Contacts of the helix formed by residues 89 - 107 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SO4 2.9 30.4 + - - +
87A THR 3.3 2.6 + - - -
88A VAL* 1.3 76.3 - - - +
90A SER* 1.3 55.3 + - - +
91A GLN* 3.4 8.8 - - - +
92A GLU* 2.8 47.5 + - - +
93A GLN* 3.0 29.6 + - - +
87B THR* 3.7 19.7 - - + -
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Residues in contact with SER 90 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A SO4 3.1 19.9 + - - -
89A ASN* 1.3 73.3 - - - +
91A GLN* 1.3 67.5 + - - +
93A GLN* 3.2 18.1 + - - +
94A LYS* 2.9 38.6 + - - +
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Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2A SO4 2.7 26.7 + - - +
89A ASN* 3.4 11.4 - - - +
90A SER* 1.3 70.7 - - - +
92A GLU* 1.3 60.9 + - + +
94A LYS* 3.1 11.7 + - - +
95A ARG* 2.7 32.1 + - - +
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Residues in contact with GLU 92 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85A ARG* 3.3 24.6 + - - -
87A THR 4.4 0.9 - - - +
88A VAL* 3.4 12.5 - - + -
89A ASN* 2.8 50.1 + - - +
91A GLN* 1.3 79.5 - - + +
93A GLN* 1.3 66.4 + - - +
95A ARG* 4.3 3.8 - - - +
96A LEU* 2.9 27.4 + - - +
203A TYR* 3.3 25.9 - - + +
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Residues in contact with GLN 93 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ILE* 6.2 0.2 - - + -
88A VAL* 3.6 33.2 - - + +
89A ASN 3.0 17.8 + - - +
90A SER* 3.5 20.4 + - - +
92A GLU* 1.3 75.4 - - - +
94A LYS* 1.3 64.4 + - + +
96A LEU* 3.5 9.8 + - + +
97A LEU* 3.2 29.3 + - + +
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Residues in contact with LYS 94 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A SER* 2.9 26.0 + - - +
91A GLN* 3.4 12.1 - - - +
93A GLN* 1.3 78.8 - - + +
95A ARG* 1.3 64.4 + - - +
97A LEU* 3.6 10.6 + - + +
98A MSE 3.1 32.3 + - + +
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Residues in contact with ARG 95 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A GLN 2.7 19.3 + - - +
92A GLU* 4.0 3.4 - - - +
94A LYS* 1.3 73.6 - - - +
96A LEU* 1.3 58.0 + - - +
98A MSE 3.3 31.4 + - - +
99A ASP* 2.8 65.9 + - - +
102A ILE* 5.0 4.0 - - - +
178A ARG* 5.9 5.8 - - - +
203A TYR* 3.4 17.7 - - - +
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Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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84A ILE* 3.6 39.9 - - + -
88A VAL* 6.0 0.7 - - + -
92A GLU 2.9 16.6 + - - +
93A GLN* 3.8 9.4 - - + +
95A ARG* 1.3 77.6 - - - +
97A LEU* 1.3 53.7 + - + +
99A ASP* 3.4 2.8 + - - +
100A LEU* 2.7 44.7 + - + +
127A ILE* 4.7 7.0 - - + -
198A PHE* 3.8 13.5 - - + -
200A ILE* 3.6 31.0 - - + -
203A TYR* 3.8 27.6 + - + -
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Residues in contact with LEU 97 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.8 31.3 - - + -
93A GLN* 3.2 17.6 + - + +
94A LYS* 3.7 10.3 - - + +
96A LEU* 1.3 78.0 - - + +
98A MSE 1.3 67.5 + - - +
100A LEU* 4.1 4.4 - - + +
101A ASP* 3.0 26.3 + - - +
120A PHE* 6.3 1.3 - - + -
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Residues in contact with MSE 98 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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94A LYS* 3.1 23.7 + - + +
95A ARG* 3.6 32.1 - - - +
97A LEU* 1.3 79.9 - - - +
99A ASP* 1.3 70.7 + - - +
101A ASP* 3.5 4.1 - - - +
102A ILE* 2.9 44.8 + - + +
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Residues in contact with ASP 99 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ARG* 2.8 62.4 + - - +
96A LEU 4.0 2.0 - - - +
98A MSE 1.3 73.8 - - - +
100A LEU* 1.3 65.5 + - - +
102A ILE* 3.9 10.6 - - - +
103A SER* 2.9 26.3 + - - -
197A ASP* 4.7 0.7 - - - +
198A PHE* 3.6 43.9 - - + +
203A TYR* 4.7 1.9 + - - -
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Residues in contact with LEU 100 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 3.7 29.6 - - + -
96A LEU* 2.7 27.3 + - + +
97A LEU* 4.1 4.5 - - + +
99A ASP* 1.3 72.9 - - - +
101A ASP* 1.3 57.8 + - - +
103A SER* 3.5 2.2 + - - -
104A MSE 3.0 41.6 + - - +
115A PHE* 3.8 40.6 - - + -
117A GLY 4.5 10.8 - - - +
118A ALA* 4.6 1.1 - - + -
127A ILE* 4.0 31.0 - - + -
198A PHE* 4.1 15.4 - - + -
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 5.2 13.4 - - + +
97A LEU 3.0 18.6 + - - +
98A MSE 3.5 5.1 - - - +
100A LEU* 1.3 74.5 - - - +
102A ILE* 1.3 68.7 + - - +
103A SER 3.1 1.3 - - - -
104A MSE 3.3 5.0 + - - +
105A ARG* 2.8 71.2 + - - +
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Residues in contact with ILE 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95A ARG* 5.0 3.6 - - - +
98A MSE 2.9 36.6 + - + +
99A ASP* 3.9 18.8 - - - +
101A ASP* 1.3 75.4 + - - +
103A SER* 1.3 63.0 + - - +
105A ARG* 4.5 12.6 - - - +
106A THR* 2.4 47.0 + - + +
107A VAL* 4.9 5.8 - - + -
175A VAL* 4.9 16.6 - - + -
197A ASP* 5.7 1.6 - - - +
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Residues in contact with SER 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99A ASP 2.9 18.9 + - - -
100A LEU* 3.5 6.7 - - - -
102A ILE* 1.3 79.0 - - - +
104A MSE 1.3 59.8 + - - +
107A VAL* 2.9 42.6 + - - +
113A VAL 5.0 0.9 + - - -
115A PHE* 3.7 20.4 + - - +
197A ASP* 2.9 32.8 + - - -
198A PHE* 4.6 1.6 - - - -
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Residues in contact with MSE 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46A PHE* 4.0 31.0 - - - +
100A LEU* 3.0 32.1 + - - +
101A ASP* 4.2 3.1 - - - +
103A SER* 1.3 78.3 - - - +
105A ARG* 1.3 66.4 + - + +
106A THR 3.5 0.2 + - - -
107A VAL 4.7 1.6 + - - +
115A PHE* 3.3 30.7 - - + +
116A TYR* 2.8 29.6 - - - +
117A GLY* 3.6 20.0 - - - -
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Residues in contact with ARG 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101A ASP* 2.8 51.1 + - - +
102A ILE* 4.5 11.9 - - - +
104A MSE 1.3 82.9 - - + +
106A THR* 1.3 74.7 + - + +
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Residues in contact with THR 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 2.4 38.8 + - + +
104A MSE 3.3 0.4 - - - -
105A ARG* 1.3 104.3 - - + +
107A VAL* 1.3 67.1 + - - +
108A ASP* 3.3 8.8 + - - +
168A HIS* 5.6 0.3 - - - -
173A LEU* 4.0 24.8 - - - +
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Residues in contact with VAL 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102A ILE* 4.2 5.2 - - + +
103A SER* 2.9 33.4 + - - +
104A MSE 4.7 1.4 - - - +
106A THR* 1.3 87.3 - - - +
108A ASP* 1.3 58.2 + - - +
109A CYS* 4.1 3.8 + - + -
112A THR* 3.3 25.8 + - + +
113A VAL 5.7 1.3 - - - +
114A THR* 6.1 1.2 - - - -
168A HIS* 5.5 1.3 - - + -
169A LEU* 3.9 18.8 - - + -
173A LEU* 3.8 18.6 - - + -
175A VAL* 6.1 0.4 - - + -
197A ASP* 3.8 23.3 - - - +
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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