Contacts of the helix formed by residues 98 - 114 (chain A) in PDB entry 2B9S
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 MET 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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93A HIS* 6.3 0.2 - - + -
94A ASP* 3.4 37.2 - - + +
95A TYR* 3.0 21.3 + - + +
97A ARG* 1.3 77.6 - - - +
99A GLU* 1.3 66.0 + - - +
100A VAL* 3.3 1.5 + - + +
101A PHE* 3.6 8.1 - - + +
102A ARG* 3.1 24.3 + - - +
191A GLY 5.6 0.7 - - - +
196A MET* 3.7 31.6 - - - +
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Residues in contact with GLU 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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97A ARG 3.7 2.8 + - - +
98A MET* 1.3 73.2 - - - +
100A VAL* 1.3 59.0 + - + +
102A ARG* 3.8 25.0 + - - +
103A ARG* 2.9 46.6 + - - +
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Residues in contact with VAL 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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98A MET* 3.3 2.1 - - + +
99A GLU* 1.3 75.0 - - + +
101A PHE* 1.3 62.5 + - - +
103A ARG* 3.5 29.5 + - - +
104A ASN* 3.0 39.9 + - - +
193A HIS 3.8 15.7 - - - +
194A PRO* 3.4 29.4 - - + +
196A MET* 3.8 10.1 - - + -
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Residues in contact with PHE 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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87A PHE* 4.1 20.2 - + - -
90A MET* 3.7 31.0 - - + -
95A TYR* 3.2 60.1 - + + +
96A TYR* 4.3 2.2 - - - -
98A MET* 3.4 2.9 + - + +
100A VAL* 1.3 77.7 - - - +
102A ARG* 1.3 57.5 + - - +
104A ASN 3.4 0.7 + - - -
105A PHE* 3.0 29.7 + - + +
186A LEU* 3.8 31.2 - - + -
187A PHE 4.0 7.9 - - - -
188A ARG* 5.0 0.4 - - + -
196A MET* 3.3 26.8 - - + +
197A GLY* 3.2 30.8 - - - -
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Residues in contact with ARG 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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87A PHE* 4.0 21.9 - - + -
95A TYR 4.7 0.2 - - - +
96A TYR* 2.9 49.1 + - - +
97A ARG* 4.2 8.3 - - - +
98A MET 3.1 20.5 + - - +
99A GLU* 3.8 25.5 + - - +
101A PHE* 1.3 74.5 - - - +
103A ARG* 1.3 66.0 + - - +
105A PHE* 3.8 4.4 - - - +
106A PHE* 3.1 25.8 + - - +
123A LEU* 3.6 42.6 + - + +
124A GLU* 5.1 5.5 - - - +
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Residues in contact with ARG 103 (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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99A GLU* 2.9 33.4 + - - +
100A VAL* 3.8 39.0 - - - +
102A ARG* 1.3 76.4 - - - +
104A ASN* 1.3 72.4 + - - +
106A PHE* 3.3 5.6 + - - +
107A GLU* 3.1 26.0 + - + +
194A PRO 5.2 1.8 + - - -
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Residues in contact with ASN 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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100A VAL* 3.0 18.7 + - - +
103A ARG* 1.3 83.7 + - - +
105A PHE* 1.3 65.7 + - - +
107A GLU* 3.5 6.9 + - - +
108A SER* 3.1 26.9 + - - -
194A PRO 2.7 29.6 + - - +
195A LEU* 3.4 11.9 - - - +
196A MET 2.7 29.9 + - - +
197A GLY 3.8 2.2 - - - -
198A LYS* 3.5 15.3 - - + +
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Residues in contact with PHE 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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83A VAL* 3.4 27.6 - - + -
84A ALA* 4.4 3.1 - - - -
87A PHE* 3.4 55.0 - + + -
101A PHE* 3.0 18.5 + - + +
102A ARG 3.8 7.6 - - - +
104A ASN* 1.3 77.0 - - - +
106A PHE* 1.3 64.6 + - + +
108A SER* 3.2 4.6 + - - -
109A TRP* 2.8 72.4 + + + +
123A LEU* 4.0 16.4 - - + -
128A PHE* 4.2 5.2 - + - -
186A LEU* 3.9 20.6 - - + -
197A GLY* 3.3 14.6 + - - +
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Residues in contact with PHE 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 ARG 3.1 19.7 + - - +
103A ARG* 3.8 5.6 - - - +
104A ASN 3.3 0.2 - - - -
105A PHE* 1.3 80.7 - - - +
107A GLU* 1.3 57.7 + - - +
109A TRP* 3.8 19.2 - + - +
110A ARG* 2.9 59.7 + - + +
120A ILE* 3.7 25.8 - - + -
121A ARG 3.7 16.6 - - - -
122A ARG* 3.6 13.0 - - - -
123A LEU* 3.5 49.4 - - + -
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Residues in contact with GLU 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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103A ARG* 3.1 18.8 + - + +
104A ASN* 3.9 7.4 - - - +
106A PHE* 1.3 76.5 - - - +
108A SER* 1.3 64.4 + - - +
110A ARG* 3.5 5.9 + - - +
111A GLU* 3.1 29.6 + - - +
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Residues in contact with SER 108 (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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83A VAL* 5.2 2.9 - - - -
104A ASN 3.1 14.1 + - - -
105A PHE* 3.5 10.1 - - - -
107A GLU* 1.3 76.1 - - - +
109A TRP* 1.3 60.9 + - - +
111A GLU* 3.3 28.9 + - - +
112A ILE* 3.6 13.2 + - - +
186A LEU* 5.8 0.2 - - - -
198A LYS* 3.8 9.9 - - - +
199A LEU* 3.0 43.3 + - - +
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Residues in contact with TRP 109 (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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67A ILE* 4.0 23.1 - - + -
74A PHE* 5.0 0.7 - + - -
76A MET* 3.8 15.3 - - - -
80A GLU* 3.0 32.2 + - - +
83A VAL* 3.8 21.3 - - + +
84A ALA* 3.7 20.8 - - + +
105A PHE* 2.8 43.4 + + + +
106A PHE* 3.8 18.2 - + - +
107A GLU 3.3 0.2 - - - -
108A SER* 1.3 73.2 - - - +
110A ARG* 1.3 57.9 + - - +
112A ILE* 3.1 11.4 + - + +
113A LEU* 3.0 50.3 + - + +
120A ILE* 4.1 12.6 - - + -
126A CYS* 3.8 24.0 - - - -
128A PHE* 4.1 13.7 - + - -
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Residues in contact with ARG 110 (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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106A PHE* 2.9 51.2 + - + +
107A GLU* 3.8 6.7 - - - +
109A TRP* 1.3 72.7 - - - +
111A GLU* 1.3 57.2 + - - +
112A ILE 3.1 1.6 - - - -
113A LEU* 3.7 13.2 - - + -
114A ASP* 2.7 74.5 + - - +
118A HIS* 3.6 9.3 + - - -
120A ILE* 3.3 28.9 + - - -
121A ARG* 3.7 20.4 + - - +
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Residues in contact with GLU 111 (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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107A GLU* 3.1 22.3 + - - +
108A SER* 3.4 18.3 + - - +
109A TRP 3.3 0.2 - - - -
110A ARG* 1.3 76.2 - - - +
112A ILE* 1.3 63.4 + - + +
114A ASP* 4.1 6.5 + - - +
115A LYS* 3.8 15.8 + - - +
198A LYS* 6.0 1.2 - - - -
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Residues in contact with ILE 112 (chain A).
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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77A THR* 5.1 0.2 - - - +
79A GLU* 3.6 43.3 - - + +
80A GLU* 3.7 29.0 - - + +
83A VAL* 3.6 35.7 - - + -
108A SER 3.9 12.1 - - - +
109A TRP* 3.1 7.9 + - + +
111A GLU* 1.3 77.7 - - + +
113A LEU* 1.3 65.1 + - - +
114A ASP 3.2 0.2 - - - -
115A LYS* 3.3 27.7 + - - +
116A ARG* 5.4 0.3 - - - +
199A LEU* 3.8 17.3 - - + -
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Residues in contact with LEU 113 (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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74A PHE* 3.9 28.5 - - + -
80A GLU* 3.6 35.0 - - + +
109A TRP* 3.0 54.3 + - + +
110A ARG* 3.4 15.0 + - - +
112A ILE* 1.3 76.3 - - - +
114A ASP* 1.3 57.2 + - - +
115A LYS 3.1 5.4 + - - -
116A ARG* 3.2 19.0 + - - +
118A HIS* 3.0 27.3 + - + -
120A ILE* 4.0 24.5 - - + -
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Residues in contact with ASP 114 (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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110A ARG* 2.7 57.1 + - - +
111A GLU* 4.4 6.0 - - - +
112A ILE 3.2 0.4 - - - -
113A LEU* 1.3 68.8 - - - +
115A LYS* 1.3 63.1 + - - +
116A ARG 3.2 6.6 + - - +
118A HIS* 2.8 26.3 - - - -
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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