Contacts of the helix formed by residues 921 - 928 (chain D) in PDB entry 3KKA
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 TYR 921 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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913D LEU* 4.0 0.2 - - - -
918D MET* 3.0 25.6 + - + +
919D GLN 3.0 1.8 - - - -
920D GLN* 1.3 92.6 - - + +
922D THR* 1.3 66.1 + - - +
923D GLU 3.3 2.9 - - - -
924D HIS* 3.0 39.8 + + + +
925D PHE* 3.2 30.4 + - + -
948D GLY 4.1 6.5 - - - -
949D VAL* 3.7 38.1 - - + +
950D ARG 4.7 0.9 + - - -
951D LEU* 3.9 12.8 + - - +
954D HIS* 2.8 44.7 - + + +
958D ILE* 4.1 12.3 - - + -
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Residues in contact with THR 922 (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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909D VAL* 4.9 0.9 - - + -
910D SER* 4.0 31.5 + - - +
913D LEU* 3.6 19.1 - - + +
919D GLN* 2.7 27.5 + - - +
920D GLN 3.5 0.8 - - - -
921D TYR* 1.3 76.6 - - - +
923D GLU* 1.3 56.0 + - - +
925D PHE* 3.3 6.3 + - - +
926D MET* 2.9 46.9 + - + +
917E LYS* 4.2 29.8 + - + +
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Residues in contact with GLU 923 (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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920D GLN 5.0 2.3 + - - +
921D TYR 3.3 1.0 - - - -
922D THR* 1.3 74.5 - - - +
924D HIS* 1.3 64.6 + - + +
926D MET* 4.3 0.9 - - - +
927D ALA* 2.7 41.0 + - - +
917E LYS* 3.3 23.4 - - + +
918E MET* 5.5 0.2 - - - +
957E ARG* 2.9 43.6 + - - -
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Residues in contact with HIS 924 (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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920D GLN 3.9 15.0 + - - -
921D TYR* 3.0 38.7 + + + +
923D GLU* 1.3 80.0 + - + +
925D PHE* 1.3 62.9 + - - +
927D ALA* 3.6 5.0 + - - +
928D ALA* 3.2 23.9 + - - +
947D ILE* 3.5 37.6 - - + +
948D GLY* 4.0 18.2 + - - -
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Residues in contact with PHE 925 (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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909D VAL* 4.1 11.7 - - + -
912D TRP* 3.8 27.1 - + - -
913D LEU* 3.7 27.1 - - + -
921D TYR* 3.2 29.7 + - + -
922D THR 3.4 7.2 - - - +
924D HIS* 1.3 77.8 - - - +
926D MET* 1.3 60.7 + - - +
928D ALA* 3.1 8.8 + - - +
930D TYR* 2.9 53.6 + - + +
936D VAL* 4.2 8.5 - - + -
939D MET* 3.6 30.7 - - + -
944D ILE* 5.5 1.8 - - + -
947D ILE* 3.8 20.6 - - + -
949D VAL* 5.1 1.1 - - + -
958D ILE* 4.3 17.9 - - + -
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Residues in contact with MET 926 (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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909D VAL* 3.7 30.3 - - + -
910D SER 5.3 0.2 - - - +
922D THR* 2.9 33.9 + - + +
923D GLU* 3.1 6.7 + - - +
925D PHE* 1.3 74.5 - - - +
927D ALA* 1.3 63.6 + - - +
929D GLY* 3.0 14.4 + - - -
930D TYR 3.7 4.0 - - - +
931D THR* 3.6 44.0 - - - +
915E SER 3.6 16.6 - - - +
916E ILE* 3.7 27.1 - - - +
917E LYS* 4.6 1.3 - - + -
957E ARG* 3.4 36.1 + - - +
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Residues in contact with ALA 927 (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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923D GLU* 2.7 23.7 + - - +
924D HIS* 4.1 5.6 - - - +
926D MET* 1.3 73.1 - - - +
928D ALA* 1.3 59.0 + - - +
929D GLY 3.2 1.0 + - - -
957E ARG* 3.8 12.1 - - - +
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Residues in contact with ALA 928 (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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924D HIS 3.2 11.3 + - - +
925D PHE 3.1 6.4 + - - +
927D ALA* 1.3 76.9 - - - +
929D GLY* 1.3 60.4 + - - +
930D TYR* 3.4 14.4 + - + -
947D ILE* 3.4 35.2 - - + -
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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