - - - +
105C ARG* 1.3 64.2 + - + +
106C THR 3.3 0.5 + - - -
107C VAL 4.9 0.3 + - - -
115C PHE* 2.6 39.0 - - + +
116C TYR* 3.4 25.6 - - - +
117C GLY* 3.4 5.2 - - - -
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Residues in contact with ARG 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 ASP* 3.0 45.4 + - - +
102C ILE* 3.2 2.0 + - - +
104C MSE 1.3 80.0 - - + +
106C THR* 1.3 73.1 + - + +
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Residues in contact with THR 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 ILE* 2.7 33.6 + - + +
103C SER 4.0 0.2 + - - -
104C MSE 3.2 1.6 + - - -
105C ARG* 1.3 95.7 - - + +
107C VAL* 1.3 74.9 + - - +
108C ASP* 4.7 2.5 - - - +
173C LEU* 3.6 37.3 - - + +
175C VAL* 5.8 0.9 - - - +
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Residues in contact with VAL 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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102C ILE* 6.2 0.2 - - + -
103C SER* 3.1 27.6 + - - +
104C MSE 4.9 0.6 + - - -
106C THR* 1.3 84.9 - - - +
108C ASP* 1.3 70.9 + - - +
109C CYS 4.3 2.5 - - - +
112C THR* 3.0 32.1 - - + +
113C VAL 5.6 3.8 - - - +
168C HIS* 3.5 17.0 + - + -
169C LEU* 4.0 23.6 - - + -
173C LEU* 4.1 5.6 - - + -
197C ASP* 3.0 28.9 - - - +
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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