Contacts of the helix formed by residues 116 - 126 (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 ARG 116 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112B ALA 3.1 9.6 + - - -
113B VAL 3.2 12.2 + - - +
114B ALA 4.6 2.7 - - - +
115B ARG* 1.3 79.8 - - - +
117B VAL* 1.3 60.1 + - - +
118B VAL 3.6 1.1 - - - -
119B GLU* 2.7 51.7 + - + +
120B GLY* 2.9 25.2 + - - -
135B GLU 5.8 0.2 + - - -
137B LEU* 3.6 27.9 - - + +
138B LEU* 3.0 41.4 + - - +
139B GLY* 4.4 1.3 - - - -
248B PHE* 4.6 9.4 - - + -
270B PRO 6.0 0.4 - - - +
271B ASN* 6.6 0.4 - - - -
278D ILE* 4.3 3.8 - - - +
283D ARG* 5.7 2.4 - - - +
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Residues in contact with VAL 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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111B LEU 3.8 19.5 - - - +
112B ALA* 3.0 15.9 + - + -
115B ARG* 4.1 10.3 - - + +
116B ARG* 1.3 74.3 - - - +
118B VAL* 1.3 62.6 + - + +
120B GLY* 3.2 0.5 + - - -
121B ALA* 2.9 28.6 + - - +
105D LEU* 4.4 9.6 - - + -
108D ALA* 3.9 21.8 - - + +
109D LEU* 4.4 11.2 - - + -
112D ALA* 4.5 17.9 - - + -
118D VAL* 4.5 9.2 - - + -
273D VAL* 4.6 1.3 - - + -
275D THR* 4.0 21.0 - - + +
278D ILE* 5.1 0.9 - - - -
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Residues in contact with VAL 118 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B ALA* 4.4 10.0 + - + -
116B ARG 3.6 0.2 - - - -
117B VAL* 1.3 77.0 - - + +
119B GLU* 1.3 64.0 - - - +
121B ALA* 3.4 3.5 + - - +
122B ALA* 3.1 22.7 + - + +
125B ARG* 5.3 0.7 + - - -
273B VAL* 4.0 39.3 - - + -
117D VAL* 4.6 3.6 - - + -
118D VAL* 4.4 30.6 - - + +
121D ALA* 4.3 16.2 - - + -
125D ARG* 3.7 25.6 - - - +
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Residues in contact with GLU 119 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116B ARG* 2.7 60.4 + - + +
117B VAL 3.2 0.4 - - - -
118B VAL* 1.3 81.0 - - - +
120B GLY* 1.3 56.6 + - - +
122B ALA* 3.3 8.0 + - - +
123B TYR* 3.0 26.6 + - + +
137B LEU* 3.8 10.5 - - + +
270B PRO* 3.9 41.2 + - + +
271B ASN* 5.5 0.5 - - - -
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Residues in contact with GLY 120 (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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116B ARG 2.9 19.4 + - - -
117B VAL 3.2 1.5 + - - -
119B GLU* 1.3 74.9 - - - +
121B ALA* 1.3 63.6 + - - +
123B TYR* 3.2 2.8 + - - +
124B ALA* 3.1 18.2 + - - +
137B LEU* 3.8 23.3 - - - +
275D THR* 4.7 0.7 - - - -
276D PRO* 3.2 21.1 - - - +
278D ILE* 4.9 2.7 - - - -
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Residues in contact with ALA 121 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B VAL 2.9 16.6 + - - +
118B VAL 3.7 4.7 - - - +
119B GLU 3.4 0.2 - - - -
120B GLY* 1.3 75.2 - - - +
122B ALA* 1.3 57.5 + - - +
124B ALA* 3.4 2.4 + - - +
125B ARG* 2.9 52.4 + - - +
118D VAL* 4.3 12.1 - - + -
267D TYR* 5.2 0.7 - - - -
273D VAL* 4.6 12.1 - - + -
274D ILE 3.3 21.8 + - - +
275D THR* 4.6 1.2 - - + +
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Residues in contact with ALA 122 (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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118B VAL* 3.1 14.5 + - + +
119B GLU* 3.6 11.2 - - + +
121B ALA* 1.3 74.6 - - - +
123B TYR* 1.3 55.5 + - - +
125B ARG* 3.5 19.0 - - - +
126B ASP* 2.8 51.3 + - - +
28C ARG* 4.7 12.3 - - - +
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Residues in contact with TYR 123 (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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119B GLU* 3.0 14.5 + - + +
120B GLY* 3.2 12.6 - - - +
122B ALA* 1.3 79.0 - - - +
124B ALA* 1.3 60.1 + - - +
126B ASP* 3.6 0.4 + - - -
127B GLY 3.6 1.4 + - - -
128B LEU* 3.1 76.9 + - + +
129B TRP* 3.5 23.0 - + + -
130B LYS 4.7 0.9 + - - -
131B ALA 5.1 0.2 + - - -
136B LEU* 3.6 40.8 - - + +
137B LEU* 4.3 9.4 - - + -
40C ARG* 6.0 3.1 - - - -
30D LEU* 4.3 15.9 - - - +
276D PRO* 3.8 18.2 - - + -
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Residues in contact with ALA 124 (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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120B GLY 3.1 9.4 + - - +
121B ALA 3.8 5.6 - - - +
123B TYR* 1.3 78.6 - - - +
125B ARG* 1.3 65.4 + - - +
127B GLY* 3.0 14.6 + - - -
129B TRP* 4.0 26.7 - - + +
260D LEU 4.9 1.0 - - - +
262D PRO* 4.6 1.9 - - - +
267D TYR* 3.6 36.4 + - + +
274D ILE* 4.0 12.3 - - + +
276D PRO* 4.4 7.0 - - + -
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Residues in contact with ARG 125 (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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118B VAL 5.3 0.6 + - - -
121B ALA* 2.9 41.0 + - - +
122B ALA* 3.5 26.9 - - - +
124B ALA* 1.3 77.3 - - - +
126B ASP* 1.3 64.6 + - - +
127B GLY 3.1 3.2 + - - -
28C ARG* 6.1 1.7 - - - +
118D VAL* 3.7 19.6 - - - +
262D PRO* 4.0 14.9 - - - +
267D TYR* 3.8 40.0 + - + +
273D VAL* 6.3 1.0 - - - +
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Residues in contact with ASP 126 (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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122B ALA* 2.8 31.7 + - - +
123B TYR* 4.1 4.1 - - - +
124B ALA 3.2 0.4 - - - -
125B ARG* 1.3 80.9 + - - +
127B GLY* 1.3 60.7 + - - +
128B LEU* 3.4 23.0 + - + +
24C VAL 4.7 9.7 - - - +
25C GLU* 5.6 0.3 - - - -
26C VAL 4.9 7.5 - - - +
28C ARG* 2.7 52.0 + - - +
262D PRO* 4.6 2.0 - - - -
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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