Contacts of the helix formed by residues 398 - 408 (chain A) in PDB entry 3DAN
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 VAL 398 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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328A PRO* 3.8 31.4 - - + +
329A LEU* 4.3 6.1 - - + -
332A SER* 3.6 22.9 - - - -
395A ASP* 3.1 30.4 + - + +
397A PHE* 1.3 77.1 - - - +
399A GLY* 1.3 71.3 + - - +
400A ASP 3.4 0.5 + - - -
401A GLY* 3.1 11.8 + - - -
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Residues in contact with GLY 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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397A PHE 3.9 1.0 + - - -
398A VAL* 1.3 80.5 - - - +
400A ASP* 1.3 65.2 + - - -
402A GLU* 2.9 28.1 + - - +
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Residues in contact with ASP 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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398A VAL 3.4 1.0 + - - -
399A GLY* 1.3 71.4 - - - -
401A GLY* 1.3 61.9 + - - +
402A GLU 2.9 1.7 + - - -
403A ALA* 3.0 22.9 + - - +
404A LEU* 5.3 0.2 - - - +
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Residues in contact with GLY 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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396A ARG 3.4 19.0 - - - +
397A PHE* 3.6 15.4 - - - -
398A VAL 3.1 8.2 + - - -
399A GLY 3.0 2.4 - - - -
400A ASP* 1.3 78.1 - - - +
402A GLU* 1.3 62.1 + - - +
404A LEU* 2.9 31.8 + - - +
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Residues in contact with GLU 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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397A PHE 3.3 15.7 + - - +
399A GLY* 2.9 19.5 + - - +
401A GLY* 1.3 78.4 - - - +
403A ALA* 1.3 61.2 + - - +
405A LEU* 3.1 42.3 + - + +
416A THR* 5.5 1.6 - - - +
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Residues in contact with ALA 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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400A ASP 3.0 15.6 + - - +
402A GLU* 1.3 78.8 - - - +
404A LEU* 1.3 65.0 + - + +
405A LEU 3.2 1.9 + - - -
406A LYS* 3.7 20.3 + - - +
407A TYR* 5.0 0.9 - - - -
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Residues in contact with LEU 404 (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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385A VAL* 4.3 17.5 - - + +
386A PHE* 3.9 24.0 - - + -
396A ARG* 4.6 17.5 - - + +
397A PHE* 3.8 17.4 - - + -
401A GLY* 2.9 22.1 + - - +
403A ALA* 1.3 80.0 - - + +
405A LEU* 1.3 54.6 + - - +
406A LYS 2.9 6.3 - - - -
407A TYR* 2.9 45.2 + - + +
408A VAL 3.9 1.6 + - - -
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Residues in contact with LEU 405 (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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335A TYR* 3.5 57.2 - - + +
397A PHE* 3.6 20.4 - - + -
402A GLU* 3.1 39.0 + - + +
404A LEU* 1.3 73.6 - - - +
406A LYS* 1.3 61.2 + - - +
407A TYR 2.9 7.5 + - - -
408A VAL* 3.1 21.9 + - + -
415A GLU* 3.3 27.8 + - + +
416A THR* 4.1 18.4 - - + -
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Residues in contact with LYS 406 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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403A ALA 3.7 13.3 + - - +
404A LEU 2.9 0.2 - - - -
405A LEU* 1.3 79.5 - - - +
407A TYR* 1.3 100.6 + - + +
408A VAL 3.5 0.2 - - - -
409A TRP* 2.9 19.8 + - - -
414A PRO* 3.7 15.8 - - + +
416A THR* 4.2 19.5 - - + +
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Residues in contact with TYR 407 (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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74A ALA* 4.8 6.1 - - + -
339A ARG* 5.3 0.2 - - - +
380A THR* 3.7 17.3 - - - +
385A VAL* 3.5 40.4 - - + -
386A PHE* 3.8 19.6 - - + -
403A ALA 5.1 0.7 - - - -
404A LEU* 2.9 29.9 + - + +
405A LEU 2.9 1.0 - - - -
406A LYS* 1.3 119.0 + - + +
408A VAL* 1.3 61.1 + - - +
409A TRP* 3.5 37.9 + + + +
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Residues in contact with VAL 408 (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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335A TYR* 4.4 16.6 - - + +
338A LEU* 4.5 6.1 - - + -
339A ARG* 4.5 14.1 - - + +
380A THR* 5.0 2.5 - - - -
386A PHE* 4.9 0.4 - - + -
397A PHE* 3.5 39.3 - - + -
404A LEU 4.1 0.2 - - - +
405A LEU* 3.1 20.7 + - + +
407A TYR* 1.3 77.2 - - - +
409A TRP* 1.3 62.1 + - - +
410A TRP* 3.9 24.2 + - + +
413A GLY 3.4 0.7 - - - +
415A GLU* 3.0 38.6 + - + +
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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