Contacts of the helix formed by residues 98 - 115 (chain B) in PDB entry 2CUK
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 LEU 98 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B SER* 5.1 0.2 - - - -
74B VAL* 4.2 40.6 - - + +
94B THR 4.1 11.4 - - - +
96B GLY 5.4 2.7 - - - +
97B VAL* 1.3 75.8 - - + +
99B THR* 1.3 69.6 + - - +
100B GLU 3.5 1.6 - - - -
101B ALA* 3.6 2.5 + - - +
102B THR* 2.8 37.6 + - - +
155B ILE* 4.6 10.5 - - + -
280B SER* 3.7 16.8 - - - +
285B THR* 3.6 21.8 - - + -
289B MET* 4.0 27.4 - - + -
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Residues in contact with THR 99 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLY* 3.2 28.0 + - - -
97B VAL 3.5 0.2 - - - -
98B LEU* 1.3 82.6 - - - +
100B GLU* 1.3 72.2 + - - +
102B THR* 3.4 2.8 + - - -
103B ALA* 3.1 20.6 + - - +
154B ARG* 3.7 45.9 + - + +
155B ILE* 4.0 16.1 - - - +
158B ALA* 4.1 10.1 - - + -
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Residues in contact with GLU 100 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96B GLY 4.8 0.4 + - - -
97B VAL 5.1 2.3 + - - +
98B LEU 3.5 0.2 - - - -
99B THR* 1.3 79.9 - - + +
101B ALA* 1.3 61.1 + - - +
103B ALA* 3.1 4.6 + - - +
104B ASP* 2.8 35.5 + - - +
158B ALA* 4.1 13.6 - - - +
162B ARG* 2.6 32.5 + - - +
143D GLN* 3.6 32.6 - - + +
165D ALA 5.2 0.3 - - - +
166D PHE 4.7 2.8 - - - +
167D GLY* 5.6 0.9 - - - -
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Residues in contact with ALA 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B VAL 5.5 0.4 + - - -
98B LEU 3.6 7.0 + - - +
99B THR 3.4 0.4 - - - -
100B GLU* 1.3 78.4 - - - +
102B THR* 1.3 58.8 + - - +
104B ASP* 3.2 5.7 + - - -
105B LEU 3.0 15.1 + - - -
279B GLY 3.2 11.8 - - - +
280B SER* 4.1 8.5 - - - -
285B THR* 3.5 31.2 + - + +
115D ARG* 2.9 27.3 + - - +
141D ASP* 3.5 14.4 - - - +
143D GLN* 4.5 1.0 + - - -
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Residues in contact with THR 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B LEU* 2.8 27.6 + - - +
99B THR 3.8 3.4 - - - -
101B ALA* 1.3 77.1 - - - +
103B ALA* 1.3 57.9 + - - +
105B LEU* 3.3 2.3 + - - +
106B THR* 2.8 32.4 + - - -
155B ILE* 3.8 32.5 - - + +
228B THR* 4.2 26.2 - - - +
279B GLY* 3.5 24.1 + - - -
280B SER* 4.2 4.5 + - - -
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Residues in contact with ALA 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99B THR 3.1 9.8 + - - +
100B GLU 3.4 8.7 - - - +
102B THR* 1.3 78.7 - - - +
104B ASP* 1.3 61.4 + - - +
106B THR* 3.2 1.6 + - - -
107B LEU* 3.1 28.9 + - - +
155B ILE* 4.4 2.6 - - - +
158B ALA* 3.5 32.8 - - + -
159B VAL* 3.9 19.5 - - + -
162B ARG* 3.8 15.0 - - - +
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Residues in contact with ASP 104 (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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100B GLU 2.8 14.9 + - - +
101B ALA* 3.2 10.1 + - - +
103B ALA* 1.3 76.8 - - - +
105B LEU* 1.3 58.0 + - - +
107B LEU* 3.2 4.5 + - - +
108B ALA* 2.9 27.1 + - - +
162B ARG* 2.8 31.6 + - - +
111D LEU* 4.0 13.5 - - + +
115D ARG* 3.9 13.8 + - + +
141D ASP* 4.9 1.9 - - - +
142D LEU* 4.1 14.2 + - + +
143D GLN* 2.8 27.5 + - - +
166D PHE* 3.2 17.2 - - - -
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Residues in contact with LEU 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B ALA 3.0 15.6 + - - +
102B THR 3.8 4.3 - - - +
104B ASP* 1.3 74.2 - - - +
106B THR* 1.3 67.1 + - - +
108B ALA* 3.1 3.4 + - + +
109B LEU* 3.0 44.9 + - + +
228B THR* 4.3 4.0 - - + -
253B ASP* 3.7 25.4 - - + +
275B THR* 4.1 2.2 - - + +
278B ILE* 4.1 18.6 - - + +
279B GLY* 3.7 22.4 - - - +
115D ARG* 4.0 19.7 - - + +
117D VAL* 4.1 25.4 - - + -
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Residues in contact with THR 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102B THR* 2.8 20.8 + - - +
103B ALA 3.2 8.3 + - - -
105B LEU* 1.3 77.4 - - - +
107B LEU* 1.3 61.6 + - + +
109B LEU* 3.4 3.7 + - - +
110B LEU* 3.1 20.3 + - - +
155B ILE* 4.9 0.2 - - - +
159B VAL* 3.9 25.1 - - + +
198B SER* 3.6 24.5 - - - +
200B HIS* 4.1 6.8 - - + -
226B LEU* 4.0 13.5 - - + +
228B THR* 3.0 34.5 + - + +
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Residues in contact with LEU 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 ALA 3.1 19.2 + - - +
104B ASP 3.7 7.4 - - - +
106B THR* 1.3 76.2 - - - +
108B ALA* 1.3 64.2 + - - +
110B LEU* 3.2 24.8 + - + +
111B LEU* 3.0 30.2 + - + +
142B LEU* 6.2 0.4 - - + -
159B VAL* 3.6 29.6 - - + +
162B ARG* 3.7 30.1 - - + -
163B ALA* 4.4 8.5 - - + +
166B PHE* 4.1 27.1 - - + -
168B MET* 6.1 0.4 - - - -
226B LEU* 6.5 0.2 - - + -
111D LEU* 4.0 2.7 - - + -
166D PHE* 3.9 16.6 - - + -
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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
----------------------------------------------------------
104B ASP 2.9 15.1 + - - +
105B LEU* 3.1 13.4 + - + +
107B LEU* 1.3 76.2 - - - +
109B LEU* 1.3 57.6 + - - +
111B LEU* 3.4 3.0 + - - +
112B ALA* 2.8 30.6 + - - +
108D ALA 5.6 1.2 - - - +
111D LEU* 3.6 32.5 - - + +
112D ALA* 5.1 0.4 - - - +
115D ARG* 5.2 1.3 - - + -
117D VAL* 3.8 25.5 - - + +
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Residues in contact with LEU 109 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105B LEU* 3.0 35.4 + - + +
106B THR 3.7 6.5 - - - +
108B ALA* 1.3 74.8 - - - +
110B LEU* 1.3 65.5 + - - +
112B ALA* 3.6 2.2 - - - +
113B VAL* 2.9 31.6 + - - +
226B LEU* 4.3 5.8 - - + -
228B THR* 3.8 19.5 - - + -
251B GLY* 3.9 26.2 - - - +
252B LEU 4.0 10.8 - - - -
253B ASP* 4.0 0.7 - - + +
273B VAL* 3.7 36.1 - - + +
275B THR* 3.9 20.2 - - + +
117D VAL* 4.6 4.3 - - + -
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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 THR 3.1 11.7 + - - +
107B LEU* 3.2 26.9 + - + +
109B LEU* 1.3 78.8 - - - +
111B LEU* 1.3 58.2 + - + +
113B VAL* 3.9 1.0 - - - +
114B ALA* 2.8 33.4 + - - +
142B LEU* 4.5 19.5 - - + -
147B LEU* 5.4 6.5 - - + -
159B VAL* 6.5 0.2 - - + -
163B ALA* 5.8 0.2 - - + -
168B MET* 4.2 25.6 - - + -
196B VAL* 3.9 35.4 - - + -
224B ILE* 4.2 15.7 - - + -
226B LEU* 3.7 20.8 - - + +
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Residues in contact with LEU 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 LEU* 3.0 18.1 + - + +
108B ALA* 3.8 3.6 - - - +
110B LEU* 1.3 75.5 - - + +
112B ALA* 1.3 66.1 + - - +
114B ALA* 4.5 2.5 - - + -
115B ARG* 3.0 33.1 + - + +
117B VAL* 3.8 4.0 - - - +
142B LEU* 3.8 27.4 - - + -
166B PHE* 3.8 28.5 - - + -
104D ASP* 3.8 21.5 - - + +
107D LEU 4.0 0.4 - - - -
108D ALA* 3.7 29.6 - - + +
111D LEU* 3.7 29.2 - - + -
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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 2.8 22.3 + - - +
109B LEU* 3.3 9.4 + - - +
111B LEU* 1.3 71.4 - - - +
113B VAL* 1.3 58.2 + - - +
116B ARG* 3.1 8.1 + - - -
117B VAL* 3.0 38.0 + - + -
118B VAL* 4.4 9.1 + - + -
273B VAL* 4.4 18.5 - - + +
108D ALA* 5.1 0.4 - - - +
112D ALA* 6.4 1.3 - - + -
117D VAL* 4.4 17.9 - - + -
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Residues in contact with VAL 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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109B LEU 2.9 21.4 + - - +
110B LEU 3.9 2.2 - - - +
112B ALA* 1.3 74.9 - - - +
114B ALA* 1.3 65.8 + - - +
116B ARG* 3.2 14.2 + - - +
224B ILE* 4.0 18.4 - - + -
226B LEU* 5.1 0.9 - - + -
248B PHE* 3.4 13.6 - - + -
249B GLY* 3.9 13.9 - - - -
250B ALA 3.5 46.0 - - - +
251B GLY* 3.7 7.6 - - - +
271B ASN* 4.1 7.4 - - - +
273B VAL* 3.9 18.6 - - + +
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Residues in contact with ALA 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* 2.8 24.4 + - + +
111B LEU* 4.3 2.2 - - - +
113B VAL* 1.3 74.9 - - - +
115B ARG* 1.3 62.0 - - + +
116B ARG 3.8 0.2 + - - -
139B GLY* 3.2 5.9 - - - -
140B LEU* 2.8 36.4 + - + +
142B LEU* 4.1 24.0 - - + -
224B ILE* 3.9 20.4 - - + +
248B PHE* 3.9 6.1 - - - -
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Residues in contact with ARG 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 LEU* 3.0 22.9 + - + +
112B ALA 4.0 0.2 - - - -
114B ALA* 1.3 82.0 - - + +
116B ARG* 1.3 72.0 + - - +
117B VAL* 3.2 10.9 + - + -
137B LEU 4.6 4.1 + - - +
139B GLY* 4.5 2.7 - - - -
140B LEU 3.5 28.3 - - - +
141B ASP* 5.3 1.6 + - - +
142B LEU* 6.1 1.1 - - + -
101D ALA* 2.8 33.1 + - - +
104D ASP* 3.9 16.8 + - + +
105D LEU* 4.0 17.9 - - + +
108D ALA* 5.3 1.1 - - + -
278D ILE* 2.8 45.1 + - - +
279D GLY* 2.9 13.3 + - - -
280D SER 4.0 0.2 - - - -
281D ALA* 3.3 28.3 + - - +
282D GLY* 3.8 4.4 - - - +
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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
------------------------------------------------------------
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