Contacts of the helix formed by residues 104 - 118 (chain A) in PDB entry 3DBI
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 SER 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 LYS 3.9 0.2 - - - -
103A HIS* 1.3 79.6 - - - +
105A ALA* 1.3 58.7 + - - +
106A GLU* 3.6 8.4 + - - +
107A GLU* 2.8 34.7 + - - +
108A GLU* 3.0 31.5 + - - +
129A PHE* 3.6 16.0 - - - -
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Residues in contact with ALA 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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104A SER* 1.3 73.9 - - - +
106A GLU* 1.3 59.6 + - - +
108A GLU* 3.5 1.5 + - - +
109A ARG* 3.1 27.5 + - - +
129A PHE* 3.4 23.6 - - + +
130A LEU* 3.7 30.4 - - + +
131A SER 5.2 0.2 - - - +
134A GLU* 4.8 8.1 - - - +
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Residues in contact with GLU 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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104A SER* 3.3 7.9 + - - +
105A ALA* 1.3 78.3 - - - +
107A GLU* 1.3 60.2 + - + +
109A ARG* 3.2 11.6 + - + +
110A GLN* 2.9 54.1 + - + +
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Residues in contact with GLU 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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100A ASP 4.3 1.9 - - - +
101A GLY* 3.5 17.2 - - - +
102A LYS* 3.4 33.4 - - + +
103A HIS* 3.2 10.8 + - - +
104A SER* 2.8 35.9 + - - +
106A GLU* 1.3 80.4 - - + +
108A GLU* 1.3 57.1 + - - +
110A GLN* 3.4 19.9 + - - +
111A ALA* 3.1 27.2 + - - +
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Residues in contact with GLU 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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67A VAL* 5.2 0.2 - - - -
69A THR* 3.4 22.8 - - + +
70A ASN 5.0 1.0 + - - -
101A GLY* 3.4 23.3 - - - +
102A LYS 5.1 1.3 - - - +
104A SER 3.0 20.3 + - - +
105A ALA 3.8 5.2 - - - +
106A GLU 3.3 0.2 - - - -
107A GLU* 1.3 73.0 - - - +
109A ARG* 1.3 65.1 + - - +
111A ALA* 3.5 3.5 + - - +
112A ILE* 3.3 26.9 + - - +
125A ILE* 4.6 5.5 - - + +
127A PRO* 3.6 5.3 - - - +
128A ARG* 3.1 27.9 + - - +
129A PHE* 3.3 17.4 + - + -
130A LEU* 2.9 37.4 + - + +
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Residues in contact with ARG 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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105A ALA 3.1 14.5 + - - +
106A GLU* 3.4 13.7 - - - +
108A GLU* 1.3 74.8 - - - +
110A GLN* 1.3 59.2 + - + +
112A ILE* 3.3 5.8 + - - +
113A GLN* 2.9 32.7 + - + +
130A LEU* 4.0 14.9 - - + +
134A GLU* 2.8 44.3 + - - +
137A ASP* 5.0 7.5 + - - +
138A ILE* 3.7 34.5 - - + +
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Residues in contact with GLN 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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102A LYS* 6.0 1.6 - - - -
106A GLU* 2.9 46.8 + - + +
107A GLU* 3.6 19.2 - - - +
108A GLU 3.4 0.2 - - - -
109A ARG* 1.3 74.4 - - + +
111A ALA* 1.3 52.2 + - - +
113A GLN* 3.2 8.1 + - - +
114A TYR* 2.8 36.3 + - - +
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Residues in contact with ALA 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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67A VAL* 4.0 11.4 - - + -
99A ALA* 3.8 19.3 - - + +
100A ASP 3.7 19.1 - - - +
101A GLY* 3.9 9.4 - - - -
107A GLU 3.1 16.8 + - - +
108A GLU 3.7 6.1 - - - +
109A ARG 3.3 0.2 - - - -
110A GLN* 1.3 73.6 - - - +
112A ILE* 1.3 65.0 + - - +
114A TYR* 3.4 6.0 + - - +
115A LEU* 3.2 27.9 + - - +
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Residues in contact with ILE 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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67A VAL* 4.0 18.4 - - + -
108A GLU 3.3 14.6 + - - +
109A ARG* 3.3 7.6 + - - +
111A ALA* 1.3 74.9 - - - +
113A GLN* 1.3 57.9 + - - +
115A LEU* 3.3 4.7 + - - +
116A LEU* 2.9 43.9 + - + +
123A ILE* 3.7 18.5 - - + +
125A ILE* 3.9 21.3 - - + -
130A LEU* 3.8 23.1 - - + -
135A ILE* 4.9 4.3 - - + -
138A ILE* 4.1 24.0 - - + -
146A ILE* 4.5 14.8 - - + -
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Residues in contact with GLN 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 ARG* 2.9 22.4 + - + +
110A GLN* 3.5 9.2 - - + +
112A ILE* 1.3 77.6 - - - +
114A TYR* 1.3 51.5 + - - +
116A LEU* 3.2 22.7 + - - +
117A ASP* 2.8 70.3 + - - +
138A ILE* 5.4 2.6 - - - +
142A HIS* 4.4 15.0 + - - -
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Residues in contact with TYR 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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97A LEU* 4.8 1.5 - - + +
98A LEU 4.3 7.9 - - - -
99A ALA* 3.8 26.7 - - + -
110A GLN 2.8 20.2 + - - +
111A ALA* 3.7 4.9 - - - +
112A ILE 3.3 0.2 - - - -
113A GLN* 1.3 70.8 - - - +
115A LEU* 1.3 66.1 + - + +
117A ASP* 3.4 9.5 + - + +
118A LEU* 3.1 50.7 + - + +
90C GLU* 6.6 0.9 - - + -
94C ARG 4.2 5.2 + - - -
95C GLN* 3.3 36.8 + - + +
96C LEU 5.1 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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65A GLY* 4.0 3.8 - - - -
66A LEU 3.8 21.1 - - - +
67A VAL* 4.0 16.8 - - + -
97A LEU* 3.9 26.0 - - + +
99A ALA* 3.8 24.7 - - + -
111A ALA 3.2 16.0 + - - +
112A ILE 3.3 5.6 + - - +
114A TYR* 1.3 83.1 - - + +
116A LEU* 1.3 64.2 + - - +
118A LEU* 3.5 5.1 + - + -
119A ARG 3.1 4.5 + - - -
120A CYS* 3.1 45.0 + - - -
123A ILE* 3.8 20.6 - - + -
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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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112A ILE* 2.9 34.4 + - + +
113A GLN* 3.2 22.6 + - - +
115A LEU* 1.3 77.3 - - - +
117A ASP* 1.3 57.7 + - - +
119A ARG* 3.1 21.5 + - - +
120A CYS 4.9 0.9 - - - +
123A ILE* 3.7 17.7 - - + -
138A ILE* 4.1 6.5 - - + -
142A HIS* 3.6 45.5 - - + +
144A GLN* 3.8 42.7 + - + +
146A ILE* 4.7 4.7 - - + -
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Residues in contact with ASP 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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113A GLN* 2.8 49.3 + - - +
114A TYR* 3.6 9.7 - - + +
115A LEU 3.3 0.2 - - - -
116A LEU* 1.3 75.9 - - - +
118A LEU* 1.3 61.9 + - + +
119A ARG* 3.1 13.4 + - - -
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Residues in contact with LEU 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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61A THR* 4.7 3.3 + - - +
63A THR* 5.8 1.7 - - - +
97A LEU* 4.2 13.2 - - + -
114A TYR* 3.1 58.3 + - + +
115A LEU* 3.9 8.5 - - + +
116A LEU 3.3 0.2 - - - -
117A ASP* 1.3 75.2 - - + +
119A ARG* 1.3 78.4 + - - +
120A CYS* 4.9 4.4 - - - +
95C GLN* 3.6 32.8 - - + +
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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