Contacts of the helix formed by residues 98 - 112 (chain D) in PDB entry 4KZX
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 ALA 98 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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96D LEU 3.4 2.2 + - - -
97D CYS* 1.3 72.6 - - - +
99D ILE* 1.3 63.1 + - + +
100D ALA 3.3 0.4 - - - -
101D GLN* 3.1 5.1 + - - +
102D ALA* 2.9 23.6 + - - +
169D ASP* 3.9 38.5 + - - +
170D THR 4.2 11.0 - - - -
171D ALA* 4.3 3.6 - - + -
186D VAL* 4.1 15.0 - - + +
188D ILE* 2.9 27.5 - - + +
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Residues in contact with ILE 99 (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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34D TYR* 2.7 18.4 - - + +
35D SER* 2.6 50.0 - - - +
97D CYS* 1.7 42.0 + - - -
98D ALA* 1.3 73.0 - - + +
100D ALA* 1.3 60.7 + - - +
102D ALA* 3.3 3.0 + - - +
103D GLU* 3.1 28.1 + - + +
169D ASP* 5.5 5.6 - - - +
170D THR 5.3 1.8 - - - +
171D ALA* 4.1 21.1 - - + -
173D ARG* 4.1 22.2 - - - +
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Residues in contact with ALA 100 (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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33D GLY* 5.6 11.7 - - - +
34D TYR 5.9 0.7 - - - -
35D SER* 6.0 0.2 - - - -
53D THR* 6.2 3.1 - - + +
94D ARG* 3.6 29.8 - - + +
97D CYS* 2.4 38.5 + - + +
99D ILE* 1.3 69.0 - - - +
101D GLN* 1.3 61.6 + - - +
103D GLU* 3.5 6.1 + - - +
104D SER* 2.9 26.5 + - - -
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Residues in contact with GLN 101 (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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94D ARG* 2.2 41.3 + - - +
95D GLY* 3.8 10.7 - - - +
98D ALA* 3.1 7.2 + - - +
100D ALA* 1.3 78.3 + - - +
102D ALA* 1.3 65.0 + - - +
104D SER* 3.1 25.6 + - - -
105D LEU* 3.2 7.3 + - - +
122D VAL* 3.6 31.1 - - + +
125D PHE* 4.2 11.0 - - - +
126D ILE* 3.7 26.7 - - + +
186D VAL* 4.2 14.8 - - + +
188D ILE* 4.1 11.0 - - + -
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Residues in contact with ALA 102 (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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98D ALA 2.9 14.0 + - - +
99D ILE* 3.7 7.0 - - - +
101D GLN* 1.3 72.3 - - - +
103D GLU* 1.3 67.5 + - - +
104D SER 2.9 2.0 - - - -
105D LEU* 2.8 15.3 + - - +
106D ARG* 3.1 10.0 + - - +
171D ALA* 4.5 8.1 - - + +
173D ARG* 3.8 26.3 - - + +
184D ILE* 4.6 7.9 - - + +
186D VAL* 3.5 26.9 - - + +
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Residues in contact with GLU 103 (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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26D THR* 5.1 4.6 - - - +
30D ALA* 4.3 28.9 - - + +
33D GLY* 5.5 7.9 - - - -
34D TYR 5.6 6.7 - - - +
99D ILE* 3.1 14.5 + - + +
100D ALA* 3.7 7.2 - - - +
102D ALA* 1.3 77.0 - - - +
104D SER* 1.3 61.9 + - - +
106D ARG* 3.1 30.7 + - - +
107D TYR* 2.9 37.8 + - + -
173D ARG* 2.8 41.4 + - - +
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Residues in contact with SER 104 (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 ALA 2.9 17.7 + - - -
101D GLN* 3.1 23.3 + - - -
102D ALA 2.9 0.6 - - - -
103D GLU* 1.3 78.4 - - - +
105D LEU* 1.3 57.5 + - - +
107D TYR* 3.1 10.1 + - - +
108D LYS* 2.8 43.5 + - - +
122D VAL* 5.0 4.3 - - - -
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Residues in contact with LEU 105 (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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101D GLN 3.2 7.1 + - - +
102D ALA* 2.8 13.1 + - - +
104D SER* 1.3 72.0 - - - +
106D ARG* 1.3 67.8 + - - +
108D LYS* 3.0 7.0 + - + -
109D LEU* 2.9 42.6 + - + +
118D ALA* 3.7 30.3 - - + -
119D CYS* 4.8 8.5 - - - -
122D VAL* 5.2 6.3 - - + +
136D VAL* 4.4 9.4 - - + -
138D VAL* 4.1 15.0 - - + -
184D ILE* 2.6 52.0 - - + -
186D VAL* 5.9 0.7 - - + -
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Residues in contact with ARG 106 (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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30D ALA* 5.8 5.7 - - - +
102D ALA 3.1 8.0 + - - +
103D GLU* 3.1 30.6 + - - +
105D LEU* 1.3 76.9 - - - +
107D TYR* 1.3 70.8 + - + +
109D LEU* 3.6 2.5 + - - +
110D LEU* 2.9 45.3 + - + +
173D ARG* 5.8 9.5 - - + +
174D HIS 4.2 8.9 + - - -
175D VAL* 3.8 35.2 - - + +
176D LEU* 3.5 30.8 + - - +
184D ILE* 5.1 4.9 - - + +
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Residues in contact with TYR 107 (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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30D ALA* 3.0 18.7 + - + +
31D GLU* 2.8 47.0 + - + +
54D ARG* 3.4 30.5 - - - -
103D GLU* 2.9 25.4 + - + +
104D SER* 3.4 11.2 - - - +
106D ARG* 1.3 90.1 - - + +
108D LYS* 1.3 59.9 + - + +
110D LEU* 3.7 12.7 - - + +
111D GLY* 2.8 27.4 + - - -
113D LEU* 4.7 0.2 - - - +
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Residues in contact with LYS 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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104D SER* 2.8 32.0 + - - +
105D LEU* 3.0 5.8 + - - +
107D TYR* 1.3 72.7 - - + +
109D LEU* 1.3 51.9 - - - +
111D GLY 3.1 0.3 + - - -
113D LEU* 1.4 69.4 - - + +
117D ARG 5.2 0.7 - - - -
118D ALA* 3.8 38.6 - - + +
121D GLY* 5.4 3.4 - - - -
122D VAL* 4.0 24.6 - - + +
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Residues in contact with LEU 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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105D LEU* 2.9 47.5 + - + +
106D ARG* 4.0 3.1 - - - +
108D LYS* 1.3 73.0 - - - +
110D LEU* 1.3 58.7 + - - +
112D GLY* 2.8 24.1 + - - -
113D LEU* 3.5 4.9 - - - +
114D ALA 3.6 24.9 - - - +
115D VAL* 4.9 8.1 - - + -
118D ALA* 4.2 3.6 - - + -
119D CYS* 6.3 0.2 - - - -
138D VAL* 5.3 7.0 - - + -
142D LEU* 6.1 5.2 - - + -
175D VAL* 4.9 15.9 - - + -
177D LEU* 5.3 8.7 - - + -
178D ARG* 5.3 5.4 + - - -
182D LEU* 5.2 8.5 - - + -
184D ILE* 4.0 15.3 - - + -
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Residues in contact with LEU 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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106D ARG* 2.9 38.6 + - + +
107D TYR* 3.8 13.7 - - + +
109D LEU* 1.3 76.1 - - - +
111D GLY* 1.3 65.9 + - - +
112D GLY* 3.2 0.7 + - - -
175D VAL* 5.6 1.5 - - + +
176D LEU 5.7 4.9 - - - +
177D LEU* 5.2 6.7 - - + +
178D ARG* 4.8 20.2 + - - +
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Residues in contact with GLY 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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107D TYR 2.8 16.0 + - - -
109D LEU 3.0 0.6 - - - -
110D LEU* 1.3 82.0 - - - +
112D GLY* 1.3 64.5 + - - +
113D LEU* 3.3 8.1 - - - -
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Residues in contact with GLY 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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109D LEU 2.8 11.4 + - - -
110D LEU 3.0 0.8 - - - -
111D GLY* 1.3 77.7 - - - +
113D LEU* 1.3 92.9 + - - +
117D ARG* 5.1 1.0 + - - -
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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