Contacts of the helix formed by residues 96 - 112 (chain A) in PDB entry 4B23
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 SER 96 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A PHE* 1.3 79.0 - - - +
97A LYS* 1.3 59.8 + - - +
98A LEU* 3.5 8.5 + - - +
99A LYS* 2.9 32.2 + - - +
100A SER* 2.9 25.1 + - - -
15Y T 3.8 13.9 - - - -
16Y T 3.2 46.1 + - - -
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Residues in contact with LYS 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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87A VAL* 5.4 1.4 - - - +
91A HIS* 3.6 37.7 - - + -
95A PHE 3.7 0.6 + - - -
96A SER* 1.3 71.7 - - - +
98A LEU* 1.3 62.5 + - - +
100A SER* 3.3 9.8 + - - -
101A GLN* 3.2 20.8 + - - +
16Y T 2.8 24.6 + - - +
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Residues in contact with LEU 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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96A SER* 3.2 7.3 + - - +
97A LYS* 1.3 79.8 - - - +
99A LYS* 1.3 64.8 + - + +
101A GLN* 3.1 12.7 + - + +
102A GLU* 3.0 46.9 + - + +
137A LYS* 5.2 1.6 - - + -
8X A 4.1 15.0 - - + +
9X T 3.2 54.7 - - - +
10X C 4.3 13.9 - - - +
15Y T 5.1 5.2 - - - +
16Y T 4.7 0.4 + - - -
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Residues in contact with LYS 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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49A ILE* 3.3 31.2 + - + +
50A THR* 2.7 33.9 + - + -
52A GLN* 2.8 34.6 + - - +
54A LEU* 3.8 2.8 - - + +
95A PHE* 4.3 10.1 - - + -
96A SER* 2.9 24.4 + - - +
98A LEU* 1.3 78.0 - - + +
100A SER* 1.3 53.7 + - - +
102A GLU* 3.2 11.7 + - - +
103A ILE* 2.8 44.3 + - + +
7X A 6.1 2.5 - - - -
16Y T 3.1 30.3 + - - +
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Residues in contact with SER 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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87A VAL* 3.7 25.5 - - - +
90A LEU* 3.8 16.9 - - - +
91A HIS* 3.3 26.0 + - - +
95A PHE* 3.5 10.5 - - - +
96A SER 2.9 19.4 + - - -
97A LYS* 3.3 12.8 - - - -
98A LEU 3.2 0.2 - - - -
99A LYS* 1.3 76.8 - - - +
101A GLN* 1.3 61.4 + - - +
103A ILE* 3.5 4.2 + - - +
104A HIS* 3.1 24.1 + - - +
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Residues in contact with GLN 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 VAL* 4.0 27.3 - - + +
97A LYS 3.2 7.8 + - - +
98A LEU* 3.1 16.2 + - + +
100A SER* 1.3 79.9 - - - +
102A GLU* 1.3 65.2 + - + +
104A HIS* 3.2 9.0 + - - +
105A ILE* 3.1 45.8 + - + +
137A LYS* 5.4 4.7 - - + -
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Residues in contact with GLU 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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49A ILE* 4.1 17.8 - - + +
52A GLN* 4.9 3.1 - - - +
98A LEU* 3.0 26.0 + - + +
99A LYS* 3.8 16.5 - - - +
101A GLN* 1.3 76.1 - - + +
103A ILE* 1.3 57.6 + - - +
105A ILE* 3.3 11.2 + - - +
106A VAL* 2.9 33.2 + - - +
137A LYS* 3.6 30.2 - - + +
138A GLY* 3.3 18.8 + - - +
8X A 5.7 0.2 - - - +
9X T 3.1 37.6 - - - +
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Residues in contact with ILE 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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46A ILE* 3.7 38.7 - - + +
49A ILE* 4.5 15.7 - - + -
50A THR* 4.1 3.6 - - - +
66A PHE* 4.9 5.6 - - + -
82A ILE* 4.3 14.4 - - + -
90A LEU* 4.7 7.0 - - + -
95A PHE* 3.3 46.0 - - + -
99A LYS* 2.8 28.5 + - + +
100A SER* 3.8 4.9 - - - +
102A GLU* 1.3 70.6 - - - +
104A HIS* 1.3 65.5 - - - +
106A VAL* 3.3 8.0 + - - +
107A ALA* 3.0 21.8 + - - +
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Residues in contact with HIS 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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82A ILE* 3.5 16.1 + - - -
83A MET* 2.9 47.9 + - + +
85A THR 3.0 24.5 + - - -
86A ASP* 4.7 2.0 - - - -
87A VAL* 4.3 16.4 - - + -
90A LEU* 4.2 8.7 - - + +
100A SER 3.1 14.3 + - - +
101A GLN* 3.5 13.3 + - - +
103A ILE* 1.3 77.5 - - - +
105A ILE* 1.3 64.3 + - - +
107A ALA* 3.2 4.7 + - - +
108A GLU* 3.0 20.3 + - - +
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Residues in contact with ILE 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 GLN* 3.1 36.5 + - + +
102A GLU* 3.6 7.6 - - - +
103A ILE 3.2 0.4 - - - -
104A HIS* 1.3 75.4 - - + +
106A VAL* 1.3 60.9 + - + +
108A GLU* 3.2 17.8 + - - +
109A ALA* 2.9 29.3 + - + +
136A ILE* 6.0 4.7 - - + -
137A LYS* 3.9 37.2 - - + +
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Residues in contact with VAL 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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42A TYR* 4.1 15.0 - - + +
45A ILE* 4.2 9.6 - - + -
46A ILE* 3.9 20.4 - - + -
49A ILE* 4.1 18.6 - - + -
102A GLU 2.9 21.6 + - - +
103A ILE* 3.6 7.0 - - - +
104A HIS 3.3 0.2 - - - -
105A ILE* 1.3 76.9 - - + +
107A ALA* 1.3 58.8 + - - +
109A ALA* 3.3 7.9 + - - +
110A ALA* 2.9 27.7 + - - +
115A ILE* 3.6 15.8 - - + +
136A ILE* 3.9 28.9 - - + -
137A LYS 5.3 0.2 - - - +
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Residues in contact with ALA 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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42A TYR* 5.3 3.4 - - - -
46A ILE* 5.3 0.2 - - - -
79A PRO* 3.7 21.4 - - + +
82A ILE* 3.5 43.1 - - + -
83A MET* 4.1 7.0 - - + +
103A ILE 3.0 8.0 + - - +
104A HIS 3.4 9.6 - - - +
105A ILE 3.2 0.2 - - - -
106A VAL* 1.3 78.9 - - - +
108A GLU* 1.3 55.8 + - - +
110A ALA* 3.3 2.1 + - - -
111A LEU* 2.9 29.3 + - - +
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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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83A MET* 3.3 36.7 - - + -
104A HIS* 3.0 9.8 + - - +
105A ILE* 3.2 23.4 + - - +
107A ALA* 1.3 76.0 - - - +
109A ALA* 1.3 66.9 + - - +
111A LEU* 3.2 2.8 + - - +
112A ASN* 2.7 63.1 + - - +
114A GLN* 4.3 6.6 - - - +
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Residues in contact with ALA 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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105A ILE* 2.9 19.3 + - + +
106A VAL* 3.5 8.3 - - - +
108A GLU* 1.3 86.7 - - - +
110A ALA* 1.3 60.0 + - - +
112A ASN 3.3 0.7 + - - -
113A LYS 3.1 3.5 + - - -
114A GLN* 2.7 46.8 + - + +
115A ILE* 3.7 18.4 - - + -
136A ILE* 6.2 2.7 - - + -
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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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42A TYR* 3.6 35.9 - - + -
79A PRO* 4.1 11.7 - - + -
106A VAL 2.9 12.2 + - - +
107A ALA 3.7 4.5 - - - +
108A GLU 3.3 0.2 - - - -
109A ALA* 1.3 74.8 - - - +
111A LEU* 1.3 64.6 + - - +
113A LYS* 3.1 15.3 + - - +
114A GLN 4.9 0.4 - - - +
115A ILE* 3.7 13.4 - - + +
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Residues in contact with LEU 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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79A PRO* 3.7 18.3 - - + +
80A LYS* 3.9 29.8 - - + +
83A MET* 3.4 35.2 - - + -
107A ALA 2.9 8.7 + - - +
108A GLU* 3.3 9.2 - - - +
110A ALA* 1.3 78.2 - - - +
112A ASN* 1.3 64.1 + - - +
113A LYS* 3.4 14.7 + - - +
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Residues in contact with ASN 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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83A MET* 5.2 2.6 - - - +
108A GLU* 2.7 52.4 + - - +
110A ALA 3.2 0.2 - - - -
111A LEU* 1.3 77.3 - - - +
113A LYS* 1.3 65.6 + - - +
114A GLN* 2.9 31.4 + - + +
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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