Contacts of the helix formed by residues 3096 - 3104 (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 PHE3096 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3091D TYR* 3.4 34.8 - + - -
3092D ILE* 3.7 23.6 - - + -
3095D HIS* 1.3 84.6 - - + +
3097D LYS* 1.3 50.5 + - - +
3098D GLY 2.5 5.1 + - - -
3099D VAL* 2.5 55.7 + - + -
3100D TRP* 3.2 6.3 + - + +
3702D BOG 4.1 29.8 - - + -
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Residues in contact with LYS3097 (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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3095D HIS 2.4 13.2 + - - -
3096D PHE* 1.3 70.1 - - - +
3098D GLY* 1.3 63.3 - - - +
3100D TRP* 3.3 3.9 + - - +
3101D ASN* 2.8 27.3 + - + +
3356D HIS* 3.3 46.4 - - + +
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Residues in contact with GLY3098 (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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3096D PHE 2.5 6.9 + - - -
3097D LYS* 1.3 76.1 - - - +
3099D VAL* 1.3 60.0 + - - -
3101D ASN* 3.0 22.9 + - - +
3102D ILE* 3.2 14.7 + - - +
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Residues in contact with VAL3099 (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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3096D PHE* 2.5 35.3 + - + +
3098D GLY* 1.3 68.1 - - - -
3100D TRP* 1.3 73.6 + - + +
3102D ILE* 2.6 47.4 + - + +
3103D VAL* 3.1 8.7 + - + +
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Residues in contact with TRP3100 (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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3092D ILE* 2.7 31.5 + - + -
3093D LEU* 3.1 40.1 + - + -
3095D HIS 2.7 25.1 + - - -
3096D PHE* 3.2 4.6 + - + +
3097D LYS 3.6 5.2 - - - +
3099D VAL* 1.3 89.2 - - + +
3101D ASN* 1.3 57.3 + - - +
3103D VAL* 3.5 19.5 + - + +
3104D ASN* 2.8 37.3 + - - +
3112D ILE* 4.4 18.4 - - + -
3356D HIS* 3.2 35.0 - - + +
3357D PHE* 3.7 30.5 - + + -
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Residues in contact with ASN3101 (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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3097D LYS* 2.8 17.8 + - + +
3098D GLY* 3.1 16.2 - - - +
3099D VAL 3.0 0.2 - - - -
3100D TRP* 1.3 77.3 - - - +
3102D ILE* 1.3 60.9 + - - +
3104D ASN* 3.5 10.0 + - - +
3105D ASN* 3.1 36.9 + - - +
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Residues in contact with ILE3102 (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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3098D GLY 3.4 7.6 - - - +
3099D VAL* 2.6 48.0 + - + +
3101D ASN* 1.3 74.7 - - + +
3103D VAL* 1.3 65.2 + - + +
3105D ASN* 3.1 33.8 + - - +
3108D LEU* 5.3 4.7 - - + -
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Residues in contact with VAL3103 (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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3099D VAL* 3.1 7.9 + - + +
3100D TRP* 4.0 18.4 - - + +
3102D ILE* 1.3 75.7 - - + +
3104D ASN* 1.3 67.6 + - - +
3105D ILE* 2.6 39.9 + - - +
3108D LEU* 3.4 44.9 - - + -
3109D ARG* 4.0 13.4 - - - +
3112D ILE* 4.5 10.1 - - + -
3357D PHE* 4.1 19.1 - - + -
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Residues in contact with ASN3104 (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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3100D TRP 2.8 28.1 + - - +
3101D ASN* 3.7 12.4 + - - +
3102D ILE 3.3 0.6 - - - -
3103D VAL* 1.3 72.5 - - - +
3105D ASN* 1.3 63.9 + - - +
3109D ARG* 4.4 20.2 + - - +
3356D HIS 3.3 12.5 + - - -
3357D PHE* 3.3 16.1 - - - -
3358D LYS* 3.0 54.9 + - - +
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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