Contacts of the helix formed by residues 98 - 118 (chain A) in PDB entry 4OE4
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 THR 98 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75A GLU* 5.4 3.1 - - + +
76A ARG* 4.0 25.9 + - + +
96A GLN 4.5 1.3 - - - +
97A ALA* 1.3 74.1 - - - +
99A GLU* 1.3 64.9 + - - +
100A LYS* 3.3 9.8 + - - +
101A ASP* 2.8 41.7 + - - +
102A VAL* 2.9 26.8 + - - +
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Residues in contact with GLU 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 THR* 1.3 73.7 - - - +
100A LYS* 1.3 63.9 + - - +
102A VAL* 3.3 5.5 + - - +
103A MET* 3.0 36.9 + - - +
269A GLN* 5.9 0.8 + - - -
273A GLN* 3.2 36.8 + - + +
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Residues in contact with LYS 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 THR* 3.2 8.6 + - - +
99A GLU* 1.3 80.4 - - + +
101A ASP* 1.3 59.8 + - - +
103A MET* 3.2 31.1 + - - +
104A ASN* 2.8 61.0 + - - +
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Residues in contact with ASP 101 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LEU* 3.5 21.7 - - + +
65A ILE* 3.4 16.1 - - + +
70A ILE* 4.5 7.4 - - - +
76A ARG* 2.7 47.1 + - - -
97A ALA* 4.1 3.1 - - + -
98A THR* 2.8 44.8 + - - +
100A LYS* 1.3 75.2 - - - +
102A VAL* 1.3 52.6 + - - +
104A ASN* 3.0 11.2 + - - +
105A ALA* 2.7 32.1 + - - +
263A ILE* 5.1 0.4 - - - -
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Residues in contact with VAL 102 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97A ALA* 4.1 15.9 - - + -
98A THR 2.9 22.5 + - - +
99A GLU* 3.6 8.3 - - - +
101A ASP* 1.3 73.7 - - - +
103A MET* 1.3 58.2 + - - +
105A ALA* 3.0 8.9 + - - +
106A VAL* 2.8 32.5 + - + +
263A ILE* 4.3 7.6 - - + -
269A GLN 5.4 0.2 - - - +
270A VAL* 4.1 25.4 - - + +
273A GLN* 3.7 20.9 - - + -
274A VAL* 3.5 33.9 - - + +
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Residues in contact with MET 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 GLU* 3.0 32.9 + - - +
100A LYS* 3.4 34.1 - - + +
102A VAL* 1.3 76.0 - - - +
104A ASN* 1.3 59.5 + - - +
106A VAL* 3.4 8.5 + - - +
107A LYS* 2.9 28.4 + - - +
273A GLN* 3.3 27.4 - - - +
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Residues in contact with ASN 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A ILE* 3.8 16.0 - - + +
70A ILE* 5.9 4.6 - - + +
100A LYS* 2.8 52.6 + - - +
101A ASP* 3.4 15.0 + - - +
103A MET* 1.3 70.4 - - - +
105A ALA* 1.3 60.6 + - - +
107A LYS* 3.6 12.6 - - - +
108A ALA* 2.8 30.0 + - - +
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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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65A ILE* 3.9 11.4 - - + +
101A ASP 2.7 16.5 + - - +
102A VAL* 3.3 9.9 - - - +
104A ASN* 1.3 72.5 - - - +
106A VAL* 1.3 63.1 + - - +
108A ALA* 3.2 3.5 + - - +
109A ALA 3.0 18.2 + - - -
232A VAL* 3.6 16.6 - - + +
261A ASN* 3.7 17.3 + - + -
263A ILE* 3.7 29.8 - - + -
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Residues in contact with VAL 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 VAL* 2.8 30.4 + - + +
103A MET* 3.7 8.1 - - - +
105A ALA* 1.3 75.0 - - - +
107A LYS* 1.3 62.7 + - - +
109A ALA* 3.4 4.0 + - - +
110A LYS* 3.1 23.3 + - + +
204A PHE* 3.7 31.8 - - + -
232A VAL* 3.8 16.8 - - + -
273A GLN 5.4 0.7 - - - +
274A VAL* 4.6 8.5 - - - -
277A ASP* 3.6 35.2 - - + +
279A ASP* 5.8 0.2 - - + -
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Residues in contact with LYS 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 MET 2.9 18.2 + - - +
104A ASN* 3.6 14.8 - - - +
105A ALA 3.2 0.2 - - - -
106A VAL* 1.3 76.2 - - - +
108A ALA* 1.3 67.0 + - - +
110A LYS* 3.2 6.1 + - + +
111A ASP* 2.7 61.1 + - - +
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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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65A ILE* 4.3 0.9 - - + -
66A ASN* 3.7 34.3 - - + +
104A ASN 2.8 21.4 + - - +
105A ALA 3.2 1.1 + - - +
107A LYS* 1.3 72.2 - - - +
109A ALA* 1.3 62.4 + - - +
111A ASP* 3.3 7.9 + - - +
112A ALA* 3.0 26.0 + - - +
258A GLY* 3.6 3.4 - - - +
261A ASN* 3.4 23.6 - - - +
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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 12.6 + - - +
106A VAL* 3.7 7.9 - - - +
108A ALA* 1.3 77.4 - - - +
110A LYS* 1.3 60.5 + - - +
112A ALA 3.5 0.9 + - - -
113A LYS* 3.3 13.7 + - - +
204A PHE* 4.3 11.4 - - + -
230A THR* 2.7 34.1 + - - +
231A VAL 4.2 5.2 - - - +
232A VAL* 4.1 13.0 - - + -
258A GLY 3.2 12.3 + - - -
261A ASN* 3.8 9.6 - - - +
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Residues in contact with LYS 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 VAL* 3.1 15.6 + - + +
107A LYS* 3.7 9.0 - - + +
109A ALA* 1.3 76.0 - - - +
111A ASP* 1.3 65.7 + - - +
113A LYS* 3.4 19.9 + - - +
114A LYS 4.8 0.5 + - - -
204A PHE* 5.5 5.5 - - + +
230A THR* 4.8 0.2 - - - -
279A ASP* 5.3 11.4 - - + +
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Residues in contact with ASP 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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66A ASN* 5.8 2.7 - - - +
107A LYS* 2.7 54.9 + - - +
108A ALA* 3.8 7.5 - - - +
110A LYS* 1.3 81.0 - - - +
112A ALA* 1.3 59.8 + - - +
113A LYS 3.3 0.4 + - - -
114A LYS* 4.9 3.1 + - - +
115A ASP* 5.3 4.7 + - - -
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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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66A ASN* 5.4 0.7 - - - +
108A ALA 3.0 15.6 + - - +
109A ALA 4.1 1.6 - - - +
110A LYS 3.3 0.4 - - - -
111A ASP* 1.3 77.2 - - - +
113A LYS* 1.3 65.4 + - - +
114A LYS 3.5 0.9 - - - -
115A ASP* 3.4 8.5 + - - +
116A TRP* 3.0 22.2 + - - +
230A THR* 4.2 1.8 - - + -
256A PRO* 6.1 0.4 - - + -
257A LYS 3.3 26.2 - - - +
258A GLY 3.7 12.8 - - - +
259A VAL* 3.9 10.5 - - + +
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Residues in contact with LYS 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 3.3 8.9 + - - +
110A LYS* 3.4 17.9 - - - +
111A ASP 3.3 2.0 - - - -
112A ALA* 1.3 76.1 - - - +
114A LYS* 1.3 60.4 + - - +
116A TRP* 3.0 4.0 + - - +
117A TYR* 2.9 44.0 + - + -
200A PRO* 3.8 12.3 - - - -
201A LEU 2.9 28.9 + - - -
202A GLU* 3.1 20.9 + - - +
203A GLY 3.6 9.7 + - - -
204A PHE 4.8 0.2 - - - +
228A GLY 3.5 23.6 - - - +
229A ASN* 4.3 4.9 + - - +
230A THR* 3.8 23.7 + - + +
510B PHE* 5.4 0.6 - - - -
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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 LYS 4.8 1.2 + - - -
111A ASP 4.9 2.3 + - - +
112A ALA 3.5 0.2 - - - -
113A LYS* 1.3 77.9 - - - +
115A ASP* 1.3 63.2 + - - +
117A TYR* 3.7 23.6 - - + +
118A ASN* 2.9 43.1 + - - +
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Residues in contact with ASP 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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111A ASP 5.3 4.4 + - - -
112A ALA* 3.4 10.6 + - - +
114A LYS* 1.3 80.6 - - - +
116A TRP* 1.3 57.8 + - - +
118A ASN* 4.0 7.4 + - - -
119A LEU* 3.2 24.9 + - - +
256A PRO* 6.1 1.4 - - + +
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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 3.0 17.9 + - - +
113A LYS 3.0 3.8 + - - +
115A ASP* 1.3 75.6 - - - +
117A TYR* 1.3 65.5 + - - +
118A ASN 3.1 1.6 - - - -
119A LEU* 3.0 41.6 + - + +
124A ARG* 3.4 38.6 - - + -
127A ILE* 3.8 10.5 - - + -
128A PHE* 4.2 11.4 - + - -
225A ALA* 2.8 35.2 + - + -
228A GLY* 3.5 22.1 - - - -
229A ASN 3.1 24.0 + - - -
230A THR* 3.9 3.8 - - + -
255A LEU* 4.1 9.2 - - + -
256A PRO* 3.5 26.2 - - + -
259A VAL* 3.5 37.1 - - + +
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Residues in contact with TYR 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 LYS* 2.9 47.0 + - + -
114A LYS* 3.7 23.3 - - + +
116A TRP* 1.3 74.1 - - - +
118A ASN* 1.3 83.9 + - - +
119A LEU 3.3 0.6 - - - +
124A ARG* 3.5 14.6 + - - +
200A PRO* 3.9 24.5 - - + -
228A GLY* 3.5 24.7 - - - +
510B PHE* 3.7 31.5 - + - -
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Residues in contact with ASN 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* 2.9 29.4 + - - +
115A ASP* 4.0 7.6 + - - +
117A TYR* 1.3 96.8 + - - +
119A LEU* 1.3 61.4 + - - +
120A PRO* 3.4 8.5 - - - +
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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
------------------------------------------------------------
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