Contacts of the helix formed by residues 104 - 122 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102A GLY 3.3 2.0 + - - -
103A LYS* 1.3 71.6 - - - +
105A TYR* 1.3 65.7 + - - +
106A HIS* 2.7 38.8 + - - +
107A ASP* 3.0 32.3 + - - +
108A VAL 3.2 7.8 + - - -
289A HIS* 2.8 21.7 + - - +
290A VAL 4.2 2.4 - - - +
291A SER* 3.2 32.8 - - - +
294A TRP* 5.8 2.9 - - - +
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Residues in contact with TYR 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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99A ALA* 3.9 13.9 + - + -
103A LYS 3.2 6.7 + - - -
104A ASP* 1.3 75.5 + - - +
106A HIS* 1.3 81.6 + + - +
108A VAL* 4.3 7.6 - - - -
109A LEU* 2.8 36.0 + - + +
133A VAL* 3.9 20.4 - - + -
134A ASP* 3.0 31.7 + - + +
168A TYR* 3.5 61.6 + + + -
291A SER* 4.0 11.0 - - - -
503A B12 3.7 29.9 - - + +
504A GOL 3.9 5.0 + - - -
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Residues in contact with HIS 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104A ASP* 2.7 31.9 + - - +
105A TYR* 1.3 104.1 + + - +
107A ASP* 1.3 60.2 + - - +
110A ARG* 3.1 31.9 + - - +
133A VAL* 3.5 37.1 - - + +
134A ASP* 2.7 29.1 + - + -
135A THR* 4.0 14.7 - - + +
291A SER* 4.7 5.8 - - - -
294A TRP* 6.1 7.4 - + + -
504A GOL 5.1 4.4 - - - -
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Residues in contact with ASP 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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103A LYS* 3.6 26.7 + - - +
104A ASP* 3.0 28.7 + - - +
106A HIS* 1.3 77.9 - - - +
108A VAL* 1.3 65.8 + - - +
110A ARG* 4.0 3.9 - - - +
111A GLU* 3.1 24.3 + - - +
289A HIS* 5.2 6.1 + - - +
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Residues in contact with VAL 108 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.2 7.0 - - + -
103A LYS* 3.7 39.5 - - + +
104A ASP 3.2 2.7 + - - +
105A TYR* 3.3 7.2 + - - +
107A ASP* 1.3 79.3 - - - +
109A LEU* 1.3 70.7 + - + +
111A GLU* 3.2 11.5 + - - +
112A LYS* 3.3 16.5 + - - +
260A GLU* 3.6 39.9 - - + +
261A MET* 4.1 22.7 - - + -
505A PO4 4.0 9.6 - - - +
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Residues in contact with LEU 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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73A ILE* 4.3 6.1 - - + +
75A LEU* 4.1 25.4 - - + -
105A TYR* 2.8 24.5 + - + +
108A VAL* 1.3 87.8 - - + +
110A ARG* 1.3 61.5 + - - +
112A LYS* 3.3 7.3 + - - +
113A LEU* 3.0 28.2 + - - +
133A VAL* 4.0 13.2 - - + -
168A TYR* 3.6 53.6 - - + +
169A LEU 3.6 9.0 - - - +
170A ALA* 3.6 24.7 - - + +
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Residues in contact with ARG 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 HIS 3.1 21.3 + - - +
107A ASP* 4.0 4.5 - - - +
109A LEU* 1.3 77.7 - - - +
111A GLU* 1.3 53.9 + - - +
113A LEU* 3.3 15.7 + - - -
114A ASP* 2.7 60.0 + - - +
117A GLU* 4.8 6.3 + - - -
131A SER* 3.5 37.8 + - - +
132A MET* 4.6 4.0 - - - +
133A VAL* 4.3 10.1 - - + +
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Residues in contact with GLU 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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103A LYS* 4.8 9.2 - - - +
107A ASP 3.1 18.3 + - - +
108A VAL* 3.2 6.2 + - - +
110A ARG* 1.3 78.0 - - - +
112A LYS* 1.3 89.5 + - - +
114A ASP* 3.4 10.6 + - + +
115A LEU* 3.2 44.0 + - - +
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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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17A ILE* 2.7 47.7 + - + +
19A VAL* 4.3 7.4 - - + -
73A ILE* 4.3 13.2 - - + -
75A LEU* 4.5 17.9 - - + -
108A VAL* 3.5 16.2 - - - +
109A LEU* 3.3 7.6 + - - +
110A ARG 3.2 0.2 - - - -
111A GLU* 1.3 94.7 + - - +
113A LEU* 1.3 60.6 + - - +
115A LEU* 3.2 8.8 + - + +
116A LEU* 3.0 31.9 + - - +
260A GLU* 5.2 0.4 - - - -
505A PO4 2.6 40.5 + - - -
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Residues in contact with LEU 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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73A ILE* 3.9 29.8 - - + -
109A LEU 3.0 22.1 + - - +
110A ARG* 3.7 14.1 - - - +
112A LYS* 1.3 73.8 - - - +
114A ASP* 1.3 65.6 + - - +
116A LEU* 3.1 10.1 + - + +
117A GLU* 2.9 25.7 + - - +
131A SER* 3.8 26.2 - - - +
132A MET 3.6 27.4 - - - +
133A VAL* 4.7 0.9 - - + -
170A ALA* 3.8 7.9 - - + -
171A GLU* 3.9 22.2 - - - +
172A MET* 4.2 13.3 - - + +
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Residues in contact with ASP 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 ARG* 2.7 61.0 + - - +
111A GLU* 3.5 9.7 - - + +
113A LEU* 1.3 72.6 - - - +
115A LEU* 1.3 56.9 + - + +
117A GLU* 3.6 15.9 + - - +
118A ASP* 3.0 27.7 + - - +
131A SER* 5.6 0.2 - - - -
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Residues in contact with LEU 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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13A TYR* 3.6 22.6 + - - +
17A ILE* 3.8 37.0 - - + -
111A GLU* 3.2 39.8 + - - +
112A LYS* 3.2 10.2 + - + +
113A LEU 3.1 0.8 - - - -
114A ASP* 1.3 74.8 - - + +
116A LEU* 1.3 60.4 + - - +
118A ASP* 3.4 6.6 + - + +
119A PHE* 3.0 27.9 + - - +
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Residues in contact with LEU 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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10A LEU* 3.9 19.9 - - + +
13A TYR* 3.9 19.1 - - + -
14A ALA* 4.0 21.1 - - + -
17A ILE* 4.0 13.0 - - + -
19A VAL* 4.8 4.9 - - + -
22A ILE* 4.6 6.5 - - + -
71A VAL* 5.0 2.2 - - + -
73A ILE* 3.8 28.3 - - + -
112A LYS 3.0 17.0 + - - +
113A LEU* 3.1 15.0 + - + +
115A LEU* 1.3 75.7 - - - +
117A GLU* 1.3 63.4 + - - +
119A PHE* 3.3 6.8 - - - +
120A LEU* 3.2 25.5 + - - +
172A MET* 4.1 19.3 - - + -
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Residues in contact with GLU 117 (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 ARG* 4.8 6.4 + - - -
113A LEU 2.9 14.1 + - - +
114A ASP* 3.7 21.8 - - - +
116A LEU* 1.3 76.2 - - - +
118A ASP* 1.3 58.8 + - - +
120A LEU* 3.1 5.6 + - - +
121A LYS* 2.9 51.5 + - + +
129A THR* 3.4 22.5 + - - +
131A SER* 4.6 7.2 + - - +
172A MET* 4.0 18.0 - - - -
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Residues in contact with ASP 118 (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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114A ASP 3.0 17.3 + - - +
115A LEU* 4.0 7.0 - - + +
116A LEU 3.4 0.2 - - - -
117A GLU* 1.3 74.6 - - + +
119A PHE* 1.3 65.0 + - - +
121A LYS* 4.2 9.1 - - - +
122A SER* 3.0 31.3 + - - -
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Residues in contact with PHE 119 (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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6A LEU* 4.0 15.0 - - + -
9A GLU* 3.8 24.2 - - + -
10A LEU* 3.7 35.4 - - + -
13A TYR* 3.6 39.9 - + + -
115A LEU 3.0 13.7 + - - +
116A LEU 3.3 8.5 - - - +
118A ASP* 1.3 77.4 - - - +
120A LEU* 1.3 65.9 + - + +
122A SER* 2.8 22.9 + - - -
123A LYS* 3.4 42.8 - - - +
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Residues in contact with LEU 120 (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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6A LEU* 3.9 23.6 - - + -
10A LEU* 4.6 10.8 - - + -
116A LEU 3.2 7.8 + - - +
117A GLU 3.1 6.7 + - - +
119A PHE* 1.3 90.6 - - + +
121A LYS* 1.3 66.8 + - - +
122A SER 3.1 1.6 - - - -
123A LYS* 3.1 20.9 + - - +
124A HIS 3.6 1.9 + - - -
127A ILE* 3.5 25.2 - - + +
129A THR* 4.3 8.5 - - + -
172A MET* 3.5 31.9 - - + -
174A THR* 4.2 8.1 - - + -
176A ILE* 3.8 28.9 - - + -
178A PHE* 4.5 5.4 - - + -
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Residues in contact with LYS 121 (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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117A GLU* 2.9 40.0 + - + +
118A ASP* 3.9 12.8 - - - +
120A LEU* 1.3 76.8 - - - +
122A SER* 1.3 61.6 + - - +
123A LYS 3.3 0.7 + - - +
124A HIS 3.9 15.7 - - - -
127A ILE* 4.1 20.8 + - + +
128A ARG* 4.4 1.4 - - - +
129A THR* 2.8 45.0 + - + +
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Residues in contact with SER 122 (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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118A ASP* 3.0 19.6 + - - -
119A PHE* 2.8 21.0 + - - -
121A LYS* 1.3 75.8 - - - +
123A LYS* 1.3 67.4 + - - +
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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
------------------------------------------------------------
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