Contacts of the helix formed by residues 3537 - 3541 (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 ASN3537 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2139C TRP* 3.7 14.3 - - - -
3228D VAL* 3.2 27.2 + - + +
3337D ILE* 4.2 4.6 - - - +
3341D ILE* 4.2 9.0 - - + -
3373D TYR* 3.9 2.3 - - - -
3533D GLY 4.1 11.0 + - - +
3534D LEU 3.7 17.2 + - - +
3535D MET 2.5 15.1 + - - +
3536D GLY* 1.3 74.6 - - - +
3538D PRO* 1.3 83.2 - - - +
3539D ILE* 2.7 49.0 + - - +
3540D CYS* 2.9 12.8 + - - +
3541D SER 3.9 1.2 + - - -
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Residues in contact with PRO3538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2127C PRO* 4.6 8.1 - - + -
2139C TRP* 3.3 33.0 - - + -
2142C PHE* 3.4 45.3 - - + -
3373D TYR 5.2 2.9 - - - +
3374D GLN* 6.2 0.2 - - - -
3536D GLY 3.6 5.1 - - - +
3537D ASN* 1.3 87.0 - - - +
3539D ILE* 1.3 52.8 + - + +
3540D CYS 2.5 15.1 + - - -
3541D SER* 2.5 32.7 + - - +
3544D TYR* 4.3 13.7 - - + -
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Residues in contact with ILE3539 (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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2139C TRP* 4.6 6.7 - - + -
3334D LEU* 4.9 15.0 - - + +
3337D ILE* 3.8 19.7 - - + -
3338D GLY* 4.2 19.3 - - - -
3341D ILE* 5.4 2.0 - - + -
3361D PHE* 5.0 2.7 - - + -
3537D ASN* 2.7 28.6 + - - +
3538D PRO* 1.3 74.7 - - + +
3540D CYS* 1.3 67.0 + - - +
3541D SER 3.3 2.1 + - - -
3544D TYR* 3.8 27.2 - - + +
3545D TRP* 3.3 43.9 + - + -
3550D PHE* 3.8 22.4 - - + -
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Residues in contact with CYS3540 (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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3341D ILE* 4.4 2.5 - - - -
3361D PHE* 3.8 31.9 - - - -
3363D PRO* 3.1 30.0 - - + +
3366D LEU* 6.2 0.2 - - + -
3367D PHE* 3.6 2.1 - - - -
3373D TYR* 2.9 20.2 + - + -
3534D LEU 3.7 16.2 - - - -
3535D MET* 3.0 33.0 - - - +
3537D ASN* 2.9 6.2 + - - +
3538D PRO 2.5 7.7 + - - -
3539D ILE* 1.3 84.5 - - - +
3541D SER* 1.3 60.0 + - - -
3545D TRP* 4.9 0.7 - - - -
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Residues in contact with SER3541 (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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2127C PRO* 3.4 17.3 - - - +
3367D PHE* 3.9 1.3 - - - -
3373D TYR* 3.4 18.7 - - - -
3538D PRO 2.5 26.4 + - - -
3540D CYS* 1.3 74.0 - - - +
3542D PRO* 1.3 72.0 - - - +
3543D GLN* 3.1 17.9 + - - -
3544D TYR* 3.1 21.3 + - - +
3545D TRP* 3.0 20.1 + - - +
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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