Contacts of the helix formed by residues 98 - 115 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73D SER* 5.9 0.2 - - - -
74D VAL* 4.2 32.8 - - + +
94D THR 5.3 0.7 - - - +
96D GLY 3.3 2.4 - - - +
97D VAL* 1.3 82.4 - - + +
99D THR* 1.3 64.7 + - - +
100D GLU 3.5 1.8 - - - -
101D ALA* 3.6 2.9 + - - +
102D THR* 2.8 41.2 + - - +
155D ILE* 4.2 15.9 - - + -
280D SER* 3.7 32.3 - - - +
285D THR* 3.9 12.3 - - + -
289D MET* 4.5 15.7 - - + -
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Residues in contact with THR 99 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
96D GLY* 3.2 23.0 + - - -
97D VAL 3.5 0.6 - - - -
98D LEU* 1.3 80.7 - - - +
100D GLU* 1.3 72.6 + - - +
102D THR* 3.7 2.1 - - - -
103D ALA* 3.0 21.8 + - - +
154D ARG* 3.5 47.3 - - + +
155D ILE* 3.9 17.6 - - - +
158D ALA* 4.1 9.0 - - + -
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Residues in contact with GLU 100 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
141B ASP* 5.9 0.2 - - - +
143B GLN* 3.5 35.2 - - + +
166B PHE 4.4 1.6 - - - +
167B GLY* 5.6 0.5 - - - -
97D VAL 5.0 2.5 + - - +
98D LEU 3.5 0.4 - - - -
99D THR* 1.3 84.5 - - - +
101D ALA* 1.3 58.6 + - - +
103D ALA* 3.2 3.2 + - - +
104D ASP* 2.9 35.8 + - - +
158D ALA* 4.0 14.4 - - - +
161D LYS* 4.8 7.8 + - - -
162D ARG* 2.4 32.2 + - - +
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Residues in contact with ALA 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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115B ARG* 2.8 30.1 + - - +
141B ASP* 3.6 11.4 + - - +
143B GLN* 4.6 0.8 + - - -
97D VAL 5.4 0.6 + - - -
98D LEU 3.6 6.8 + - - +
99D THR 3.4 0.6 - - - -
100D GLU* 1.3 77.3 - - - +
102D THR* 1.3 63.0 + - - +
104D ASP* 3.2 5.8 + - - -
105D LEU 3.0 10.2 + - - -
279D GLY 3.2 12.2 - - - +
280D SER* 4.1 11.7 - - - -
282D GLY 4.6 0.9 - - - +
285D THR* 3.5 27.0 + - + +
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Residues in contact with THR 102 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98D LEU* 2.8 35.4 + - - +
99D THR 3.7 3.1 - - - -
101D ALA* 1.3 76.5 - - - +
103D ALA* 1.3 58.7 + - - +
105D LEU* 3.2 3.3 + - - +
106D THR* 2.9 31.4 + - - -
155D ILE* 3.8 29.4 - - + -
228D THR* 4.1 27.8 - - - +
279D GLY* 3.4 23.2 + - - +
280D SER* 4.3 1.7 + - - -
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Residues in contact with ALA 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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99D THR 3.0 16.8 + - - +
100D GLU 3.6 4.5 - - - +
102D THR* 1.3 76.6 - - - +
104D ASP* 1.3 64.5 + - - +
106D THR* 3.2 1.7 + - - -
107D LEU* 3.1 28.2 + - - +
155D ILE* 4.4 2.2 - - - +
158D ALA* 3.6 28.3 - - + -
159D VAL* 3.8 22.0 - - + -
162D ARG* 3.8 14.6 - - - +
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Residues in contact with ASP 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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111B LEU* 3.8 13.4 - - + +
115B ARG* 3.9 13.2 + - + +
140B LEU 5.3 0.7 - - - +
141B ASP* 5.1 1.7 - - - -
142B LEU* 4.0 15.4 + - + +
143B GLN* 3.0 25.2 + - - +
166B PHE* 3.2 18.0 - - - -
100D GLU 2.9 14.8 + - - +
101D ALA* 3.5 9.5 - - - +
103D ALA* 1.3 76.4 - - - +
105D LEU* 1.3 56.9 + - - +
107D LEU* 3.3 4.3 + - - +
108D ALA* 2.9 27.9 + - - +
162D ARG* 2.9 32.4 + - - -
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Residues in contact with LEU 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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115B ARG* 4.0 15.6 - - + +
117B VAL* 4.4 20.4 - - + -
101D ALA 3.0 13.3 + - - +
102D THR 3.8 5.6 - - - +
104D ASP* 1.3 74.3 - - - +
106D THR* 1.3 66.4 + - - +
108D ALA* 3.5 2.9 - - + +
109D LEU* 3.0 30.0 + - + +
228D THR* 4.4 4.9 - - + -
253D ASP* 3.3 41.7 - - + +
275D THR* 4.2 5.8 - - + +
278D ILE* 4.1 24.7 - - + +
279D GLY* 3.3 22.7 - - - +
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Residues in contact with THR 106 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102D THR* 2.9 20.6 + - - +
103D ALA 3.2 8.3 + - - -
105D LEU* 1.3 78.1 - - - +
107D LEU* 1.3 62.3 + - + +
109D LEU* 3.4 4.0 + - - +
110D LEU* 3.1 21.7 + - - +
159D VAL* 3.9 18.4 - - + +
198D SER* 3.6 24.0 - - - +
200D HIS* 3.9 13.2 - - + -
226D LEU* 3.9 14.1 - - + +
228D THR* 3.1 31.0 + - + +
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Residues in contact with LEU 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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111B LEU* 4.0 3.4 - - + -
166B PHE* 3.7 27.1 - - + -
103D ALA 3.1 17.7 + - - +
104D ASP 3.6 7.0 - - - +
106D THR* 1.3 74.8 - - - +
108D ALA* 1.3 66.3 + - - +
110D LEU* 3.3 21.6 + - + +
111D LEU* 3.0 31.8 + - + +
142D LEU* 6.1 0.4 - - + -
159D VAL* 3.9 28.0 - - + +
162D ARG* 3.7 22.2 - - + -
163D ALA* 4.5 7.4 - - + +
166D PHE* 4.0 27.4 - - + -
168D MET* 6.3 0.2 - - - -
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Residues in contact with ALA 108 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108B ALA 5.6 1.4 - - - +
111B LEU* 3.7 30.4 - - + +
112B ALA* 5.1 0.4 - - - +
115B ARG* 5.3 1.8 - - + -
117B VAL* 3.9 24.4 - - + +
104D ASP 2.9 14.5 + - - +
105D LEU* 3.5 14.8 - - + +
106D THR 3.3 0.4 - - - -
107D LEU* 1.3 77.6 - - - +
109D LEU* 1.3 57.7 + - - +
111D LEU* 3.4 2.8 + - - +
112D ALA* 2.8 29.7 + - - +
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Residues in contact with LEU 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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117B VAL* 4.4 6.5 - - + -
105D LEU* 3.0 21.2 + - + +
106D THR* 3.8 4.0 - - - +
108D ALA* 1.3 75.0 - - - +
110D LEU* 1.3 64.6 - - - +
112D ALA* 3.7 2.4 - - - +
113D VAL* 3.0 30.5 + - - +
226D LEU* 4.2 6.5 - - + -
228D THR* 3.9 24.9 - - + -
251D GLY* 3.9 14.8 - - - +
252D LEU 3.8 25.8 - - - -
253D ASP* 3.9 2.7 - - + +
273D VAL* 3.8 27.4 - - + +
275D THR* 3.7 34.1 - - + +
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Residues in contact with LEU 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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106D THR 3.1 8.9 + - - +
107D LEU* 3.3 23.5 + - + +
109D LEU* 1.3 76.3 - - - +
111D LEU* 1.3 59.0 + - + +
113D VAL* 3.9 0.9 - - - +
114D ALA* 2.8 33.8 + - - +
142D LEU* 4.1 22.0 - - + -
147D LEU* 5.4 3.8 - - + -
163D ALA* 5.8 1.6 - - + -
168D MET* 4.0 26.2 - - + -
196D VAL* 3.9 37.5 - - + -
224D ILE* 4.1 17.9 - - + -
226D LEU* 3.7 22.4 - - + +
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Residues in contact with LEU 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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104B ASP* 4.0 19.3 - - + +
107B LEU 4.0 0.2 - - - -
108B ALA* 3.6 30.7 - - + +
111B LEU* 3.7 29.2 - - + -
107D LEU* 3.0 16.5 + - + +
108D ALA 3.9 3.1 - - - +
110D LEU* 1.3 76.2 - - + +
112D ALA* 1.3 60.7 + - - +
114D ALA* 4.5 2.2 - - - -
115D ARG* 2.9 39.7 + - + +
117D VAL* 4.0 3.5 - - - +
142D LEU* 3.7 28.5 - - + -
166D PHE* 3.9 28.5 - - + -
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Residues in contact with ALA 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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108B ALA* 5.6 0.2 - - - -
117B VAL* 4.5 11.4 - - + -
108D ALA 2.8 19.4 + - - +
109D LEU* 3.7 9.2 - - - +
111D LEU* 1.3 76.0 - - - +
113D VAL* 1.3 58.3 + - - +
116D ARG* 3.1 8.5 + - - -
117D VAL* 3.0 36.5 + - + -
118D VAL* 4.2 23.7 + - + -
273D VAL* 4.5 11.2 - - + +
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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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109D LEU 3.0 21.3 + - - +
110D LEU 3.9 2.5 - - - +
112D ALA* 1.3 74.2 - - - +
114D ALA* 1.3 67.5 + - - +
116D ARG* 3.2 15.1 + - - +
224D ILE* 4.0 19.3 - - + -
226D LEU* 5.2 0.7 - - + -
248D PHE* 3.6 12.5 - - + -
249D GLY* 4.0 13.7 - - - -
250D ALA 3.5 44.2 - - - +
251D GLY* 3.8 6.1 - - - +
271D ASN* 4.3 6.3 - - - +
273D VAL* 3.8 20.2 - - + +
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Residues in contact with ALA 114 (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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110D LEU* 2.8 23.7 + - + +
111D LEU* 4.3 3.4 - - - +
113D VAL* 1.3 75.1 - - - +
115D ARG* 1.3 62.0 + - + +
116D ARG 3.8 0.2 + - - -
139D GLY* 3.3 5.9 - - - -
140D LEU* 2.8 42.3 + - + +
142D LEU* 4.2 17.7 - - + -
224D ILE* 3.9 21.1 - - + -
248D PHE* 4.0 6.4 - - - -
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Residues in contact with ARG 115 (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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101B ALA* 2.9 34.3 + - - +
104B ASP* 3.9 11.7 + - + +
105B LEU* 4.0 21.7 - - + +
108B ALA* 5.2 1.1 - - + -
278B ILE* 2.8 46.4 + - - +
279B GLY* 2.9 11.5 + - - -
281B ALA* 3.3 29.7 + - - +
282B GLY* 3.8 5.1 - - - +
111D LEU* 2.9 31.6 + - + +
114D ALA* 1.3 77.5 - - + +
116D ARG* 1.3 72.3 + - - +
117D VAL* 3.2 5.3 + - + +
137D LEU 4.7 3.3 - - - +
139D GLY* 4.6 2.6 - - - -
140D LEU 3.7 24.9 - - - +
141D ASP* 4.8 3.2 + - - +
142D LEU* 6.1 1.6 - - + -
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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