Contacts of the helix formed by residues 107 - 117 (chain D) in PDB entry 3K75
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 GLY 107 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101D THR* 4.4 2.5 - - - -
105D GLY 3.7 4.9 + - - -
106D ILE* 1.3 77.3 - - - +
108D PRO* 1.3 65.8 - - - +
109D SER 3.3 2.7 - - - -
110D ALA* 3.3 7.5 + - - +
111D ALA* 2.8 32.7 + - - +
113E LYS* 5.4 7.8 - - - +
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Residues in contact with PRO 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ILE* 5.0 4.8 - - + +
101D THR* 4.4 11.6 - - + +
107D GLY* 1.3 80.1 - - - +
109D SER* 1.3 68.3 + - - +
111D ALA* 3.4 7.9 - - + +
112D ARG* 3.0 39.4 + - - +
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Residues in contact with SER 109 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107D GLY 3.3 1.2 - - - -
108D PRO* 1.3 80.0 - - - +
110D ALA* 1.3 63.0 + - - +
111D ALA 3.1 1.0 + - - -
112D ARG* 3.1 16.4 + - - +
113D LYS* 3.3 28.4 + - - +
109E SER* 4.9 11.0 + - - -
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Residues in contact with ALA 110 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D GLY 5.1 0.2 - - - +
106D ILE* 4.4 2.0 - - + -
107D GLY* 3.3 13.7 + - - +
109D SER* 1.3 79.8 - - - +
111D ALA* 1.3 60.6 + - - +
113D LYS* 3.6 13.1 + - - +
114D LEU* 3.2 30.2 + - + +
136D GLN* 3.6 27.1 - - - +
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Residues in contact with ALA 111 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ILE* 3.7 18.8 - - + -
100D LEU* 3.6 14.2 - - + +
101D THR* 4.2 6.7 - - - +
106D ILE* 3.8 17.0 - - + -
107D GLY 2.8 18.4 + - - +
108D PRO* 3.4 11.4 - - + +
109D SER 3.0 0.2 - - - -
110D ALA* 1.3 77.0 - - - +
112D ARG* 1.3 62.2 + - - +
114D LEU* 3.5 4.5 + - - -
115D VAL* 3.2 25.5 + - - +
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Residues in contact with ARG 112 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D THR* 5.9 6.3 - - + +
94D SER* 5.8 4.2 + - - +
97D ILE* 3.6 35.0 - - + +
108D PRO* 3.0 22.5 + - - +
109D SER* 3.1 10.5 + - - +
111D ALA* 1.3 75.6 - - - +
113D LYS* 1.3 65.5 + - + +
115D VAL* 3.2 3.7 + - - +
116D ASP* 3.1 33.2 + - - +
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Residues in contact with LYS 113 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D SER* 3.3 24.9 + - - +
110D ALA* 3.8 14.3 - - - +
111D ALA 3.3 0.2 - - - -
112D ARG* 1.3 76.9 - - + +
114D LEU* 1.3 62.0 + - + +
116D ASP* 3.9 6.9 + - - +
117D GLU* 3.5 32.1 + - - +
105E GLY* 4.9 10.3 + - - -
107E GLY* 4.8 17.2 - - - +
135E HIS* 5.8 9.0 - - + -
229E SER* 4.8 3.9 + - - +
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Residues in contact with LEU 114 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D LEU* 4.1 5.6 - - + -
106D ILE* 3.8 37.2 - - + -
110D ALA* 3.2 20.1 + - + +
111D ALA* 3.8 7.2 - - - +
112D ARG 3.2 0.4 - - - -
113D LYS* 1.3 76.7 - - + +
115D VAL* 1.3 57.9 + - - +
117D GLU* 3.5 3.7 + - - +
118D GLY 3.3 2.8 + - - -
119D ILE* 2.6 73.2 + - + +
125D LEU* 4.1 8.1 - - + -
131D LYS* 4.2 13.0 - - + +
132D LEU* 3.5 26.0 - - + -
136D GLN* 5.6 0.4 - - - +
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Residues in contact with VAL 115 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93D THR* 4.3 22.9 - - + +
96D SER* 4.6 10.5 - - - -
97D ILE* 3.2 36.1 - - + -
100D LEU* 3.9 13.2 - - + -
111D ALA 3.2 5.4 + - - +
112D ARG* 3.2 8.4 + - + +
114D LEU* 1.3 74.4 - - - +
116D ASP* 1.3 60.8 + - - +
118D GLY* 2.6 28.8 + - - -
119D ILE 3.9 6.7 - - - +
120D LYS* 4.5 21.5 + - + +
232E GLU* 4.8 3.5 - - - +
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Residues in contact with ASP 116 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ARG* 3.1 24.4 + - - +
113D LYS* 4.2 7.1 - - - +
115D VAL* 1.3 82.1 - - - +
117D GLU* 1.3 59.4 + - + +
118D GLY 3.2 3.1 + - - -
229E SER* 5.5 2.5 - - - +
230E LYS 4.2 0.2 - - - +
231E GLY* 3.3 26.4 - - - -
232E GLU* 3.3 22.4 + - - +
233E THR* 4.7 10.0 + - - -
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Residues in contact with GLU 117 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113D LYS* 3.5 21.1 + - - +
114D LEU* 4.0 7.7 - - - +
115D VAL 3.1 0.8 - - - -
116D ASP* 1.3 78.6 - - + +
118D GLY* 1.3 60.1 + - - +
119D ILE* 3.4 14.2 + - + +
131D LYS* 3.3 43.7 + - + +
227E THR* 5.4 1.2 - - - +
228E LEU 4.1 3.0 - - - +
229E SER* 3.3 32.2 + - - +
230E LYS* 3.5 32.0 + - + +
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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