Contacts of the helix formed by residues 155 - 165 (chain D) in PDB entry 1CCW
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 SER 155 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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150D HIS* 3.2 20.9 + - - -
152D THR* 3.7 14.4 - - - -
153D PRO 3.8 1.4 + - - -
154D ASP* 1.3 73.1 - - - +
156D ARG* 1.3 58.7 + - - +
157D LEU 3.5 1.6 - - - -
158D LEU* 3.4 13.7 + - - +
159D ALA* 2.8 27.0 + - - +
170D ASN* 4.1 6.4 + - - -
193D ASP* 5.1 0.8 - - - +
194D TRP* 3.5 32.1 - - - +
197D CYS* 3.7 9.5 - - - -
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Residues in contact with ARG 156 (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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8D TRP* 6.0 0.7 - - - -
16D GLN* 4.2 14.8 + - - -
19D GLU* 5.4 3.6 + - - +
20D VAL* 3.5 32.9 - - + +
23D GLN* 3.3 18.6 + - - +
154D ASP* 2.7 39.2 + - - +
155D SER* 1.3 78.5 - - - +
157D LEU* 1.3 63.8 + - - +
159D ALA* 3.3 3.3 + - - +
160D GLU* 3.1 25.3 + - - +
189D LYS* 3.9 13.1 - - - +
193D ASP* 3.5 37.8 + - + +
196D TYR* 3.6 44.9 - - + -
197D CYS* 4.1 2.7 - - - -
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Residues in contact with LEU 157 (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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20D VAL* 3.5 20.0 - - + +
21D LEU* 4.2 13.0 - - + -
23D GLN* 3.9 26.0 - - + +
24D TRP* 3.7 28.3 - - + +
27D GLY* 4.2 17.7 - - - -
102D ASN* 6.1 0.2 - - - +
104D TYR* 4.1 11.7 - - - +
128D VAL* 3.7 25.1 - - + -
154D ASP 5.4 0.4 + - - -
155D SER 3.5 0.2 - - - -
156D ARG* 1.3 75.5 - - - +
158D LEU* 1.3 68.8 + - - +
160D GLU* 3.2 1.9 + - - +
161D ILE* 3.0 40.9 + - + +
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Residues in contact with LEU 158 (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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95D ILE* 4.3 26.0 - - + -
99D THR* 4.4 10.3 - - + -
104D TYR* 5.1 1.9 + - - +
127D GLY* 4.6 0.4 - - - -
128D VAL* 3.8 33.7 - - + +
148D ALA* 5.2 1.6 - - + -
150D HIS* 3.6 43.3 - - + +
152D THR* 4.3 8.7 - - + +
154D ASP 5.7 0.4 + - - +
155D SER* 3.4 13.4 + - - +
156D ARG 3.4 0.6 - - - -
157D LEU* 1.3 78.8 - - - +
159D ALA* 1.3 58.2 + - - +
161D ILE* 3.3 1.9 + - + +
162D ILE* 2.9 55.5 + - + +
170D ASN* 5.7 0.7 - - - +
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Residues in contact with ALA 159 (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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155D SER* 2.8 21.6 + - - +
156D ARG 3.6 4.3 - - - +
158D LEU* 1.3 70.1 - - - +
160D GLU* 1.3 66.1 + - - +
162D ILE* 4.0 8.3 - - - -
163D HIS* 3.1 35.4 + - + +
170D ASN* 3.9 22.2 - - - +
197D CYS* 4.0 15.0 - - + +
200D LEU* 3.9 13.9 - - + -
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Residues in contact with GLU 160 (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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17D ARG* 2.8 40.6 + - - -
20D VAL* 4.5 2.2 - - + -
21D LEU* 4.1 23.1 - - + -
30D VAL* 3.5 14.5 - - + +
32D LEU* 4.5 2.4 - - - +
156D ARG 3.1 18.1 + - - +
157D LEU* 3.6 8.1 - - - +
159D ALA* 1.3 74.7 - - - +
161D ILE* 1.3 62.7 + - - +
163D HIS* 4.4 0.3 - - - +
164D ALA* 3.1 27.0 + - - +
196D TYR* 2.5 36.3 + - + +
200D LEU* 3.7 23.1 - - + +
204D TYR* 5.0 2.3 + - - -
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Residues in contact with ILE 161 (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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26D THR* 3.3 33.4 - - - +
30D VAL* 4.0 15.5 - - + -
127D GLY 3.7 15.0 - - - +
128D VAL* 3.9 16.4 - - - +
131D GLY 3.6 27.4 - - - +
132D VAL* 3.7 11.9 - - + +
135D CYS* 4.1 5.3 - - - +
157D LEU* 3.0 38.4 + - + +
158D LEU* 3.8 4.5 - - - +
160D GLU* 1.3 78.1 - - - +
162D ILE* 1.3 59.6 + - + +
164D ALA 3.5 0.9 + - - -
165D GLY* 2.8 25.6 + - - -
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Residues in contact with ILE 162 (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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95D ILE* 5.2 0.7 - - + -
127D GLY* 5.3 0.4 - - - -
135D CYS* 4.2 13.0 - - - -
148D ALA* 4.0 15.9 - - + -
158D LEU* 2.9 46.6 + - + +
159D ALA* 3.7 9.0 - - - +
161D ILE* 1.3 75.1 - - + +
163D HIS* 1.3 91.3 + - + +
165D GLY* 3.2 7.1 + - - -
166D GLY 3.2 0.5 + - - -
167D TRP* 2.9 65.1 + - + +
169D SER 3.7 16.4 - - - +
170D ASN* 4.3 5.6 - - + +
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Residues in contact with HIS 163 (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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39D LEU* 3.5 19.9 - - - +
159D ALA* 3.1 28.5 + - + +
160D GLU 4.4 1.1 - - - +
162D ILE* 1.3 89.2 - - + +
164D ALA* 1.3 64.1 + - - +
165D GLY 3.0 1.6 - - - -
166D GLY 3.0 10.6 + - - -
167D TRP 3.0 22.6 + - - -
169D SER 4.0 3.6 - - - -
170D ASN* 3.7 25.5 + - + +
197D CYS 5.2 1.0 + - - -
200D LEU* 3.9 17.3 - - + -
201D VAL* 3.8 17.5 - - + +
204D TYR* 3.9 20.9 - - + -
211D ILE* 3.4 33.9 - - + +
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Residues in contact with ALA 164 (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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29D GLU 5.3 0.2 - - - +
30D VAL* 4.2 15.7 - - + -
31D ASP 5.3 0.4 - - - +
34D GLU* 5.9 0.2 - - - +
35D ALA* 3.9 26.5 - - + +
38D TYR* 4.1 3.1 - - - -
132D VAL* 3.9 22.4 - - + -
136D ARG* 2.9 32.5 + - - +
160D GLU 3.1 19.6 + - - +
163D HIS* 1.3 76.1 - - - +
165D GLY* 1.3 57.1 - - - +
166D GLY 3.2 1.7 + - - -
204D TYR* 4.0 3.2 + - - +
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Residues in contact with GLY 165 (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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38D TYR* 4.1 0.3 - - - -
132D VAL* 4.0 3.8 - - - +
135D CYS* 3.6 12.1 - - - +
136D ARG* 3.5 35.5 - - - +
139D LEU* 3.9 4.2 - - - +
161D ILE 2.8 15.8 + - - -
162D ILE 3.3 8.3 - - - -
163D HIS 3.0 1.0 - - - -
164D ALA* 1.3 76.0 - - - +
166D GLY* 1.3 57.9 + - - +
167D TRP* 3.4 12.4 - - - -
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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
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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