Contacts of the helix formed by residues 3552 - 3561 (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 GLY3552 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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2048C MET* 3.6 15.7 - - - +
3547D PRO* 2.5 38.7 + - - +
3548D SER 3.7 2.1 + - - -
3550D PHE 3.8 0.2 - - - +
3551D GLY* 1.3 71.7 - - - +
3553D GLU* 1.3 67.2 + - - -
3554D VAL 3.0 3.5 + - - -
3555D GLY 3.1 5.0 + - - -
3556D PHE* 2.9 17.5 + - - +
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Residues in contact with GLU3553 (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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3547D PRO* 3.1 33.0 - - + +
3552D GLY* 1.3 68.3 - - - -
3554D VAL* 1.3 56.2 + - + +
3556D PHE* 2.8 17.8 + - - +
3557D LYS* 2.6 37.7 + - - +
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Residues in contact with VAL3554 (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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3315D ILE* 4.0 27.6 - - + +
3316D LEU* 5.6 2.2 - - + -
3319D GLU* 3.1 44.9 - - + +
3552D GLY 3.0 1.3 + - - -
3553D GLU* 1.3 82.4 - - + +
3555D GLY* 1.3 65.3 + - - +
3556D PHE 2.8 2.8 + - - -
3557D LYS* 3.0 13.8 + - - +
3558D ILE* 3.2 14.1 + - + +
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Residues in contact with GLY3555 (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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3316D LEU* 4.6 9.8 - - - +
3335D ILE* 3.3 25.2 - - - +
3550D PHE* 3.7 17.3 + - - +
3551D GLY 4.6 2.2 + - - -
3552D GLY 3.1 6.8 + - - -
3554D VAL* 1.3 85.0 - - - +
3556D PHE* 1.3 60.0 + - - +
3558D ILE* 3.4 22.5 - - - +
3559D ILE* 4.1 1.9 + - - +
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Residues in contact with PHE3556 (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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3545D TRP* 3.5 46.2 - + - -
3546D LYS* 4.3 8.3 - - - -
3547D PRO* 3.8 22.7 - - + -
3550D PHE* 3.2 40.4 - + - +
3552D GLY 2.9 11.2 + - - +
3553D GLU* 2.8 29.9 + - - +
3555D GLY* 1.3 75.5 - - - +
3557D LYS* 1.3 68.7 + - - +
3559D ILE* 2.8 20.3 + - + +
3560D ASN* 3.0 25.9 + - - -
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Residues in contact with LYS3557 (chain D).
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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3553D GLU 2.6 14.6 + - - +
3554D VAL* 3.4 11.7 - - - +
3556D PHE* 1.3 72.1 - - - +
3558D ILE* 1.3 66.8 + - - +
3560D ASN* 2.6 26.4 + - + +
3561D THR* 2.8 37.6 + - + +
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Residues in contact with ILE3558 (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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3311D ARG* 4.1 12.6 - - - +
3312D VAL* 3.8 11.7 - - + -
3315D ILE* 3.5 39.5 - - + -
3316D LEU* 6.4 0.4 - - + -
3335D ILE* 3.3 14.4 - - + -
3339D GLU* 2.7 31.4 - - - +
3554D VAL* 3.2 12.5 + - + +
3555D GLY* 3.4 20.4 - - - +
3556D PHE 3.1 0.2 - - - -
3557D LYS* 1.3 79.0 - - - +
3559D ILE* 1.3 64.4 + - - +
3561D THR* 3.1 27.2 + - - +
3562D ALA* 3.5 4.0 + - - +
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Residues in contact with ILE3559 (chain D).
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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3335D ILE* 3.0 48.2 - - + +
3338D GLY* 3.3 35.0 - - - +
3339D GLU* 3.5 7.9 - - - +
3342D LYS* 3.3 14.2 - - + +
3361D PHE* 4.4 8.7 - - + -
3539D ILE* 4.6 1.3 - - + -
3545D TRP* 4.4 17.0 - - + -
3550D PHE* 3.8 30.1 - - + -
3555D GLY 4.4 0.9 - - - +
3556D PHE 2.8 14.9 + - - +
3558D ILE* 1.3 76.1 - - - +
3560D ASN* 1.3 62.1 + - - +
3561D THR 2.9 5.5 + - - -
3562D ALA* 3.3 9.5 + - - +
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Residues in contact with ASN3560 (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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3342D LYS* 2.8 27.2 + - - +
3545D TRP* 3.6 31.0 - - - -
3556D PHE* 3.0 48.8 + - - +
3557D LYS* 2.6 16.4 + - - +
3559D ILE* 1.3 71.2 - - - +
3561D THR* 1.3 63.1 + - + +
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Residues in contact with THR3561 (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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3342D LYS* 4.4 0.4 - - - +
3557D LYS* 2.8 50.0 + - + +
3558D ILE* 3.1 11.9 + - - +
3560D ASN* 1.3 82.6 - - + +
3562D ALA* 1.3 56.2 + - - +
3566D SER* 4.4 6.9 + - - -
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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