Contacts of the helix formed by residues 97 - 113 (chain D) in PDB entry 2ODE
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 97 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95D THR* 3.6 1.8 - - - +
96D ARG* 1.3 81.5 - - - +
98D THR* 1.3 53.5 + - - +
99D ALA* 3.6 7.6 + - - +
100D LYS* 3.5 41.2 + - - +
101D LEU* 2.7 37.4 + - - +
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Residues in contact with THR 98 (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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96D ARG 4.2 1.8 + - - -
97D SER* 1.3 71.8 + - - +
99D ALA* 1.3 58.3 + - - +
101D LEU* 3.2 10.6 + - + +
102D VAL* 2.9 42.9 + - + +
138D PRO 6.1 1.3 - - - +
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Residues in contact with ALA 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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97D SER* 3.3 8.1 + - - +
98D THR* 1.3 78.6 - - - +
100D LYS* 1.3 58.4 + - + +
102D VAL* 3.6 5.4 + - - +
103D SER* 3.1 27.6 + - - -
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Residues in contact with LYS 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95D THR* 3.7 18.2 - - + -
97D SER* 3.3 24.0 + - - +
99D ALA* 1.3 74.7 - - + +
101D LEU* 1.3 60.2 + - - +
103D SER* 3.6 5.3 - - - -
104D LYS* 2.8 46.7 + - + +
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Residues in contact with LEU 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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92D PHE* 3.3 31.0 - - + -
95D THR* 3.6 14.1 - - + +
96D ARG 6.3 0.4 - - - -
97D SER 2.7 22.7 + - - +
98D THR* 3.5 11.0 - - + +
100D LYS* 1.3 73.4 - - - +
102D VAL* 1.3 62.2 + - + +
104D LYS* 4.6 0.4 - - - -
105D ALA* 2.9 26.9 + - - +
138D PRO* 3.5 37.5 - - + +
139D SER* 4.2 2.7 - - - -
140D LEU* 3.7 38.4 - - + +
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Residues in contact with VAL 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 THR* 2.9 36.7 + - + +
99D ALA* 4.0 5.6 - - - +
101D LEU* 1.3 75.3 - - + +
103D SER* 1.3 64.3 + - - +
105D ALA* 3.4 1.0 + - - +
106D HIS* 3.0 51.3 + - + +
138D PRO* 4.0 28.5 - - + +
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Residues in contact with SER 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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284A THR 4.9 3.9 + - - -
285A ILE* 5.2 5.2 + - - -
288A PRO* 3.5 30.5 - - - +
99D ALA 3.1 18.6 + - - -
100D LYS* 3.6 7.9 - - - -
101D LEU 3.3 0.2 - - - -
102D VAL* 1.3 75.6 - - - +
104D LYS* 1.3 59.1 + - - +
106D HIS* 3.2 7.6 + - - +
107D ARG* 2.9 35.6 + - - +
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Residues in contact with LYS 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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91D GLU* 2.8 42.6 + - - +
92D PHE* 3.8 13.2 - - + -
94D LYS 5.3 0.2 - - - -
95D THR* 2.7 41.1 + - - +
100D LYS* 2.8 32.8 + - + +
101D LEU 3.8 3.1 - - - +
103D SER* 1.3 70.6 + - - +
105D ALA* 1.3 58.5 + - - +
107D ARG* 3.2 11.6 + - - +
108D ILE* 2.9 40.2 + - + +
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Residues in contact with ALA 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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92D PHE* 3.7 16.1 - - + -
101D LEU 2.9 18.3 + - - +
102D VAL 3.7 4.5 - - - +
104D LYS* 1.3 75.9 - - - +
106D HIS* 1.3 58.0 + - - +
109D PHE* 3.0 28.1 + - - +
135D LEU* 3.5 21.1 - - + -
138D PRO* 4.1 11.2 - - + -
142D CYS* 4.7 1.3 - - - -
143D PHE* 3.4 25.2 - - + -
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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
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233A VAL* 5.7 4.7 - - + -
238A GLU 5.4 2.4 + - - -
239A GLU* 4.7 17.9 - - - +
102D VAL* 3.0 45.1 + - + +
103D SER* 3.7 5.6 - - - +
105D ALA* 1.3 76.7 - - - +
107D ARG* 1.3 61.8 + - + +
109D PHE* 3.8 2.0 - - - +
110D GLU* 3.0 39.4 + - - +
135D LEU* 3.5 45.2 + - + +
138D PRO* 4.6 2.0 - - + -
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Residues in contact with ARG 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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244A HIS* 5.6 11.7 - - + -
288A PRO* 3.7 24.8 - - + +
103D SER* 2.9 31.5 + - - +
104D LYS* 3.2 11.9 + - - +
106D HIS* 1.3 76.7 - - + +
108D ILE* 1.3 58.1 + - + +
110D GLU* 3.8 7.1 - - - +
111D GLU* 2.9 33.4 + - - +
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Residues in contact with ILE 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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85D PHE* 3.6 27.4 - - + -
88D ALA* 3.8 28.0 - - + +
89D CYS* 4.7 1.6 - - - +
92D PHE* 3.8 31.6 - - + -
104D LYS* 2.9 24.2 + - + +
107D ARG* 1.3 75.0 - - + +
109D PHE* 1.3 62.9 + - - +
111D GLU* 4.6 0.4 - - - -
112D PHE* 3.0 33.6 + - + +
113D VAL* 3.8 0.5 + - - +
143D PHE* 3.6 36.3 - - + -
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Residues in contact with PHE 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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239A GLU* 3.7 31.4 - - + +
105D ALA 3.0 18.6 + - - +
106D HIS 3.8 2.5 - - - +
108D ILE* 1.3 78.0 - - - +
110D GLU* 1.3 63.1 + - - +
113D VAL* 3.0 40.5 + - + -
114D ASP* 2.9 56.1 + - + -
128D ARG* 4.3 6.1 - - + -
131D THR* 4.0 12.1 - - + -
132D ARG* 3.7 44.0 - - + -
135D LEU* 3.5 20.9 - - + -
143D PHE* 4.6 3.1 - + + -
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Residues in contact with GLU 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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239A GLU 3.6 18.3 - - - +
240A MET* 3.6 22.5 - - - +
241A ASN* 3.0 26.2 + - - +
244A HIS* 3.0 31.9 + - - +
106D HIS* 3.0 33.4 + - + +
107D ARG* 3.9 6.9 - - - +
109D PHE* 1.3 79.1 - - - +
111D GLU* 1.3 55.4 + - - +
114D ASP* 4.6 8.6 - - - +
117D ALA* 3.2 23.2 - - - +
118D PRO* 3.6 5.1 - - - +
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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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107D ARG 2.9 19.9 + - - +
109D PHE 3.2 0.2 - - - -
110D GLU* 1.3 77.3 - - - +
112D PHE* 1.3 74.5 + - + +
117D ALA* 3.3 3.9 - - - +
118D PRO* 3.3 22.7 - - - +
119D ARG* 2.7 77.8 + - - +
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Residues in contact with PHE 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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81D GLU 4.0 4.0 - - - -
84D GLU* 3.8 25.8 - - + -
85D PHE* 3.6 61.5 - + + -
88D ALA* 4.1 14.1 - - + -
108D ILE* 3.0 24.3 + - + +
111D GLU* 1.3 89.5 - - + +
113D VAL* 1.3 60.4 + - + +
117D ALA* 3.8 6.1 - - - -
119D ARG* 3.4 49.4 - - + +
120D GLU* 3.2 1.7 - - - +
121D VAL* 2.8 33.7 + - + +
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Residues in contact with VAL 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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85D PHE* 3.8 31.2 - - + -
108D ILE 4.0 8.3 - - - +
109D PHE* 3.0 39.6 + - + +
112D PHE* 1.3 81.2 - - - +
114D ASP* 1.3 69.6 + - - +
120D GLU* 4.4 5.2 - - - +
121D VAL* 4.9 5.3 - - + +
123D ILE* 4.1 22.6 - - + +
128D ARG* 3.5 23.3 - - + -
131D THR* 4.1 11.7 - - + -
143D PHE* 4.4 8.5 - - + -
146D ALA* 5.3 0.4 - - + -
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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
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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