Contacts of the helix formed by residues 397 - 403 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140G ALA 5.8 0.2 - - - -
144G TRP* 3.2 48.9 - - - -
163G ARG* 3.9 2.6 + - - -
165G ILE* 4.5 0.9 - - - -
395G CYS 3.4 3.8 + - - -
396G ARG* 1.3 77.0 - - - +
398G LEU* 1.3 66.4 + - - +
399G ALA* 3.7 8.5 + - - +
400G GLU* 2.8 44.6 + - - +
401G GLU 3.6 5.9 + - - -
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Residues in contact with LEU 398 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136G SER* 3.9 13.7 - - - +
137G LEU* 3.8 26.2 - - + +
140G ALA* 3.2 39.9 + - + +
144G TRP* 4.9 0.2 - - - -
152G ILE* 4.0 15.5 - - + -
161G TYR* 5.2 2.0 - - - +
163G ARG* 3.7 19.3 - - - +
165G ILE* 3.6 14.3 - - + +
396G ARG 3.6 1.1 + - - -
397G SER* 1.3 72.2 - - - +
399G ALA* 1.3 64.9 + - - +
401G GLU* 2.8 40.8 + - - +
402G TYR* 3.1 23.0 + - + -
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Residues in contact with ALA 399 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G LEU* 4.9 5.8 - - - +
140G ALA 6.2 0.2 - - - -
141G ASP* 5.2 12.3 - - + +
397G SER* 3.2 9.1 - - - +
398G LEU* 1.3 79.4 - - - +
400G GLU* 1.3 52.3 + - + +
402G TYR* 2.9 9.0 + - - +
403G GLY* 2.7 35.0 + - - -
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Residues in contact with GLU 400 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
144G TRP* 5.1 5.7 - - - -
396G ARG* 2.8 50.1 + - - +
397G SER* 2.8 35.4 + - - +
398G LEU 3.2 0.2 - - - -
399G ALA* 1.3 76.7 - - + +
401G GLU* 1.3 60.5 + - - +
403G GLY 3.4 2.3 + - - -
406G THR* 3.2 34.9 + - + +
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Residues in contact with GLU 401 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161G TYR* 4.8 0.4 + - - -
163G ARG* 2.6 39.6 + - - +
396G ARG* 3.6 13.6 - - - +
397G SER 3.6 6.3 + - - +
398G LEU* 2.8 20.7 + - - +
400G GLU* 1.3 74.6 - - - +
402G TYR* 1.3 65.9 + - + +
403G GLY 3.3 0.7 - - - -
407G ILE* 3.7 23.9 - - + +
408G ASN 5.8 0.4 - - - +
426G TYR* 2.8 38.2 + - - +
430G ARG* 5.2 1.0 + - - -
468G TYR* 4.4 1.4 - - - -
519G THR* 3.8 7.5 + - - -
533G GLN* 3.4 31.3 - - - +
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Residues in contact with TYR 402 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133G GLU* 3.4 35.1 + - + +
136G SER* 6.5 1.3 - - - -
137G LEU* 3.6 37.0 - - + -
161G TYR* 4.9 9.1 + - - -
398G LEU* 3.1 32.5 + - + +
399G ALA* 2.9 7.9 + - - +
401G GLU* 1.3 85.0 - - - +
403G GLY* 1.3 63.1 + - - +
404G LEU* 3.6 1.7 + - - +
426G TYR* 3.8 16.2 + - - -
430G ARG* 3.5 35.5 + - - -
433G ASP* 4.8 4.3 + - - -
468G TYR* 2.8 23.1 + - - -
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Residues in contact with GLY 403 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399G ALA 2.7 13.9 + - - -
400G GLU 3.4 1.2 + - - -
401G GLU 3.3 1.8 - - - -
402G TYR* 1.3 82.2 - - - +
404G LEU* 1.3 61.0 + - - -
405G ASP 3.5 2.2 - - - -
406G THR* 3.4 15.3 - - - -
407G ILE* 3.0 28.9 + - - +
468G 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