Contacts of the helix formed by residues 397 - 403 (chain E) in PDB entry 3DBL
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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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144E TRP* 3.5 46.6 - - - -
163E ARG* 3.7 3.4 + - - -
165E ILE* 4.3 0.7 - - - -
395E CYS 3.5 2.2 + - - -
396E ARG* 1.3 77.0 - - - +
398E LEU* 1.3 65.6 + - - +
399E ALA* 3.7 10.3 - - - +
400E GLU* 3.2 41.4 + - - +
401E GLU 3.2 9.4 + - - -
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Residues in contact with LEU 398 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E SER* 4.2 5.6 - - - -
137E LEU* 3.9 28.0 - - + +
140E ALA* 3.7 27.0 - - + +
152E ILE* 4.0 16.2 - - + -
161E TYR* 4.8 2.7 - - - +
163E ARG* 3.9 18.8 - - + +
165E ILE* 3.7 23.1 - - + +
396E ARG 3.8 0.8 + - - -
397E SER* 1.3 70.2 - - - +
399E ALA* 1.3 67.4 + - - +
401E GLU* 3.0 32.0 + - - +
402E TYR* 2.9 40.4 + - + +
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Residues in contact with ALA 399 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137E LEU* 4.7 11.1 - - - +
140E ALA* 5.6 0.6 - - - +
141E ASP* 5.2 11.0 - - + +
397E SER* 3.7 11.2 + - - +
398E LEU* 1.3 78.5 - - - +
400E GLU* 1.3 58.8 + - + +
402E TYR* 3.2 1.6 + - - +
403E GLY* 2.8 28.8 + - - -
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Residues in contact with GLU 400 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144E TRP* 5.5 3.9 - - - -
396E ARG* 3.3 37.1 + - - +
397E SER* 3.2 31.4 + - - +
398E LEU 3.2 0.2 - - - -
399E ALA* 1.3 80.0 - - + +
401E GLU* 1.3 62.6 + - - +
402E TYR 3.3 0.3 + - - -
403E GLY 3.3 3.5 + - - -
406E THR* 2.8 46.9 + - + +
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Residues in contact with GLU 401 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161E TYR* 3.9 8.1 + - - -
163E ARG* 2.7 49.1 + - - +
396E ARG* 3.9 3.4 - - - +
397E SER 3.2 2.0 + - - -
398E LEU* 3.0 18.9 + - - +
400E GLU* 1.3 79.7 - - - +
402E TYR* 1.3 71.4 + - + +
407E ILE* 3.8 21.0 - - - +
426E TYR* 2.7 38.0 + - - +
430E ARG* 4.3 4.5 + - - -
519E THR* 4.2 1.5 + - - -
534E LEU* 3.3 37.5 - - + +
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Residues in contact with TYR 402 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133E GLU* 3.5 30.8 + - + +
137E LEU* 3.9 26.7 - - + -
161E TYR* 5.1 5.9 + - - -
398E LEU* 2.9 37.7 + - + +
399E ALA 4.0 2.7 - - - +
401E GLU* 1.3 103.4 - - + +
403E GLY* 1.3 62.2 + - - +
404E LEU* 3.6 0.9 + - - +
426E TYR* 4.7 1.2 + - - -
430E ARG* 3.2 52.8 - - - +
433E ASP* 4.3 6.8 + - - -
468E TYR* 2.5 28.0 + - - +
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Residues in contact with GLY 403 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399E ALA 2.8 19.3 + - - -
400E GLU 3.3 2.4 + - - -
402E TYR* 1.3 74.6 - - - +
404E LEU* 1.3 65.8 + - - -
405E ASP 3.1 3.6 - - - -
406E THR* 3.7 10.3 - - - -
407E ILE* 3.1 25.3 + - - +
468E TYR* 4.1 0.2 - - - -
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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