Contacts of the helix formed by residues 98 - 119 (chain A) in PDB entry 4OE5
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 98 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A THR* 4.4 14.5 - - + +
96A TYR 3.5 2.7 + - - +
97A ALA* 1.3 75.0 - - - +
99A LYS* 1.3 65.9 + - - +
100A SER* 3.9 12.7 - - - -
101A LEU* 3.0 23.8 + - - +
102A LEU* 3.0 25.1 + - - +
268A LEU* 4.3 7.6 - - + -
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Residues in contact with LYS 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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98A ASP* 1.3 75.6 - - - +
100A SER* 1.3 62.8 + - - +
102A LEU* 3.3 10.7 + - - +
103A ASN* 2.9 38.2 + - - +
268A LEU* 4.2 15.1 - - + +
272A THR* 4.6 12.3 - - + +
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Residues in contact with SER 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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98A ASP* 3.2 13.1 - - - -
99A LYS* 1.3 80.4 - - - +
101A LEU* 1.3 62.7 + - - +
103A ASN* 3.6 7.9 + - - +
104A LYS* 3.1 21.8 + - - +
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Residues in contact with LEU 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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66A CYS* 3.9 26.5 - - + -
68A VAL* 3.7 23.1 - - + -
73A VAL* 3.7 35.7 - - + -
75A THR* 4.3 7.0 - - + -
97A ALA* 4.0 19.5 - - + -
98A ASP* 3.0 22.2 + - - +
100A SER* 1.3 74.2 + - - +
102A LEU* 1.3 56.1 + - - +
104A LYS* 3.2 19.8 + - + +
105A ALA* 2.7 32.6 + - - +
262A VAL* 5.0 1.8 - - + -
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Residues in contact with LEU 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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97A ALA* 3.6 26.7 - - + +
98A ASP 3.0 24.6 + - - +
99A LYS* 3.7 4.0 - - - +
101A LEU* 1.3 75.4 - - - +
103A ASN* 1.3 58.3 + - - +
105A ALA* 3.1 6.3 + - - +
106A ILE* 2.8 34.6 + - - +
231A LEU* 3.9 7.7 - - + +
262A VAL* 3.9 18.6 - - + -
264A ALA* 4.6 3.4 - - + -
268A LEU* 4.6 4.5 - - + -
269A PHE* 3.8 41.5 - - + -
272A THR* 3.9 34.1 - - + +
273A VAL* 5.9 0.7 - - + -
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Residues in contact with ASN 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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99A LYS* 2.9 28.4 + - - +
100A SER* 3.8 7.1 - - - +
102A LEU* 1.3 74.8 - - - +
104A LYS* 1.3 64.0 + - - +
106A ILE* 3.2 13.6 + - - +
107A GLU* 2.9 24.9 + - - +
272A THR* 4.1 16.0 - - - +
276A SER* 5.9 1.2 - - - -
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Residues in contact with LYS 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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68A VAL* 4.3 18.8 - - + -
71A GLU* 2.8 34.7 + - - -
73A VAL* 4.9 6.6 - - - +
100A SER 3.1 17.9 + - - +
101A LEU* 3.2 18.1 + - + +
103A ASN* 1.3 76.6 - - - +
105A ALA* 1.3 62.1 + - - +
107A GLU* 3.5 5.6 + - - +
108A ALA* 3.1 25.3 + - + +
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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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68A VAL* 3.8 23.1 - - + -
101A LEU 2.7 17.4 + - - +
102A LEU* 3.4 10.1 - - - +
104A LYS* 1.3 70.9 - - - +
106A ILE* 1.3 65.5 + - - +
109A ALA* 3.0 22.3 + - - +
231A LEU* 4.0 12.8 - - + -
260A GLN* 3.2 31.8 + - + +
262A VAL* 4.3 5.6 - - + -
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Residues in contact with ILE 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 LEU 2.8 18.5 + - - +
103A ASN* 3.5 20.6 - - - +
105A ALA* 1.3 75.4 - - - +
107A GLU* 1.3 58.7 + - - +
109A ALA* 3.2 3.4 + - - +
110A LEU* 2.8 54.0 + - + +
203A PHE* 3.5 45.3 - - + -
231A LEU* 3.7 18.6 - - + -
272A THR* 4.8 10.8 - - + -
273A VAL* 5.0 1.8 - - + -
276A SER* 4.1 19.1 - - - +
278A HIS* 4.5 4.5 - - + -
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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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103A ASN 2.9 16.3 + - - +
104A LYS* 3.8 7.0 - - - +
106A ILE* 1.3 79.1 - - - +
108A ALA* 1.3 62.6 + - - +
110A LEU* 3.4 8.8 + - - +
111A ALA* 3.1 23.4 + - - +
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Residues in contact with ALA 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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68A VAL* 4.4 7.0 - - + -
104A LYS* 3.1 19.8 + - + +
107A GLU* 1.3 74.1 - - - +
109A ALA* 1.3 64.8 + - - +
111A ALA* 3.5 7.6 + - - +
112A ALA* 3.4 15.1 + - - +
257A ASN* 3.2 37.2 + - - +
260A GLN* 3.8 4.3 - - - +
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Residues in contact with ALA 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 3.0 18.8 + - - +
106A ILE* 3.7 3.6 - - - +
108A ALA* 1.3 73.2 - - - +
110A LEU* 1.3 67.9 + - - +
112A ALA* 3.0 10.9 + - - -
113A ARG* 3.0 11.1 + - - +
203A PHE* 5.0 1.8 - - + -
229A VAL* 3.6 27.5 - - + +
230A VAL 5.0 1.1 - - - +
231A LEU* 4.5 8.3 - - + -
257A ASN 3.4 22.2 - - - +
260A GLN* 3.6 12.2 - - + +
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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 ILE* 2.8 32.1 + - + +
107A GLU* 3.7 8.3 - - - +
109A ALA* 1.3 77.6 - - - +
111A ALA* 1.3 60.1 + - - +
112A ALA 3.3 0.9 + - - -
113A ARG* 3.4 21.1 + - - +
114A LYS* 4.5 2.4 + - - +
202A GLY* 3.6 40.2 - - - +
203A PHE* 3.9 8.7 - - + +
229A VAL* 4.8 0.4 - - + -
278A HIS* 3.3 46.2 - - + +
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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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107A GLU 3.1 16.8 + - - +
108A ALA* 3.9 7.9 - - - +
109A ALA 3.2 0.2 - - - -
110A LEU* 1.3 76.9 - - - +
112A ALA* 1.3 57.8 + - - +
113A ARG 3.5 0.2 - - - -
114A LYS* 5.0 2.8 + - - +
115A GLU* 5.6 0.9 + - - +
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Residues in contact with ALA 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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108A ALA 3.4 3.1 + - - +
109A ALA 3.0 5.8 + - - +
111A ALA* 1.3 76.4 - - - +
113A ARG* 1.3 66.7 + - - +
114A LYS 3.5 1.7 + - - -
115A GLU* 3.6 8.8 + - - +
116A TRP* 3.4 18.4 + - - +
229A VAL* 4.5 1.1 - - - -
256A PRO 4.1 8.1 - - - +
257A ASN* 3.7 35.9 - - + +
258A ILE* 4.3 6.4 - - + +
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Residues in contact with ARG 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 ALA 3.0 12.0 + - - +
110A LEU* 3.4 14.1 + - - +
112A ALA* 1.3 78.1 - - - +
114A LYS* 1.3 76.0 + - - +
116A TRP* 3.1 3.0 + - - +
117A ASP* 2.8 54.5 + - - +
199A GLY 4.5 2.2 + - - -
200A LEU 3.6 19.1 + - - -
201A GLU* 4.0 28.7 + - - +
202A GLY* 3.2 31.8 - - - +
227A GLY 4.2 11.0 + - - +
229A VAL* 3.7 24.7 - - + +
499B ASN* 4.2 12.3 - - - +
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Residues in contact with LYS 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 LEU 4.5 3.0 + - - +
111A ALA 5.0 2.6 + - - +
112A ALA 3.5 0.8 - - - -
113A ARG* 1.3 92.8 - - - +
115A GLU* 1.3 62.0 + - - +
117A ASP* 3.7 6.8 - - - +
118A LEU* 3.0 36.7 + - + +
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Residues in contact with GLU 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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112A ALA* 3.6 8.1 + - - +
113A ARG 3.3 0.6 - - - -
114A LYS* 1.3 77.8 - - - +
116A TRP* 1.3 57.6 + - - +
118A LEU* 3.3 8.0 + - - +
119A LYS* 3.0 26.2 + - - +
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Residues in contact with TRP 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 ALA 3.4 5.3 + - - +
113A ARG* 3.1 6.9 + - - +
115A GLU* 1.3 74.7 - - - +
117A ASP* 1.3 61.8 + - - +
119A LYS* 3.2 19.0 + - + +
124A ARG* 2.9 51.8 + - + -
127A ILE* 3.6 25.4 - - + -
128A PHE* 4.5 4.3 - + - -
224A ALA 2.8 30.7 + - - -
227A GLY* 3.5 21.6 - - - -
228A ASN 3.3 22.6 + - - -
229A VAL* 4.6 1.3 - - + -
254A LEU* 3.7 20.2 - - + -
255A PRO* 3.6 33.0 - - + -
258A ILE* 3.4 32.7 - - + +
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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 ARG* 2.8 38.9 + - - +
114A LYS* 3.7 5.9 - - - +
116A TRP* 1.3 72.9 - - - +
118A LEU* 1.3 59.8 + - - +
119A LYS 3.6 0.9 - - - +
124A ARG* 2.8 23.0 + - - +
197A TYR 4.6 1.0 - - - +
198A ARG* 3.9 0.7 - - - +
199A GLY* 3.0 30.8 + - - +
227A GLY* 3.7 15.7 + - - +
498B ARG* 2.7 44.4 + - - -
499B ASN* 4.8 1.7 + - - -
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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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114A LYS* 3.0 28.5 + - + +
115A GLU* 3.7 7.2 - - - +
116A TRP 3.1 0.2 - - - -
117A ASP* 1.3 75.8 - - - +
119A LYS* 1.3 66.9 + - - +
120A PRO* 3.3 5.9 - - - +
495B LYS* 4.5 30.3 - - + +
498B ARG* 3.6 38.6 - - - +
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Residues in contact with LYS 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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115A GLU 3.0 12.6 + - - +
116A TRP* 3.2 21.2 + - + +
117A ASP 3.6 1.0 - - - +
118A LEU* 1.3 77.6 - - - +
120A PRO* 1.3 78.3 - - + +
121A ILE 3.5 0.5 + - - -
123A ASP* 4.8 7.9 - - + +
124A ARG* 3.0 29.3 + - + -
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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