Contacts of the helix formed by residues 3477 - 3483 (chain D) in PDB entry 1DDX
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 SER3477 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3475D TYR* 3.3 2.3 + - - +
3476D THR* 1.3 87.2 + - - +
3478D PHE* 1.3 60.2 + - - +
3479D GLU* 3.2 13.0 + - - +
3480D GLU* 2.7 43.8 + - - +
3481D LEU* 3.2 4.7 + - - +
3492D LYS* 6.3 1.1 - - - -
3498D ILE* 3.8 13.0 - - - +
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Residues in contact with PHE3478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3477D SER* 1.3 72.8 - - - +
3479D GLU* 1.3 54.9 + - - +
3481D LEU* 3.1 9.6 + - + +
3482D THR* 2.4 35.1 + - - -
3488D ALA* 3.6 20.6 - - + +
3491D LEU* 3.4 28.0 - - + -
3492D LYS* 3.7 35.7 - - + -
3495D TYR* 3.5 37.2 - + + -
3496D SER 3.3 22.4 - - - -
3498D ILE* 3.4 42.8 - - + -
3501D MET* 4.5 10.3 - - + -
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Residues in contact with GLU3479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3477D SER* 3.2 10.7 + - - +
3478D PHE* 1.3 80.8 - - - +
3480D GLU* 1.3 52.6 + - - +
3482D THR* 3.9 0.2 - - - -
3483D GLY* 2.5 44.4 + - - +
3484D GLU 3.7 11.7 - - - +
3485D LYS* 2.9 54.8 + - + +
3488D ALA* 3.5 12.0 - - + +
3489D ALA* 5.3 1.9 + - - +
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Residues in contact with GLU3480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3474D PRO 4.9 0.9 - - - -
3475D TYR* 3.5 29.2 - - + -
3476D THR* 2.8 46.2 + - - +
3477D SER* 2.7 21.1 + - - +
3479D GLU* 1.3 78.3 - - - +
3481D LEU* 1.3 64.5 + - - +
3482D THR 3.2 0.9 + - - -
3483D GLY* 3.7 4.6 + - - -
3511D LYS* 4.2 10.4 - - - +
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Residues in contact with LEU3481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3463D LEU* 4.9 1.3 - - + -
3475D TYR* 3.4 34.0 - - + -
3477D SER 3.2 5.4 + - - +
3478D PHE* 3.1 13.1 + - + +
3480D GLU* 1.3 81.0 - - - +
3482D THR* 1.3 54.4 + - + +
3491D LEU* 5.2 10.8 - - + -
3498D ILE* 4.8 7.0 - - + -
3501D MET* 4.1 18.8 - - + -
3506D ALA* 3.3 36.3 - - + +
3509D VAL* 5.0 1.6 - - + -
3510D GLU* 3.3 34.3 - - + +
3511D LYS* 2.5 34.1 + - - +
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Residues in contact with THR3482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3478D PHE 2.4 28.6 + - - -
3481D LEU* 1.3 78.6 - - + +
3483D GLY* 1.3 56.2 + - - +
3484D GLU* 3.0 23.5 + - - +
3487D MET* 3.7 20.9 - - + -
3488D ALA* 3.4 16.3 - - - +
3491D LEU* 5.2 1.2 - - + +
3509D VAL* 3.2 44.2 - - + +
3511D LYS* 2.9 25.5 - - - +
3512D PRO* 5.4 0.2 - - - +
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Residues in contact with GLY3483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3479D GLU* 2.5 31.4 + - - +
3480D GLU* 3.7 3.8 + - - -
3482D THR* 1.3 71.0 - - - +
3484D GLU* 1.3 63.2 + - - +
3485D LYS* 3.8 4.0 + - - +
3511D LYS* 4.0 13.5 - - - -
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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