Contacts of the helix formed by residues 98 - 119 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75B THR* 4.3 14.4 - - + +
96B TYR 3.6 3.0 + - - +
97B ALA* 1.3 76.3 - - - +
99B LYS* 1.3 68.2 + - - +
100B SER* 3.7 11.2 - - - -
101B LEU* 3.0 25.5 + - - +
102B LEU* 3.0 23.4 + - - +
268B LEU* 4.1 8.5 - - + -
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Residues in contact with LYS 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASP* 1.3 73.8 - - - +
100B SER* 1.3 64.0 + - - +
102B LEU* 3.4 6.8 + - - +
103B ASN* 3.0 35.2 + - - +
268B LEU* 4.1 15.6 - - + +
272B THR* 4.6 15.6 - - + +
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Residues in contact with SER 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B ASP* 3.1 13.1 - - - -
99B LYS* 1.3 78.7 - - - +
101B LEU* 1.3 61.9 + - - +
103B ASN* 3.3 8.6 + - - +
104B LYS* 3.1 21.7 + - - +
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Residues in contact with LEU 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66B CYS* 3.8 23.6 - - + -
68B VAL* 3.8 22.9 - - + -
73B VAL* 3.8 35.9 - - + -
75B THR* 4.4 7.0 - - + -
97B ALA* 3.8 23.3 - - + -
98B ASP* 3.0 22.8 + - - +
100B SER* 1.3 76.7 + - - +
102B LEU* 1.3 58.3 + - - +
104B LYS* 3.1 10.3 + - + +
105B ALA* 2.8 27.4 + - - +
262B VAL* 5.1 2.5 - - + -
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Residues in contact with LEU 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ALA* 3.8 20.9 - - + +
98B ASP 3.0 23.5 + - - +
99B LYS 3.7 4.3 - - - +
101B LEU* 1.3 75.4 - - - +
103B ASN* 1.3 58.1 + - - +
105B ALA* 3.2 5.1 + - - +
106B ILE* 2.9 35.2 + - + +
231B LEU* 3.9 6.8 - - + +
262B VAL* 3.9 17.0 - - + +
264B ALA* 4.6 7.4 - - + -
268B LEU* 4.6 4.9 - - + +
269B PHE* 3.9 44.9 - - + +
272B THR* 4.0 33.0 - - + +
273B VAL* 5.8 0.7 - - + -
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Residues in contact with ASN 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B LYS* 3.0 27.3 + - - +
100B SER* 3.8 6.5 - - - +
101B LEU 3.2 0.2 - - - -
102B LEU* 1.3 76.8 - - - +
104B LYS* 1.3 58.1 + - - +
106B ILE* 3.3 15.4 + - - +
107B GLU* 3.0 27.4 + - - +
272B THR* 4.0 17.3 - - - +
276B SER* 5.7 2.1 - - - -
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Residues in contact with LYS 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B VAL* 4.5 6.3 - - + -
100B SER 3.1 11.6 + - - +
101B LEU* 3.1 17.1 + - + +
103B ASN* 1.3 73.3 - - - +
105B ALA* 1.3 67.0 + - - +
107B GLU* 3.2 6.5 + - - +
108B ALA* 2.9 27.4 + - - +
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Residues in contact with ALA 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B VAL* 3.8 29.3 - - + +
101B LEU 2.8 12.3 + - - +
102B LEU* 3.4 12.3 - - - +
104B LYS* 1.3 76.5 - - - +
106B ILE* 1.3 57.1 + - - +
109B ALA* 2.9 17.2 + - - +
231B LEU* 4.1 16.8 - - + -
260B GLN* 2.9 32.3 + - + +
262B VAL* 4.3 5.6 - - + -
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Residues in contact with ILE 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B LEU 2.9 19.9 + - - +
103B ASN* 3.5 23.6 - - - +
104B LYS 3.2 0.2 - - - -
105B ALA* 1.3 72.7 - - - +
107B GLU* 1.3 66.1 + - - +
109B ALA* 3.2 2.4 + - - +
110B LEU* 3.0 47.0 + - + +
203B PHE* 3.7 39.0 - - + -
231B LEU* 3.6 23.8 - - + -
272B THR* 4.7 10.3 - - + -
273B VAL* 5.0 1.8 - - + -
276B SER* 4.1 17.0 - - - +
278B HIS* 4.6 4.0 - - + -
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Residues in contact with GLU 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ASN 3.0 15.1 + - - +
104B LYS* 3.8 7.2 - - - +
106B ILE* 1.3 79.0 - - - +
108B ALA* 1.3 61.3 + - - +
110B LEU* 3.4 8.9 + - - +
111B ALA* 3.1 23.7 + - - +
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Residues in contact with ALA 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68B VAL* 4.4 7.9 - - + -
104B LYS 2.9 16.1 + - - +
107B GLU* 1.3 74.0 - - - +
109B ALA* 1.3 64.9 + - - +
111B ALA* 3.5 6.8 + - - +
112B ALA* 3.3 16.3 + - - +
257B ASN* 3.3 36.9 + - - +
260B GLN* 3.9 4.7 - - - +
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Residues in contact with ALA 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105B ALA 2.9 18.3 + - - +
106B ILE* 3.7 4.5 - - - +
108B ALA* 1.3 73.2 - - - +
110B LEU* 1.3 66.2 + - - +
112B ALA* 3.1 2.6 + - - -
113B ARG 3.0 18.9 + - - -
203B PHE* 4.9 2.0 - - + -
229B VAL* 3.5 29.0 - - + +
230B VAL 5.1 0.7 - - - +
231B LEU* 4.4 9.6 - - + -
257B ASN 3.4 19.7 - - - +
260B GLN* 3.6 12.9 - - + +
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Residues in contact with LEU 110 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ILE* 3.0 30.5 + - + +
107B GLU* 3.7 7.6 - - - +
109B ALA* 1.3 77.8 - - - +
111B ALA* 1.3 61.9 + - - +
112B ALA 3.3 0.5 + - - -
113B ARG* 3.3 23.1 + - - +
114B LYS* 4.5 2.8 + - - +
202B GLY* 3.5 40.6 - - - +
203B PHE* 3.9 7.4 - - + +
278B HIS* 3.3 46.0 - - + +
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Residues in contact with ALA 111 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B GLU 3.1 16.7 + - - +
108B ALA* 3.9 7.6 - - - +
109B ALA 3.2 0.2 - - - -
110B LEU* 1.3 76.4 - - - +
112B ALA* 1.3 58.4 + - - +
114B LYS* 5.1 2.9 + - - +
115B GLU* 5.7 0.9 + - - +
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Residues in contact with ALA 112 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B ALA 3.3 4.7 + - - +
109B ALA 3.1 5.2 + - - +
111B ALA* 1.3 77.0 - - - +
113B ARG* 1.3 65.9 + - - +
114B LYS 3.5 1.7 + - - -
115B GLU* 3.6 9.8 + - - +
116B TRP* 3.4 17.2 + - - +
229B VAL* 4.6 1.1 - - - -
256B PRO 4.1 7.2 - - - +
257B ASN* 3.6 37.9 - - + +
258B ILE* 4.4 5.9 - - + +
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Residues in contact with ARG 113 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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499A ASN* 4.0 13.9 + - - -
109B ALA 3.0 10.5 + - - +
110B LEU* 3.3 18.3 + - - +
112B ALA* 1.3 77.7 - - - +
114B LYS* 1.3 69.7 + - - +
116B TRP* 3.0 4.7 + - - +
117B ASP* 2.8 58.5 + - - +
199B GLY 4.7 2.0 + - - -
200B LEU 3.6 20.1 + - - -
201B GLU* 3.8 25.8 + - - +
202B GLY* 3.3 32.0 - - - +
227B GLY 4.4 11.1 + - - +
229B VAL* 3.6 26.0 - - + +
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Residues in contact with LYS 114 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B LEU 4.5 3.1 + - - +
111B ALA 5.1 2.4 + - - +
112B ALA 3.5 1.0 + - - -
113B ARG* 1.3 93.4 - - - +
115B GLU* 1.3 57.2 + - - +
117B ASP* 3.5 7.8 + - - +
118B LEU* 3.0 39.9 + - + +
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Residues in contact with GLU 115 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111B ALA 5.7 0.4 + - - +
112B ALA* 3.6 9.9 + - - +
113B ARG 3.3 0.6 - - - -
114B LYS* 1.3 75.6 - - - +
116B TRP* 1.3 60.1 + - - +
118B LEU* 3.3 8.1 + - - +
119B LYS* 2.9 27.4 + - - +
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Residues in contact with TRP 116 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA 3.4 4.3 + - - +
113B ARG* 3.0 8.6 + - - +
115B GLU* 1.3 76.4 - - - +
117B ASP* 1.3 63.5 + - - +
119B LYS* 3.1 23.7 + - + +
124B ARG* 3.1 43.9 + - + -
127B ILE* 3.7 24.9 - - + -
128B PHE* 4.6 5.6 - + - -
224B ALA 2.8 31.6 + - - -
227B GLY* 3.4 21.2 - - - -
228B ASN 3.2 22.2 + - - -
229B VAL* 4.7 1.3 - - + -
254B LEU* 3.8 14.4 - - + -
255B PRO* 3.5 34.1 - - + -
258B ILE* 3.5 36.6 - - + +
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Residues in contact with ASP 117 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A ARG* 2.7 43.8 + - - +
499A ASN* 4.7 2.9 - - - +
113B ARG* 2.8 38.9 + - - +
114B LYS* 3.6 6.0 - - - +
116B TRP* 1.3 75.4 - - - +
118B LEU* 1.3 57.8 + - - +
119B LYS 3.5 0.9 - - - +
124B ARG* 3.0 18.5 + - - +
197B TYR 4.6 1.0 - - - +
198B ARG* 3.9 0.7 - - - +
199B GLY* 3.0 32.8 + - - +
226B MET 5.0 0.2 - - - +
227B GLY* 3.8 15.2 + - - +
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Residues in contact with LEU 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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495A LYS* 4.1 31.6 - - + +
498A ARG* 3.7 39.7 - - - +
114B LYS* 3.0 24.4 + - + +
115B GLU* 3.8 7.0 - - - +
116B TRP 3.2 0.2 - - - -
117B ASP* 1.3 74.4 - - - +
119B LYS* 1.3 68.1 + - - +
120B PRO* 3.3 7.3 - - - +
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Residues in contact with LYS 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLU 2.9 12.8 + - - +
116B TRP* 3.1 21.4 + - + +
117B ASP 3.5 1.0 - - - +
118B LEU* 1.3 77.1 - - - +
120B PRO* 1.3 72.3 - - + +
121B ILE 3.6 0.3 + - - -
123B ASP* 5.1 5.4 - - + -
124B ARG* 2.9 37.7 + - + -
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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
------------------------------------------------------------
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