Contacts of the helix formed by residues 397 - 403 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A ALA 5.8 0.2 - - - -
144A TRP* 3.2 47.6 - - - -
163A ARG* 3.8 2.6 + - - -
165A ILE* 4.5 0.7 - - - -
395A CYS 3.4 3.6 + - - -
396A ARG* 1.3 79.1 - - - +
398A LEU* 1.3 66.0 + - - +
399A ALA* 3.7 9.1 + - - +
400A GLU* 2.8 44.7 + - - +
401A GLU 3.6 6.1 + - - -
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Residues in contact with LEU 398 (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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136A SER* 3.9 13.5 - - - +
137A LEU* 3.8 26.0 - - + +
140A ALA* 3.2 38.8 + - + +
144A TRP* 4.9 0.2 - - - -
152A ILE* 4.0 15.5 - - + -
161A TYR* 5.2 2.5 - - - +
163A ARG* 3.7 18.4 - - - +
165A ILE* 3.6 14.5 - - + +
396A ARG 3.5 1.5 + - - -
397A SER* 1.3 73.3 - - - +
399A ALA* 1.3 65.9 + - - +
401A GLU* 2.8 40.1 + - - +
402A TYR* 3.2 23.0 + - + -
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Residues in contact with ALA 399 (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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137A LEU* 4.9 5.6 - - - +
140A ALA 5.8 0.6 + - - -
141A ASP* 5.2 12.1 - - + +
397A SER* 3.8 8.7 - - - +
398A LEU* 1.3 79.6 - - - +
400A GLU* 1.3 52.3 + - + +
402A TYR* 3.0 8.5 + - - +
403A GLY* 2.7 34.5 + - - -
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Residues in contact with GLU 400 (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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144A TRP* 5.1 5.7 - - - -
396A ARG* 2.8 50.2 + - - +
397A SER* 2.8 39.3 + - - +
398A LEU 3.1 0.4 + - - -
399A ALA* 1.3 76.5 - - + +
401A GLU* 1.3 60.8 + - - +
403A GLY 3.4 2.1 + - - -
406A THR* 3.1 35.2 + - + +
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Residues in contact with GLU 401 (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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161A TYR* 4.8 0.2 + - - -
163A ARG* 2.6 38.7 + - - +
396A ARG* 3.6 14.1 - - - +
397A SER 3.6 6.2 + - - +
398A LEU* 2.8 16.8 + - - +
400A GLU* 1.3 78.0 - - - +
402A TYR* 1.3 65.2 + - + +
403A GLY 3.3 0.2 - - - -
407A ILE* 3.7 25.7 - - + +
408A ASN 5.8 0.4 - - - +
426A TYR* 2.8 38.0 + - + +
430A ARG* 5.3 0.9 + - - -
468A TYR* 4.4 1.4 - - - -
519A THR* 3.8 7.3 + - - -
533A GLN* 3.4 31.7 - - - +
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Residues in contact with TYR 402 (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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133A GLU* 3.5 34.8 + - + +
136A SER* 6.5 1.3 - - - -
137A LEU* 3.5 37.9 - - + -
161A TYR* 4.9 9.3 + - - -
398A LEU* 3.2 31.4 + - + +
399A ALA* 3.0 8.3 + - - +
401A GLU* 1.3 85.0 - - - +
403A GLY* 1.3 64.4 + - - +
404A LEU* 3.6 1.7 + - - +
426A TYR* 3.8 16.4 + - - -
430A ARG* 3.5 36.1 + - - +
433A ASP* 4.8 4.0 + - - -
468A TYR* 2.8 24.5 + - - -
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Residues in contact with GLY 403 (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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399A ALA 2.7 12.2 + - - -
400A GLU 3.4 1.4 + - - -
401A GLU 3.3 1.8 - - - -
402A TYR* 1.3 81.3 - - - +
404A LEU* 1.3 60.9 + - - -
405A ASP 3.5 2.2 - - - -
406A THR* 3.4 17.0 - - - -
407A ILE* 3.0 29.1 + - - +
468A TYR* 3.8 1.1 - - - -
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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