Contacts of the helix formed by residues 97 - 110 (chain A) in PDB entry 3DAE
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 GLN 97 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90A VAL* 3.1 50.1 + - + +
91A LEU* 3.4 43.4 - - - +
92A ALA 5.0 5.5 + - - +
98A GLY* 1.3 66.1 + - - +
99A ARG* 3.3 4.9 - - - +
100A ILE* 3.4 20.4 + - - +
101A GLU* 3.2 26.7 + - - +
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Residues in contact with GLY 98 (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 GLN* 1.3 79.9 - - - +
99A ARG* 1.3 62.4 + - - +
101A GLU* 3.8 5.2 + - - +
102A ARG* 3.3 21.4 + - - +
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Residues in contact with ARG 99 (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 GLN 3.3 2.3 - - - +
98A GLY* 1.3 77.0 - - - +
100A ILE* 1.3 61.8 + - + +
102A ARG* 3.3 25.4 + - - +
103A GLU* 2.9 32.7 + - + +
254B ASP* 3.1 37.9 + - - -
255B GLU* 6.1 1.0 - - - +
256B SER* 4.1 7.5 - - - +
259B VAL* 3.7 26.3 - - - +
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Residues in contact with ILE 100 (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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66A PHE* 5.9 6.1 - - + -
84A LYS* 6.0 4.5 - - - +
86A ILE* 3.8 39.5 - - + -
90A VAL* 3.5 32.8 - - + -
97A GLN* 3.4 13.0 + - - +
98A GLY 3.2 0.4 - - - -
99A ARG* 1.3 79.1 - - + +
101A GLU* 1.3 66.4 + - - +
102A ARG 3.1 0.9 - - - -
103A GLU* 3.4 8.1 + - + +
104A ILE* 3.1 31.2 + - + +
128A ILE* 4.8 15.7 - - + -
130A MET* 4.6 10.1 - - - -
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Residues in contact with GLU 101 (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 GLN* 3.2 24.8 + - - +
98A GLY* 3.8 6.0 + - - +
100A ILE* 1.3 78.3 - - - +
102A ARG* 1.3 54.0 + - - +
104A ILE* 3.8 11.2 - - + +
105A SER* 2.6 40.6 + - - -
123A LYS* 5.6 4.5 - - - +
128A ILE* 4.4 17.8 - - - +
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Residues in contact with ARG 102 (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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98A GLY 3.3 14.9 + - - +
99A ARG* 3.3 29.1 + - - +
101A GLU* 1.3 75.9 - - - +
103A GLU* 1.3 71.5 + - - +
105A SER* 3.0 6.8 + - - -
106A TYR* 2.8 69.5 + - + +
174A VAL 4.4 13.1 + - - +
175A HIS 5.4 0.4 + - - -
176A ARG* 4.5 13.9 - - - +
196A PHE 2.7 31.1 + - - -
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Residues in contact with GLU 103 (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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84A LYS* 5.9 4.5 - - - +
99A ARG* 2.9 21.1 + - + +
100A ILE* 3.4 13.0 - - + +
102A ARG* 1.3 79.2 + - - +
104A ILE* 1.3 52.9 + - - +
106A TYR* 3.0 5.9 + - - +
107A LEU* 2.7 52.5 + - - +
130A MET* 4.4 14.2 - - + +
194A ALA 4.8 1.4 - - - +
195A ASP 2.8 30.2 - - - +
196A PHE* 3.3 22.2 - - - +
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Residues in contact with ILE 104 (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 ILE* 3.1 21.8 + - + +
101A GLU* 3.8 12.8 - - - +
103A GLU* 1.3 78.1 - - - +
105A SER* 1.3 65.4 + - - +
108A ARG* 2.9 65.3 + - + +
118A LEU* 3.7 9.0 - - - +
121A VAL* 3.5 34.1 - - + -
123A LYS* 5.4 3.6 - - + +
128A ILE* 4.3 13.9 - - + -
130A MET* 3.7 23.5 - - + +
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Residues in contact with SER 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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101A GLU 2.6 29.4 + - - -
102A ARG* 3.0 12.5 + - - -
104A ILE* 1.3 76.9 - - - +
106A TYR* 1.3 67.6 + - - +
108A ARG* 3.2 11.2 + - - +
109A LEU* 3.0 25.5 + - - +
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Residues in contact with TYR 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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102A ARG* 2.8 70.8 + - + +
103A GLU* 3.0 5.6 + - - +
105A SER* 1.3 82.2 + - - +
107A LEU* 1.3 63.3 + - + +
109A LEU* 2.9 19.9 + - + +
110A LEU* 3.1 23.1 - - + +
172A LYS 5.1 1.6 + - - -
173A ILE* 3.4 52.1 - - + +
174A VAL 5.5 1.0 + - - -
196A PHE* 4.1 22.7 - + + -
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Residues in contact with LEU 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 GLU* 2.7 36.8 + - - +
106A TYR* 1.3 73.6 - - - +
108A ARG* 1.3 61.0 + - - +
110A LEU* 3.4 19.9 - - - +
111A ARG* 3.9 11.6 + - - -
115A ILE* 4.7 3.6 - - + -
116A ILE* 3.2 45.9 - - + +
118A LEU* 3.7 27.0 + - + +
130A MET* 4.2 21.8 - - + -
132A ILE* 5.0 11.2 - - + -
194A ALA 5.5 2.2 - - - +
195A ASP 5.5 0.4 - - - +
196A PHE* 4.2 22.7 - - + -
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Residues in contact with ARG 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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104A ILE* 2.9 46.9 + - - +
105A SER* 3.4 11.4 - - - +
107A LEU* 1.3 77.3 - - - +
109A LEU* 1.3 61.7 + - - +
110A LEU 3.4 0.3 + - - -
111A ARG* 3.5 30.7 + - - +
118A LEU* 3.6 13.7 - - + -
121A VAL* 4.0 14.5 + - - +
123A LYS* 3.2 29.5 - - - +
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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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105A SER 3.0 12.0 + - - +
106A TYR* 2.9 16.4 + - + +
108A ARG* 1.3 77.9 - - - +
110A LEU* 1.3 63.9 + - + +
111A ARG* 3.8 4.4 + - - +
167A TYR* 3.9 9.7 + - - -
171A HIS* 4.1 40.2 - - + +
173A ILE* 4.9 8.5 - - + -
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Residues in contact with LEU 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 TYR* 3.1 20.7 + - - +
107A LEU* 3.4 14.4 - - - +
108A ARG 3.3 1.2 - - - -
109A LEU* 1.3 83.6 - - + +
111A ARG* 1.3 67.8 + - - +
112A HIS 3.8 2.5 + - - -
115A ILE* 4.3 18.4 - - + +
116A ILE 4.9 7.1 - - - +
117A LYS* 5.7 1.2 - - - +
167A TYR* 3.6 28.9 - - + -
168A CYS* 4.4 9.4 - - - -
171A HIS* 4.1 20.6 - - + -
173A ILE* 3.2 34.5 - - + -
196A PHE* 3.7 21.5 - - + -
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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