Contacts of the helix formed by residues 155 - 159 (chain A) in PDB entry 3RC0
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 HIS 155 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.5 27.3 - - + +
154A GLU* 1.3 81.9 + - - +
156A PRO* 1.3 65.5 - - + +
157A MET* 3.0 21.5 - - + -
158A PHE* 2.9 25.9 + - + +
159A TRP* 3.5 6.4 - - - -
218A ALA* 3.4 31.1 + - + +
219A LEU* 5.7 0.2 - - - -
221A MET* 4.1 12.8 - - + -
222A ALA* 3.7 10.7 - - + +
223A TYR* 6.4 0.2 - + - -
295A HIS 3.5 15.9 - - - +
296A MET 2.9 31.5 + - - -
297A TYR* 4.0 10.9 - - - -
298A GLY* 4.1 3.6 - - - -
484A SAM 4.9 1.6 - - - -
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Residues in contact with PRO 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLU 3.5 4.2 - - - +
155A HIS* 1.3 84.9 - - + +
157A MET* 1.3 48.7 + - - +
158A PHE 3.0 2.0 - - - -
159A TRP* 3.0 39.2 + - + +
164A ARG* 2.7 38.9 + - - -
168A LEU* 4.1 15.7 - - + -
173A VAL* 3.8 20.4 - - + -
177A VAL* 4.4 3.6 - - + -
294A ILE* 2.9 37.0 - - + +
295A HIS* 4.1 5.6 - - - +
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Residues in contact with MET 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155A HIS* 3.6 15.7 - - + -
156A PRO* 1.3 80.7 - - - +
158A PHE* 1.3 86.5 + - + +
159A TRP 4.1 1.4 - - - +
164A ARG* 3.7 7.4 + - - +
177A VAL* 3.7 29.7 - - + +
180A ASP* 5.3 6.1 - - + +
181A LEU* 3.9 29.4 - - + +
184A ILE* 3.4 31.4 - - + -
214A HIS* 4.0 15.3 - - + +
218A ALA* 4.3 3.1 - - - -
221A MET* 3.5 31.4 - - - -
295A HIS* 5.8 2.2 - - + +
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Residues in contact with PHE 158 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LEU* 3.8 32.1 - - + +
155A HIS* 2.9 23.9 + - + +
157A MET* 1.3 94.0 - - + +
159A TRP* 1.3 65.4 + - + +
160A PRO* 3.8 3.1 - - - +
214A HIS* 3.7 45.8 - + + -
215A GLN* 4.2 6.3 - - + -
218A ALA* 3.7 22.7 - - + -
450A ARG* 4.6 6.1 + - - +
474A EDO 3.6 35.9 - - - -
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Residues in contact with TRP 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A GLU* 3.5 19.3 + - - +
155A HIS 3.5 4.7 - - - -
156A PRO* 3.0 27.0 + - + +
157A MET 4.1 1.7 - - - +
158A PHE* 1.3 83.3 - - + +
160A PRO* 1.3 81.6 - - + +
161A GLU 3.4 0.9 + - - -
163A GLU* 4.3 8.3 - - + +
164A ARG* 3.0 37.9 + - + +
167A LEU* 4.0 18.8 - - + -
168A LEU* 3.8 21.5 - - + -
294A ILE* 4.1 22.2 - - + -
450A ARG* 3.4 55.4 - - + +
453A GLN* 3.6 21.5 + - - -
454A ALA* 4.5 2.7 - - + -
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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