Contacts of the helix formed by residues 1042 - 1050 (chain D) in PDB entry 3KBU
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 SER1042 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1040D LEU 3.9 0.2 + - - -
1041D GLY* 1.3 72.5 - - - -
1043D LEU* 1.3 64.9 + - - +
1044D GLU* 2.9 33.3 + - - -
1045D GLU* 2.9 29.9 + - - +
1046D LEU* 2.9 13.3 + - - +
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Residues in contact with LEU1043 (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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1026D GLU* 3.8 37.2 - - + +
1041D GLY 3.5 2.8 + - - -
1042D SER* 1.3 71.6 - - - +
1044D GLU* 1.3 61.5 + - - +
1046D LEU* 3.5 15.7 - - + +
1047D GLU* 3.2 22.5 + - - +
1053D ARG* 3.9 27.3 - - + +
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Residues in contact with GLU1044 (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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1042D SER* 2.9 24.4 + - - -
1043D LEU* 1.3 82.1 + - - +
1045D GLU* 1.3 64.9 + - + +
1046D LEU 3.3 0.2 - - - -
1047D GLU* 3.5 17.6 + - - +
1048D LYS* 3.2 20.4 + - - +
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Residues in contact with GLU1045 (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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1041D GLY* 4.5 11.1 - - - -
1042D SER* 2.9 26.5 + - - +
1044D GLU* 1.3 79.1 - - + +
1046D LEU* 1.3 64.3 + - - +
1048D LYS* 3.2 10.2 + - + +
1049D LYS* 3.0 49.3 + - + +
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Residues in contact with LEU1046 (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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992D GLU* 4.6 8.1 - - - +
1041D GLY* 3.9 21.5 - - - +
1042D SER 2.9 14.9 + - - +
1043D LEU* 3.5 18.2 - - + +
1045D GLU* 1.3 81.1 - - + +
1047D GLU* 1.3 55.5 + - - +
1049D LYS* 3.4 9.6 + - + +
1050D ARG 2.9 24.3 + - - -
1051D VAL* 3.1 44.9 + - + +
1053D ARG* 3.5 47.8 - - + +
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Residues in contact with GLU1047 (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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995D HIS* 5.6 2.3 - - - -
1043D LEU 3.2 11.3 + - - +
1044D GLU* 3.6 20.0 - - - +
1045D GLU 3.2 0.6 - - - -
1046D LEU* 1.3 76.8 - - - +
1048D LYS* 1.3 61.6 + - - +
1050D ARG* 3.4 16.7 + - - +
1051D VAL 5.2 0.4 - - - -
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Residues in contact with LYS1048 (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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1044D GLU 3.2 10.7 + - - +
1045D GLU* 3.2 13.3 + - + +
1047D GLU* 1.3 80.5 - - - +
1049D LYS* 1.3 62.6 + - + +
1050D ARG* 3.6 9.9 + - - +
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Residues in contact with LYS1049 (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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1045D GLU* 3.0 33.8 + - + +
1046D LEU* 4.0 9.9 - - + +
1048D LYS* 1.3 76.3 - - + +
1050D ARG* 1.3 70.7 + - - +
1051D VAL* 4.2 16.9 - - + +
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Residues in contact with ARG1050 (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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994D PRO* 3.6 2.1 - - - +
995D HIS* 2.9 54.5 + - + +
996D PHE 4.3 0.2 - - - -
997D ALA* 3.4 46.9 - - - +
998D SER 5.3 0.4 - - - +
1046D LEU 2.9 9.2 + - - -
1047D GLU 3.4 10.0 + - - +
1048D LYS 3.3 11.6 + - - +
1049D LYS* 1.3 82.3 - - - +
1051D VAL* 1.3 59.7 + - - +
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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
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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