Contacts of the helix formed by residues 153 - 159 (chain D) in PDB entry 1C2O
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 VAL 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69D CYS* 4.6 7.6 - - + +
70D TYR 3.7 18.6 - - - +
71D GLN* 3.8 13.0 - - + +
119D TYR* 4.2 10.5 - - + +
123D PHE* 3.4 15.9 - - - +
124D TYR 3.5 17.5 - - - +
125D SER* 3.1 30.3 - - - +
151D TYR* 3.3 16.6 + - + +
152D ARG* 1.3 74.5 - - - +
154D GLY* 1.3 65.0 + - - +
156D PHE* 3.6 12.0 + - - +
157D GLY* 2.9 17.0 + - - -
158D PHE* 4.3 2.5 - - - -
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Residues in contact with GLY 154 (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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70D TYR 5.5 0.4 - - - -
71D GLN* 6.5 0.2 - - - -
123D PHE 2.8 16.8 + - - -
124D TYR* 3.6 4.6 - - - +
153D VAL* 1.3 76.1 - - - +
155D THR* 1.3 56.9 + - - -
156D PHE* 5.0 2.9 - - - -
157D GLY 3.0 0.7 + - - -
158D PHE* 2.7 30.0 + - - +
285D GLU* 3.7 23.3 - - - -
299D PHE* 3.6 12.2 - - - +
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Residues in contact with THR 155 (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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47D PHE* 3.6 9.9 - - - -
154D GLY* 1.3 71.5 - - - -
156D PHE* 1.3 74.4 + - - +
159D LEU* 2.7 60.7 + - + +
251D LEU* 3.9 16.6 - - + -
281D LEU* 3.8 26.4 - - + +
282D VAL* 4.8 1.0 + - - +
285D GLU* 4.6 8.5 + - + +
299D PHE* 3.8 28.0 - - + +
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Residues in contact with PHE 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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46D ARG* 3.8 25.4 - - + -
47D PHE* 4.3 14.5 + + - -
70D TYR* 3.4 51.8 - + + +
94D GLU* 3.6 22.2 - - + +
152D ARG* 3.8 24.8 + - + -
153D VAL 3.7 7.9 - - - +
154D GLY* 3.2 1.5 - - - -
155D THR* 1.3 92.0 - - - +
157D GLY* 1.3 59.5 + - - +
171D VAL* 3.4 14.9 - - - +
278D ALA* 3.7 32.5 - - + -
281D LEU* 4.0 12.8 - - + -
282D VAL* 4.0 8.5 - - + -
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Residues in contact with GLY 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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152D ARG* 3.0 32.9 - - - +
153D VAL 2.9 11.1 + - - -
154D GLY 3.6 1.3 - - - -
156D PHE* 1.3 79.5 - - - +
158D PHE* 1.4 65.1 + - - +
171D VAL* 3.2 14.3 + - - +
172D GLY 2.9 24.2 + - - -
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Residues in contact with PHE 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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123D PHE* 3.5 47.8 - + - -
151D TYR* 4.7 5.6 - + - -
152D ARG 3.6 15.9 - - - -
153D VAL* 4.3 1.6 - - - -
154D GLY 2.7 13.4 + - - +
157D GLY* 1.4 82.5 - - - +
159D LEU* 1.3 67.9 + - - +
160D ALA* 2.9 12.6 + - - +
169D GLY* 4.4 2.6 - - - -
170D ASN* 3.9 16.0 + - - +
172D GLY* 4.0 13.5 - - - -
173D LEU* 4.0 18.8 - - + -
299D PHE* 3.7 10.8 - - - -
300D VAL* 3.5 29.0 - - - +
301D PRO* 3.4 35.4 - - + -
302D VAL* 5.6 1.2 - - - +
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Residues in contact with LEU 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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47D PHE* 4.2 19.2 - - + +
155D THR* 2.7 56.0 + - + +
157D GLY 5.5 0.2 - - - -
158D PHE* 1.3 70.1 - - - +
160D ALA* 1.3 63.6 + - - +
161D LEU* 4.0 14.4 - - + -
167D ALA* 4.2 19.4 - - + +
169D GLY* 4.4 4.9 + - - -
248D ALA* 4.0 21.1 - - + +
251D LEU* 4.0 17.0 - - + -
270D ILE* 5.0 0.4 - - + -
273D LEU* 4.1 22.0 - - + -
281D LEU* 5.6 0.2 - - + -
299D PHE* 3.6 20.8 - - + -
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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