Contacts of the helix formed by residues 103 - 116 (chain A) in PDB entry 2V40
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 LEU 103 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A ILE* 3.6 22.8 + - + +
102A HIS* 1.3 68.3 - - - +
104A PRO* 1.3 75.5 - - + +
106A LEU* 3.2 7.9 + - + +
107A PHE* 3.1 30.4 + - + -
135A ILE* 4.0 16.8 - - + -
136A VAL 4.4 1.8 + - - -
181A MET* 4.1 15.0 - - + -
184A LEU* 3.6 28.7 - - + -
220A LEU* 3.8 19.5 - - + -
223A TYR* 4.3 17.5 - - + -
227A ILE* 4.0 28.5 - - + -
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Residues in contact with PRO 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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102A HIS* 3.5 31.4 - - + +
103A LEU* 1.3 92.7 - - + +
105A GLY* 1.3 55.4 + - - +
107A PHE* 3.4 1.2 + - - +
108A GLU* 2.9 32.5 + - - +
136A VAL 5.3 0.2 - - - +
138A ASP* 3.9 11.4 - - - +
216A GLU* 5.9 1.1 - - - +
219A LYS* 6.0 1.6 - - + -
220A LEU* 5.3 5.2 - - + -
223A TYR* 3.6 39.1 + - + +
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Residues in contact with GLY 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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64A ASN* 4.5 14.1 - - - -
81A LEU* 6.2 0.2 - - - -
102A HIS* 3.2 20.6 + - - -
103A LEU 3.2 0.4 - - - -
104A PRO* 1.3 79.5 - - - +
106A LEU* 1.3 56.6 + - - +
108A GLU* 3.8 8.8 - - - +
109A GLU* 2.9 34.9 + - - +
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Residues in contact with LEU 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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64A ASN* 5.3 0.4 - - - +
81A LEU* 3.8 22.8 - - + +
82A LEU* 3.6 35.7 - - + -
95A ILE* 6.1 1.6 - - + -
101A ILE* 4.0 23.1 - - + -
102A HIS 3.0 13.3 + - - +
103A LEU* 3.2 16.3 + - + +
105A GLY* 1.3 76.5 - - - +
107A PHE* 1.3 67.0 + - + +
109A GLU* 3.4 7.2 + - - +
110A ALA* 3.1 21.9 + - + +
123A TRP* 5.6 4.7 - - + -
127A LEU* 4.7 7.4 - - + -
129A ILE* 4.1 25.8 - - + -
227A ILE* 4.9 5.8 - - + -
230A MET* 5.3 2.2 - - + -
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Residues in contact with PHE 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 LEU* 3.1 29.0 + - + +
104A PRO 4.1 0.7 - - - +
106A LEU* 1.3 78.6 - - + +
108A GLU* 1.3 60.4 + - - +
110A ALA* 4.0 2.0 - - - +
111A GLU* 2.8 51.3 + - - +
123A TRP* 3.9 28.3 - + - -
124A GLU* 6.1 1.1 - - + -
223A TYR* 3.4 40.6 - + + -
226A LYS* 3.5 43.7 - - + +
227A ILE* 3.1 39.0 - - + -
230A MET* 4.3 4.9 - - + -
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Residues in contact with GLU 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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104A PRO 2.9 19.7 + - - +
105A GLY* 3.8 8.4 - - - +
107A PHE* 1.3 76.5 - - - +
109A GLU* 1.3 63.9 + - - +
111A GLU* 3.9 6.4 - - - +
112A LYS* 2.9 66.9 + - + +
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Residues in contact with GLU 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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64A ASN* 4.9 1.4 + - - +
78A ASP 4.2 11.1 - - - +
79A PHE* 3.4 4.2 - - - -
80A HIS* 2.8 43.6 + - + +
81A LEU* 2.9 26.1 + - - +
82A LEU* 3.0 37.5 + - + +
105A GLY 2.9 19.4 + - - +
106A LEU* 3.7 5.9 - - - +
108A GLU* 1.3 77.6 + - - +
110A ALA* 1.3 62.1 + - - +
112A LYS* 3.7 5.6 + - - +
113A ASN* 3.3 25.8 + - - +
116A LYS* 5.0 0.5 + - - -
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Residues in contact with ALA 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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82A LEU* 4.3 13.7 - - + -
106A LEU* 3.1 15.6 + - + +
107A PHE 4.0 1.6 - - - +
109A GLU* 1.3 77.9 - - - +
111A GLU* 1.3 64.1 + - - +
113A ASN* 3.2 8.2 + - - +
114A VAL* 3.1 27.4 + - - +
120A LEU* 5.1 2.1 - - + +
123A TRP* 3.5 48.6 - - + +
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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 PHE* 2.8 34.7 + - + +
108A GLU* 4.0 5.3 + - - +
110A ALA* 1.3 79.0 - - + +
112A LYS* 1.3 57.1 + - + +
114A VAL* 3.3 10.3 + - + +
115A GLN* 3.0 34.4 + - + +
123A TRP* 5.4 5.8 - - + +
226A LYS* 2.8 32.0 + - - +
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Residues in contact with LYS 112 (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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108A GLU* 2.9 57.3 + - + +
109A GLU* 4.1 4.7 - - - +
111A GLU* 1.3 75.7 - - + +
113A ASN* 1.3 62.2 + - - +
115A GLN* 3.2 22.2 + - - +
116A LYS* 3.2 42.9 + - - +
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Residues in contact with ASN 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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77A TYR* 3.4 24.9 - - + -
78A ASP 2.9 35.0 + - - +
79A PHE* 3.5 25.3 - - - -
82A LEU* 5.4 1.2 - - - +
109A GLU* 3.3 12.6 + - - +
110A ALA* 3.2 11.3 + - - +
112A LYS* 1.3 77.2 - - - +
114A VAL* 1.3 63.0 + - - +
116A LYS* 2.8 39.8 + - - +
117A GLY 3.4 9.5 + - - +
120A LEU* 3.9 19.3 - - + +
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Residues in contact with VAL 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 ALA 3.1 15.0 + - - +
111A GLU* 3.3 11.2 + - + +
113A ASN* 1.3 75.9 - - - +
115A GLN* 1.3 60.8 + - + +
117A GLY* 3.2 19.2 + - - +
120A LEU* 4.2 15.0 - - + +
121A GLU* 5.8 5.8 - - - +
123A TRP* 3.8 29.6 - - + +
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Residues in contact with GLN 115 (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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111A GLU* 3.0 23.1 + - + +
112A LYS* 3.2 24.4 + - - +
114A VAL* 1.3 78.2 - - + +
116A LYS* 1.3 61.1 + - + +
117A GLY 3.5 0.4 + - - -
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Residues in contact with LYS 116 (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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75A VAL* 3.4 28.6 - - + +
76A GLU 3.1 21.3 - - - +
77A TYR* 4.3 2.0 - - + -
78A ASP* 3.6 28.1 + - - +
109A GLU 5.0 0.8 + - - -
112A LYS* 3.2 31.4 + - - +
113A ASN* 2.8 34.3 + - - +
115A GLN* 1.3 79.9 - - + +
117A GLY* 1.3 58.3 + - - +
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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