Contacts of the helix formed by residues 104 - 122 (chain D) in PDB entry 5D0A
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 ASP 104 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102D GLY 3.4 0.8 + - - -
103D LYS* 1.3 71.9 - - - +
105D TYR* 1.3 64.7 + - - +
106D HIS* 2.6 41.1 + - - +
107D ASP* 3.0 32.3 + - - +
108D VAL* 3.2 8.8 + - - +
288D GLY 5.9 0.2 - - - +
289D HIS* 2.8 21.3 + - - +
290D VAL 4.0 2.6 - - - +
291D SER* 3.2 32.3 - - - +
294D TRP* 5.9 2.6 - - - +
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Residues in contact with TYR 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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99D ALA* 4.0 13.6 + - + -
103D LYS 3.2 6.3 + - - -
104D ASP* 1.3 74.8 + - - +
106D HIS* 1.3 82.9 + + - +
108D VAL* 3.7 8.3 - - - -
109D LEU* 2.9 36.3 + - + +
133D VAL* 3.8 21.1 - - + -
134D ASP* 3.0 31.7 + - + -
168D TYR* 3.4 62.4 + + + -
261D MET* 5.9 0.2 - - - -
291D SER* 4.1 10.1 - - - -
503D B12 3.8 29.0 - - + +
504D GOL 3.9 5.2 + - - -
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Residues in contact with HIS 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104D ASP* 2.6 32.1 + - - +
105D TYR* 1.3 104.1 + + - +
107D ASP* 1.3 60.0 + - - +
110D ARG* 3.2 31.2 + - - +
133D VAL* 3.5 38.4 - - + +
134D ASP* 2.8 25.8 + - + -
135D THR* 3.8 15.5 - - + +
291D SER* 4.5 7.6 - - - -
294D TRP* 5.9 8.3 - + + -
504D GOL 4.9 5.3 + - - -
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Residues in contact with ASP 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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190C SER* 4.6 19.8 + - - -
103D LYS* 3.6 24.4 + - + +
104D ASP* 3.0 29.3 + - - +
106D HIS* 1.3 78.5 - - - +
108D VAL* 1.3 64.6 + - - +
110D ARG* 4.0 4.1 - - - +
111D GLU* 3.1 23.4 + - - +
289D HIS* 5.1 2.1 - - - +
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Residues in contact with VAL 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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75D LEU* 4.1 11.4 - - + -
103D LYS* 3.7 38.4 - - + +
104D ASP 3.2 13.1 + - - +
105D TYR* 3.9 7.2 - - - +
107D ASP* 1.3 77.9 - - - +
109D LEU* 1.3 74.4 + - + +
111D GLU* 3.2 15.0 + - - +
112D LYS* 3.2 15.4 + - - +
260D GLU* 3.5 29.8 - - + +
261D MET* 4.2 11.4 - - + -
505D PO4 3.9 10.1 - - - +
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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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73D ILE* 4.3 4.8 - - + +
75D LEU* 4.1 29.4 - - + -
105D TYR* 2.9 22.7 + - + +
108D VAL* 1.3 86.5 - - + +
110D ARG* 1.3 60.5 + - - +
112D LYS* 3.2 7.8 + - - +
113D LEU* 2.9 33.7 + - - +
133D VAL* 4.1 8.7 - - + -
168D TYR* 3.7 39.5 - - + +
169D LEU 3.7 17.7 - - - +
170D ALA* 3.6 31.4 - - + +
261D MET* 4.7 0.2 - - + -
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Residues in contact with ARG 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 HIS 3.2 21.2 + - - +
107D ASP* 4.0 4.7 - - - +
109D LEU* 1.3 74.2 - - - +
111D GLU* 1.3 60.5 + - - +
113D LEU* 4.2 17.3 - - - -
114D ASP* 2.8 60.8 + - - +
117D GLU* 5.0 5.1 + - - -
131D SER* 3.7 34.6 + - - +
132D MET* 4.8 3.2 - - - +
133D VAL* 4.4 9.9 - - + +
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Residues in contact with GLU 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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103D LYS* 4.6 9.0 - - - +
107D ASP 3.1 15.2 + - - +
108D VAL* 3.3 11.3 - - - +
109D LEU 3.2 0.2 - - - -
110D ARG* 1.3 79.0 - - - +
112D LYS* 1.3 97.2 + - - +
114D ASP* 3.6 8.9 - - - +
115D LEU* 3.2 39.1 + - - +
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Residues in contact with LYS 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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17D ILE* 2.7 49.2 + - + +
18D GLY* 5.1 0.4 - - - -
19D VAL* 4.6 5.6 - - + -
73D ILE* 4.4 13.2 - - + -
75D LEU* 4.5 18.8 - - + -
108D VAL* 3.2 15.5 + - - +
109D LEU* 3.2 9.5 + - - +
111D GLU* 1.3 95.4 + - - +
113D LEU* 1.3 65.6 + - - +
115D LEU* 3.2 7.6 + - + +
116D LEU* 3.0 26.8 + - - +
260D GLU* 5.3 0.2 - - - -
505D PO4 2.7 41.1 + - - -
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Residues in contact with LEU 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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71D VAL* 5.2 0.4 - - + +
73D ILE* 3.8 26.7 - - + -
109D LEU 2.9 21.3 + - - +
110D ARG* 3.9 15.0 - - - +
112D LYS* 1.3 75.2 - - - +
114D ASP* 1.3 57.3 - - - +
116D LEU* 3.1 10.8 + - + +
117D GLU* 2.8 30.5 + - - +
131D SER* 3.7 27.1 - - - +
132D MET 3.7 26.0 - - - +
133D VAL* 4.8 0.9 - - + +
170D ALA* 4.0 7.0 - - + -
171D GLU* 3.9 25.6 - - - +
172D MET* 4.1 13.7 - - + +
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Residues in contact with ASP 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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110D ARG* 2.8 58.7 + - - +
111D GLU* 3.6 8.3 - - - +
113D LEU* 1.3 76.6 - - - +
115D LEU* 1.3 57.1 + - + +
117D GLU* 3.4 15.5 + - - +
118D ASP* 3.0 28.4 + - - +
131D SER* 5.5 0.2 - - - -
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Residues in contact with LEU 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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13D TYR* 3.7 20.8 + - - +
17D ILE* 3.9 36.6 - - + -
111D GLU* 3.2 39.0 + - - +
112D LYS* 3.2 10.8 + - + +
114D ASP* 1.3 78.9 - - + +
116D LEU* 1.3 57.3 + - - +
118D ASP* 3.4 7.0 + - + +
119D PHE* 3.0 27.4 + - - +
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Residues in contact with LEU 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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10D LEU* 3.8 24.7 - - + -
13D TYR* 3.8 19.7 - - + -
14D ALA* 4.0 20.4 - - + -
17D ILE* 4.0 14.4 - - + -
19D VAL* 4.8 4.7 - - + -
22D ILE* 4.8 3.1 - - + -
71D VAL* 5.1 1.6 - - + -
73D ILE* 4.1 26.2 - - + -
112D LYS 3.0 17.9 + - - +
113D LEU* 3.5 14.6 - - + +
115D LEU* 1.3 73.0 - - - +
117D GLU* 1.3 67.5 + - - +
119D PHE* 3.3 6.4 + - - +
120D LEU* 3.2 26.0 + - - +
172D MET* 4.2 19.5 - - + -
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Residues in contact with GLU 117 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110D ARG* 5.0 4.2 + - - -
113D LEU 2.8 15.3 + - - +
114D ASP* 3.6 17.0 - - - +
116D LEU* 1.3 77.4 - - - +
118D ASP* 1.3 59.5 + - - +
120D LEU* 3.1 6.3 + - - +
121D LYS* 2.9 48.9 + - + +
129D THR* 3.4 27.5 + - - +
131D SER* 3.9 14.9 + - - -
172D MET* 4.1 13.4 - - - -
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Residues in contact with ASP 118 (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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114D ASP 3.0 17.8 + - - +
115D LEU* 3.8 7.9 - - + +
117D GLU* 1.3 77.6 - - - +
119D PHE* 1.3 57.0 + - - +
121D LYS* 4.2 9.3 - - - +
122D SER* 3.0 32.9 + - - -
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Residues in contact with PHE 119 (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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6D LEU* 4.1 8.7 - - + -
9D GLU* 3.8 29.8 - - + -
10D LEU* 3.8 34.8 - - + -
13D TYR* 3.6 37.5 - + + -
115D LEU 3.0 13.8 + - - +
116D LEU 3.3 7.6 - - - +
118D ASP* 1.3 78.3 - - - +
120D LEU* 1.3 79.9 + - + +
122D SER* 2.8 21.4 + - - -
123D LYS* 3.4 34.4 - - - +
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Residues in contact with LEU 120 (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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6D LEU* 3.9 30.3 - - + -
10D LEU* 4.7 10.3 - - + -
116D LEU 3.2 10.3 + - - +
117D GLU* 3.1 6.9 + - - +
119D PHE* 1.3 93.6 - - + +
121D LYS* 1.3 67.7 + - - +
122D SER 3.1 1.6 - - - -
123D LYS* 3.0 20.3 + - - +
124D HIS 3.9 1.7 + - - -
127D ILE* 3.7 26.5 - - + +
129D THR* 4.4 9.0 - - + -
172D MET* 3.7 33.7 - - + -
174D THR* 4.4 2.9 - - + -
176D ILE* 3.9 19.1 - - + -
178D PHE* 4.6 4.9 - - + -
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Residues in contact with LYS 121 (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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117D GLU* 2.9 37.7 + - + +
118D ASP* 3.9 12.3 - - - +
120D LEU* 1.3 77.0 - - + +
122D SER* 1.3 58.4 + - - +
123D LYS* 3.0 9.7 + - - -
124D HIS 4.1 8.6 + - - +
127D ILE* 3.9 21.6 + - - +
128D ARG* 4.4 1.2 - - - +
129D THR* 2.8 44.9 + - + +
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Residues in contact with SER 122 (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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118D ASP* 3.0 20.6 + - - -
119D PHE* 2.8 22.2 + - - -
121D LYS* 1.3 75.0 - - - +
123D LYS* 1.3 70.2 + - - +
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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