Contacts of the helix formed by residues 3043 - 3050 (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 SER3043 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3036D PHE* 5.0 1.6 - - - -
3040D SER 4.4 3.7 + - - -
3041D PRO 4.1 3.0 + - - -
3042D VAL* 1.3 78.9 - - - +
3044D ALA* 1.3 64.8 + - - +
3045D SER* 3.3 10.3 + - - -
3046D THR* 2.9 33.8 + - - -
3047D LEU* 3.3 17.3 + - - +
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Residues in contact with ALA3044 (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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3030D LEU* 3.9 9.1 - - + +
3033D PHE* 3.4 46.8 - - + +
3036D PHE* 4.2 16.3 - - + -
3042D VAL 3.8 0.2 + - - -
3043D SER* 1.3 73.8 - - - +
3045D SER* 1.3 57.1 + - - +
3047D LEU* 3.3 3.5 + - - +
3048D ALA* 2.9 30.1 + - - +
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Residues in contact with SER3045 (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* 4.8 0.7 + - - +
3030D LEU* 4.0 19.4 - - - +
3043D SER* 3.1 8.9 - - - -
3044D ALA* 1.3 77.1 - - - +
3046D THR* 1.3 66.8 + - - +
3048D ALA* 3.3 2.8 + - - +
3049D ARG* 2.9 50.9 + - - +
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Residues in contact with THR3046 (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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3042D VAL* 3.9 12.5 - - + +
3043D SER* 2.9 24.8 + - - -
3045D SER* 1.3 75.5 - - - +
3047D LEU* 1.3 57.9 + - - +
3049D ARG* 3.3 11.5 + - - +
3050D ALA* 2.9 25.6 + - - +
3079D ALA* 3.5 24.2 - - + +
3080D VAL* 6.4 0.2 - - + -
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Residues in contact with LEU3047 (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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3033D PHE* 3.5 33.4 - - + -
3036D PHE* 3.7 22.4 - - + -
3042D VAL* 3.8 19.7 - - + +
3043D SER 3.3 12.3 + - - +
3044D ALA 3.3 2.4 + - - +
3045D SER 3.2 0.4 - - - -
3046D THR* 1.3 74.8 - - - +
3048D ALA* 1.3 66.3 + - - +
3050D ALA* 2.9 12.8 + - - +
3051D GLY 3.1 0.2 + - - -
3052D PHE* 2.9 34.7 + - + +
3061D VAL* 4.0 9.9 - - + -
3073D TRP* 3.4 44.4 - - + +
3079D ALA* 4.1 3.6 - - + -
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Residues in contact with ALA3048 (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* 4.2 9.2 - - + +
3029D ARG* 2.9 33.3 + - - +
3030D LEU* 3.7 42.0 - - + +
3033D PHE* 4.3 3.5 - - + -
3044D ALA 2.9 17.5 + - - +
3045D SER* 3.6 4.0 - - - +
3047D LEU* 1.3 75.9 - - - +
3049D ARG* 1.3 61.0 + - - +
3051D GLY 3.0 2.6 + - - -
3052D PHE 3.8 12.1 - - - -
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Residues in contact with ARG3049 (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* 2.7 47.3 + - - +
3029D ARG* 4.0 1.7 + - - -
3045D SER* 2.9 38.9 + - - +
3046D THR* 3.3 9.4 - - - +
3048D ALA* 1.3 74.2 - - - +
3050D ALA* 1.3 57.6 - - - +
3051D GLY 2.9 10.2 + - - -
3080D VAL* 5.5 0.8 - - - +
3092D PHE* 3.2 15.6 - - - -
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Residues in contact with ALA3050 (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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3046D THR 2.9 7.8 + - - +
3047D LEU 2.9 7.7 + - - +
3049D ARG* 1.3 73.5 - - - +
3051D GLY* 1.3 57.9 + - - +
3052D PHE* 3.5 9.9 - - + -
3079D ALA* 3.6 42.2 - - + +
3080D VAL* 3.8 19.5 - - + +
3083D HIS* 2.8 28.2 + - - -
3092D PHE* 2.9 14.2 - - - -
3093D ILE* 4.7 0.2 - - - +
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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