Contacts of the strand formed by residues 3255 - 3257 (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 GLN3255 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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574A GLY 3.8 4.9 - - - -
575A CYS* 4.4 11.0 - - + +
577A PHE* 4.4 15.9 + - - +
3254D TYR* 1.3 83.6 - - - +
3256D VAL* 1.3 63.3 + - - +
3257D ILE* 3.6 23.1 - - + +
3260D GLU 3.4 0.7 - - - +
3261D VAL* 3.6 1.0 - - - -
3262D TYR* 2.7 42.2 + - + +
3263D PRO 2.6 29.2 + - - +
3264D PRO* 3.9 14.1 - - + +
3265D THR* 4.1 17.8 - - + +
3282D ASN 4.9 2.3 + - - +
3285D PHE* 3.4 26.3 - - - -
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Residues in contact with VAL3256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A GLU* 4.3 9.4 - - - +
574A GLY* 2.8 39.9 + - - +
575A CYS 5.3 0.2 - - - +
576A PRO* 4.7 9.0 - - - +
3254D TYR* 4.6 12.3 - - + -
3255D GLN* 1.3 75.5 - - - +
3257D ILE* 1.3 64.5 + - - +
3258D GLY 4.2 0.7 + - - -
3259D GLY* 3.7 30.7 - - - +
3260D GLU 3.1 11.7 - - - +
3261D VAL* 4.7 10.8 - - + -
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Residues in contact with ILE3257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424A GLU* 5.0 4.3 - - - +
577A PHE* 6.3 0.7 - - + -
3255D GLN* 3.6 37.5 - - + +
3256D VAL* 1.3 76.1 - - - +
3258D GLY* 1.3 72.3 + - - +
3259D GLY 3.1 0.7 - - - -
3260D GLU* 2.7 29.0 + - - +
3262D TYR* 3.8 20.4 - - + -
3282D ASN 4.7 7.4 - - - +
3285D PHE* 4.4 11.0 - - + -
3415D LEU* 4.3 30.7 - - + -
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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
------------------------------------------------------------
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