Contacts of the helix formed by residues 925 - 931 (chain A) in PDB entry 2XT6
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 THR 925 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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913A ALA 3.4 14.1 - - - +
914A VAL* 3.4 19.8 - - - +
923A GLU* 5.4 1.4 - - - +
924A PHE* 1.3 80.0 - - - +
926A PRO* 1.4 68.2 - - - +
927A LEU 4.3 0.7 - - - +
928A GLN* 3.0 35.6 + - + +
929A LEU 4.2 1.0 + - - -
943A PHE* 3.5 31.4 - - + +
945A VAL* 4.2 8.4 - - + +
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Residues in contact with PRO 926 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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846A ALA* 3.8 22.7 - - - +
847A HIS* 4.0 38.4 - - + +
864A LEU* 5.0 1.6 - - + -
912A HIS 4.6 6.7 - - - +
913A ALA* 3.4 15.3 - - - +
915A ILE* 4.7 7.6 - - + -
924A PHE* 3.3 38.8 - - + +
925A THR* 1.4 81.1 - - - +
927A LEU* 1.3 63.3 + - + +
928A GLN 3.1 1.2 + - - -
929A LEU* 3.2 22.5 + - - +
930A LEU 4.5 0.2 + - - -
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Residues in contact with LEU 927 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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843A ILE* 3.8 21.3 - - + +
846A ALA* 5.7 0.2 - - + -
847A HIS* 4.3 14.6 - - + +
883A LEU* 3.4 43.1 - - + +
886A LEU* 4.0 10.5 - - + -
887A GLY* 3.6 12.8 - - - +
890A ILE* 4.1 16.0 - - + +
913A ALA* 5.1 1.9 + - - +
925A THR* 3.2 2.6 + - - +
926A PRO* 1.3 76.0 - - + +
928A GLN* 1.3 63.2 + - - +
929A LEU 3.1 0.2 - - - -
930A LEU* 3.1 40.7 + - + +
943A PHE* 3.6 28.9 - - + -
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Residues in contact with GLN 928 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890A ILE* 5.5 0.2 - - - -
925A THR* 3.0 29.2 + - - +
927A LEU* 1.3 77.1 - - - +
929A LEU* 1.3 63.9 + - + +
931A ALA* 3.0 32.0 + - + +
932A THR* 4.4 1.9 + - - -
942A LYS* 3.7 18.9 - - - +
943A PHE* 2.6 49.7 + - - +
944A LEU* 5.3 0.6 - - - +
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Residues in contact with LEU 929 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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842A ARG* 4.0 4.9 + - - -
846A ALA* 3.5 35.4 - - + +
849A ALA* 3.7 30.1 - - + +
924A PHE* 3.7 19.3 - - + -
925A THR 4.8 0.4 - - - +
926A PRO 3.4 9.9 - - - +
927A LEU 3.1 0.6 - - - -
928A GLN* 1.3 78.6 - - + +
930A LEU* 1.3 57.1 + - - +
931A ALA 3.3 0.9 + - - -
932A THR* 3.2 26.6 + - - +
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Residues in contact with LEU 930 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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839A MET* 4.6 2.2 - - - -
842A ARG* 3.7 39.8 + - + +
843A ILE* 3.6 40.8 - - + +
846A ALA* 4.7 8.7 - - + -
887A GLY* 3.8 18.2 - - - +
890A ILE* 3.9 4.9 - - + -
891A ALA* 3.4 32.4 - - + +
927A LEU* 3.1 40.1 + - + +
928A GLN 3.1 1.0 - - - -
929A LEU* 1.3 73.6 - - - +
931A ALA* 1.4 58.2 + - - +
932A THR 3.1 8.7 + - - +
939A THR* 3.5 5.7 - - - +
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Residues in contact with ALA 931 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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890A ILE* 3.7 12.4 - - + +
928A GLN* 3.0 30.6 + - + +
930A LEU* 1.4 75.0 - - - +
932A THR* 1.4 55.3 + - - +
938A PRO* 3.5 5.9 - - - +
939A THR* 2.8 38.8 + - - -
940A GLY 4.2 1.7 + - - -
941A GLY 3.5 21.0 - - - +
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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