Contacts of the helix formed by residues 3025 - 3032 (chain D) in PDB entry 2QRA
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 GLU3025 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3022D GLU 3.2 3.2 + - - +
3023D PHE 2.8 11.3 - - - +
3024D VAL* 1.3 79.2 - - - +
3026D GLU* 1.3 73.2 + - - +
3027D PHE* 3.1 32.2 + - + +
3028D ASN* 3.2 36.4 + - - +
3029D ARG* 3.5 4.2 + - - +
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Residues in contact with GLU3026 (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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3024D VAL 3.7 4.2 + - - -
3025D GLU* 1.3 79.9 + - - +
3027D PHE* 1.3 57.4 + - - +
3029D ARG* 3.0 32.1 + - - +
3030D LEU* 2.9 26.6 + - + +
3045D SER* 4.8 1.0 + - - +
3048D ALA* 3.9 12.4 - - + +
3049D ARG* 2.7 61.2 + - - +
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Residues in contact with PHE3027 (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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3025D GLU* 3.1 19.6 + - + +
3026D GLU* 1.3 71.5 - - - +
3028D ASN* 1.3 68.3 + - - +
3029D ARG 2.8 5.6 + - - -
3030D LEU* 2.9 33.7 + - + +
3031D LYS* 3.0 57.4 + - + +
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Residues in contact with ASN3028 (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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3022D GLU* 3.0 42.7 + - - +
3023D PHE* 2.9 38.4 - - + -
3025D GLU* 3.2 22.7 + - - +
3027D PHE* 1.3 80.6 - - - +
3029D ARG* 1.3 58.6 + - - +
3031D LYS* 3.9 20.0 + - - +
3032D THR* 3.4 8.7 - - - +
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Residues in contact with ARG3029 (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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3023D PHE* 2.8 43.4 + - + +
3024D VAL 3.3 15.6 + - - -
3025D GLU 3.7 2.3 - - - +
3026D GLU* 3.0 34.2 + - - +
3027D PHE 2.8 0.8 + - - -
3028D ASN* 1.3 77.2 - - - +
3030D LEU* 1.3 62.6 + - - +
3031D LYS 3.1 2.8 + - - -
3032D THR* 3.0 23.0 + - - -
3033D PHE* 3.4 7.2 - - - -
3048D ALA* 2.9 33.3 + - + +
3049D ARG 4.0 7.1 + - - -
3051D GLY* 3.4 21.3 - - - -
3052D PHE 3.7 10.3 - - - +
3053D LEU* 3.5 21.4 - - + +
3064D PHE* 3.2 33.9 - - - -
3092D PHE* 4.2 10.5 - - - -
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Residues in contact with LEU3030 (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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3026D GLU* 2.9 14.1 + - + +
3027D PHE* 2.9 27.6 + - + +
3029D ARG* 1.3 75.8 - - - +
3031D LYS* 1.3 62.7 + - - +
3033D PHE* 3.0 20.5 + - + +
3044D ALA* 3.9 38.8 - - + +
3045D SER* 4.0 12.8 - - - +
3048D ALA* 3.7 16.1 - - + +
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Residues in contact with LYS3031 (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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3027D PHE* 3.0 55.2 + - + +
3028D ASN* 3.9 18.3 + - - +
3029D ARG 3.1 0.2 - - - -
3030D LEU* 1.3 73.9 - - - +
3032D THR* 1.3 53.9 + - + +
3033D PHE 2.7 16.0 + - - -
3034D ALA* 3.4 16.1 + - - +
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Residues in contact with THR3032 (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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3023D PHE* 3.9 11.9 - - + -
3028D ASN 3.4 15.7 - - - +
3029D ARG 3.0 18.7 + - - +
3031D LYS* 1.3 72.9 - - + +
3033D PHE* 1.3 56.4 + - - +
3034D ALA* 3.2 8.1 + - - +
3053D LEU* 3.8 17.9 - - + -
3054D TYR* 2.9 49.4 + - - +
3056D GLY* 5.8 0.3 - - - -
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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