Contacts of the helix formed by residues 397 - 403 (chain C) in PDB entry 1R4N
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 397 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140C ALA 5.8 0.2 - - - -
144C TRP* 3.2 48.0 - - - -
163C ARG* 3.9 2.4 + - - -
165C ILE* 4.6 0.4 - - - -
395C CYS 3.4 3.6 + - - -
396C ARG* 1.3 78.0 - - - +
398C LEU* 1.3 66.8 + - - +
399C ALA* 3.6 9.0 + - - +
400C GLU* 2.9 43.3 + - - +
401C GLU 3.6 6.1 + - - -
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Residues in contact with LEU 398 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C SER* 3.9 13.9 - - - +
137C LEU* 3.8 25.6 - - + +
140C ALA* 3.2 39.6 + - + +
144C TRP* 4.9 0.2 - - - -
152C ILE* 4.0 14.6 - - + -
161C TYR* 5.2 2.2 - - - +
163C ARG* 3.7 18.4 - - - +
165C ILE* 3.6 14.5 - - + +
396C ARG 3.5 1.1 + - - -
397C SER* 1.3 73.4 - - - +
399C ALA* 1.3 65.2 + - - +
401C GLU* 2.8 40.5 + - - +
402C TYR* 3.2 23.3 + - + -
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Residues in contact with ALA 399 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137C LEU* 4.9 6.0 - - - +
140C ALA 5.8 0.2 + - - -
141C ASP* 5.2 12.6 - - + +
397C SER* 3.2 9.5 + - - +
398C LEU* 1.3 80.1 - - - +
400C GLU* 1.3 52.3 + - + +
402C TYR* 3.0 8.2 + - - +
403C GLY* 2.7 34.7 + - - -
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Residues in contact with GLU 400 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144C TRP* 5.1 5.0 - - - -
396C ARG* 2.8 51.0 + - - +
397C SER* 2.9 39.0 + - - +
398C LEU 3.2 0.2 - - - -
399C ALA* 1.3 77.1 - - + +
401C GLU* 1.3 59.8 + - - +
403C GLY 3.4 2.3 + - - -
406C THR* 3.2 35.6 + - + +
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Residues in contact with GLU 401 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161C TYR* 4.8 0.4 + - - -
163C ARG* 2.6 39.1 + - - +
396C ARG* 3.6 13.2 - - - +
397C SER 3.6 5.7 + - - +
398C LEU* 2.8 16.9 + - - +
400C GLU* 1.3 79.2 - - - +
402C TYR* 1.3 66.0 + - - +
403C GLY 3.3 0.7 - - - -
407C ILE* 3.7 25.0 - - + +
408C ASN 5.9 0.4 - - - +
426C TYR* 2.7 38.3 + - + +
430C ARG* 5.3 1.2 + - - -
468C TYR* 4.4 1.2 - - - -
519C THR* 3.8 7.3 + - - -
533C GLN* 3.4 31.8 - - - +
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Residues in contact with TYR 402 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133C GLU* 3.5 35.2 + - + +
136C SER* 6.5 1.6 - - - -
137C LEU* 3.5 38.4 - - + -
161C TYR* 4.9 8.8 + - - -
398C LEU* 3.2 32.9 + - + +
399C ALA* 3.0 8.5 + - - +
401C GLU* 1.3 84.8 - - - +
403C GLY* 1.3 63.9 + - - +
404C LEU* 3.6 1.9 + - - +
426C TYR* 3.8 17.5 + - - -
430C ARG* 3.5 35.2 + - - -
433C ASP* 4.8 4.2 + - - -
468C TYR* 2.8 23.9 + - - -
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Residues in contact with GLY 403 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C ALA 2.7 11.9 + - - -
400C GLU 3.4 0.8 + - - -
401C GLU 3.3 1.8 - - - -
402C TYR* 1.3 82.1 - - - +
404C LEU* 1.3 60.7 + - - -
405C ASP 3.4 2.2 - - - -
406C THR* 3.4 16.8 - - - -
407C ILE* 3.0 28.8 + - - +
468C TYR* 3.8 0.5 - - - -
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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