Contacts of the helix formed by residues 104 - 116 (chain A) in PDB entry 4I6N
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 104 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A GLY* 3.5 4.3 - - - +
25A CYS* 3.3 22.5 - - - +
94A LEU* 3.5 39.0 - - + +
95A LEU* 3.9 23.1 - - + -
97A CYS* 5.5 5.2 - - + +
102A VAL* 4.2 14.5 + - + -
103A ASP* 1.4 73.3 - - - +
105A GLY* 1.3 67.5 + - - +
108A LEU* 3.7 23.3 + - + +
109A LYS* 4.1 24.7 - - + +
112A LYS* 4.4 15.3 - - + +
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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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24A GLY 3.5 14.4 - - - -
103A ASP* 3.1 7.1 - - - +
104A LEU* 1.3 78.7 - - - +
106A PRO* 1.3 71.6 - - - +
107A THR 3.3 2.6 + - - -
109A LYS* 3.0 31.0 + - - +
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Residues in contact with PRO 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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24A GLY* 5.0 5.2 - - - +
105A GLY* 1.3 83.1 - - - +
107A THR* 1.3 65.6 + - - +
109A LYS* 4.1 6.1 - - + -
110A GLU* 3.0 39.8 + - + +
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Residues in contact with THR 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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23A PHE 3.8 19.5 - - - +
24A GLY* 5.6 0.9 - - - -
105A GLY 3.3 1.0 - - - -
106A PRO* 1.3 82.0 - - - +
108A LEU* 1.3 60.8 + - + +
110A GLU* 4.0 2.0 - - - +
111A PHE* 3.1 27.3 + - + +
130A SER* 6.0 0.4 - - - +
132A LYS* 3.6 40.5 + - + +
133A ILE* 4.5 20.6 - - + -
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Residues in contact with LEU 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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23A PHE* 3.9 32.3 + - + +
25A CYS* 4.0 7.2 - - + -
91A ILE* 4.3 22.4 - - + -
94A LEU* 3.8 31.9 - - + -
95A LEU* 4.1 10.1 - - + +
104A LEU* 3.7 33.1 + - + +
105A GLY 3.5 2.0 + - - -
107A THR* 1.3 79.1 - - + +
109A LYS* 1.3 59.7 + - - +
111A PHE* 3.6 10.3 - - + +
112A LYS* 2.8 31.5 + - - +
133A ILE* 4.3 17.9 - - + -
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Residues in contact with LYS 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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104A LEU* 4.1 20.1 - - + +
105A GLY 3.0 22.3 + - - +
106A PRO* 3.8 5.6 - - + +
108A LEU* 1.3 77.5 - - - +
110A GLU* 1.3 62.8 + - + +
112A LYS* 3.3 6.7 + - + +
113A ASP* 2.5 68.3 + - - +
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Residues in contact with GLU 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 PRO* 3.0 27.3 + - + +
107A THR* 4.2 2.0 - - - +
109A LYS* 1.3 80.5 - - + +
111A PHE* 1.3 60.1 + - - +
113A ASP* 3.7 10.5 - - + +
114A PHE* 2.8 30.8 + - - +
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Residues in contact with PHE 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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75A TYR* 3.4 19.7 - - - -
77A SER* 5.9 0.7 - - - -
91A ILE* 4.3 17.0 - - + -
95A LEU* 3.8 16.2 - - + -
107A THR* 3.1 21.4 + - + +
108A LEU* 3.6 12.8 - - + +
110A GLU* 1.3 74.9 - - - +
112A LYS* 1.3 55.5 + - - +
114A PHE* 3.2 9.1 + + - +
115A THR* 2.7 60.0 + - + +
123A ARG 4.0 3.8 - - - -
126A CYS* 4.0 8.7 - - + -
127A LEU* 3.8 42.6 - - + -
130A SER* 5.5 6.7 - - - -
133A ILE* 6.0 7.0 - - + -
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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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75A TYR* 4.3 13.0 - - + +
95A LEU* 2.8 56.0 + - + +
96A ASN* 4.9 1.4 - - - +
97A CYS 4.6 10.3 + - - -
104A LEU* 4.4 9.9 - - + +
108A LEU 2.8 16.8 + - - +
109A LYS* 3.6 8.3 - - + +
111A PHE* 1.3 77.9 - - - +
113A ASP* 1.3 61.4 + - - +
115A THR* 3.8 5.4 - - - -
116A TYR* 2.9 56.4 + - + +
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Residues in contact with ASP 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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109A LYS* 2.5 55.2 + - - +
110A GLU* 3.7 10.8 - - - +
112A LYS* 1.3 82.4 - - - +
114A PHE* 1.3 63.2 + - - +
116A TYR* 4.1 11.3 + - - +
117A ASP* 5.2 2.3 + - - +
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Residues in contact with PHE 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 GLU 2.8 18.6 + - - +
111A PHE* 3.7 10.5 - + - +
113A ASP* 1.3 79.7 - - - +
115A THR* 1.4 69.9 + - + +
116A TYR 3.7 0.7 + - - -
117A ASP* 4.7 2.6 + - - +
118A LEU* 3.8 23.8 - - + +
126A CYS* 3.9 7.2 - - + -
301A DTT 3.7 31.6 - - - -
61C ARG* 4.7 21.5 - - + -
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Residues in contact with THR 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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75A TYR* 2.7 29.5 + - - -
111A PHE* 2.7 49.8 + - + +
112A LYS 3.6 0.3 + - - -
114A PHE* 1.4 89.8 - - + +
116A TYR* 1.3 60.8 + - - +
117A ASP 3.2 2.9 - - - -
118A LEU* 3.1 19.6 + - + -
123A ARG* 2.8 36.1 + - - +
126A CYS* 4.1 11.9 - - + -
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Residues in contact with TYR 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 TYR* 4.2 16.2 - + + -
112A LYS* 2.9 40.3 + - + +
113A ASP* 4.1 9.9 - - - +
114A PHE 3.5 1.4 - - - -
115A THR* 1.3 77.7 - - - +
117A ASP* 1.3 94.5 + - - +
118A LEU 3.4 0.2 - - - -
123A ARG* 2.9 20.9 + - - -
66C ASP* 4.4 13.8 + - - -
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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