Contacts of the helix formed by residues 739 - 749 (chain A) in PDB entry 3KSS
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 739 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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733A ALA* 5.6 0.2 - - - -
737A GLY 5.7 0.4 - - - +
738A MET* 1.3 75.8 - - - +
740A VAL* 1.3 58.3 + - - +
741A ALA* 3.7 10.2 + - - +
742A ASP* 2.7 57.1 + - - +
743A VAL* 3.1 10.6 + - - +
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Residues in contact with VAL 740 (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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728A ILE* 3.6 28.0 - - + +
730A ARG* 4.9 15.0 - - + -
733A ALA* 5.5 3.3 - - + +
738A MET 3.9 2.2 + - - -
739A THR* 1.3 72.3 - - - +
741A ALA* 1.3 64.5 + - + +
743A VAL* 3.4 10.6 + - - +
744A GLN* 3.0 40.1 + - - +
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Residues in contact with ALA 741 (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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739A THR* 2.9 10.2 - - - +
740A VAL* 1.3 83.6 - - + +
742A ASP* 1.3 50.9 + - - +
744A GLN* 2.9 18.9 + - - +
745A LEU* 2.8 34.0 + - - +
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Residues in contact with ASP 742 (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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204A ALA* 4.9 10.7 - - - +
738A MET* 4.6 11.9 - - - -
739A THR* 2.7 41.0 + - - +
741A ALA* 1.3 68.6 - - - +
743A VAL* 1.3 62.1 + - - +
745A LEU* 3.1 23.4 - - - +
746A PHE* 3.0 27.5 - - + -
791A PRO* 5.1 10.3 - - - +
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Residues in contact with VAL 743 (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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728A ILE* 3.3 35.7 - - + -
733A ALA* 4.4 15.5 - - + -
738A MET* 3.6 27.1 - - + -
739A THR 3.1 11.1 + - - +
740A VAL* 3.5 10.5 - - - +
742A ASP* 1.3 75.5 - - - +
744A GLN* 1.3 64.0 + - - +
746A PHE* 3.1 25.9 + - + +
747A VAL* 3.4 8.7 + - + +
788A ILE* 5.7 0.4 - - + -
798A LEU* 4.0 21.1 - - + +
801A VAL* 4.3 11.9 - - + -
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Residues in contact with GLN 744 (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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728A ILE* 5.0 13.7 - - + +
740A VAL* 3.0 37.9 + - - +
741A ALA* 2.9 17.0 + - - +
743A VAL* 1.3 72.3 - - + +
745A LEU* 1.3 55.4 + - - +
746A PHE 3.0 2.0 - - - -
747A VAL* 3.5 14.4 - - + -
748A THR* 2.8 45.8 + - - +
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Residues in contact with LEU 745 (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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203A LEU* 3.5 36.3 - - + -
204A ALA* 4.8 11.7 - - + +
207A LYS* 4.8 22.7 - - + +
741A ALA 2.8 9.7 + - - +
742A ASP* 3.1 31.4 - - - +
744A GLN* 1.3 76.5 - - - +
746A PHE* 1.3 59.0 + - + +
748A THR* 4.4 2.2 - - - -
749A SER* 3.0 39.2 + - - +
750A ALA 3.7 0.3 + - - -
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Residues in contact with PHE 746 (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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196A LEU* 6.4 0.4 - - + -
202A SER* 5.0 7.6 - - - -
203A LEU* 4.0 25.6 - - + -
738A MET* 4.6 5.6 - - - -
742A ASP* 3.0 33.7 - - + -
743A VAL* 3.1 12.1 + - - +
744A GLN 3.0 0.4 - - - -
745A LEU* 1.3 78.8 - - + +
747A VAL* 1.3 60.2 + - + +
750A ALA* 3.3 6.6 + - + +
751A VAL* 2.8 35.9 + - - +
772A TYR* 4.0 22.9 - + - -
786A LEU* 4.1 17.3 - - + -
787A PRO 4.5 0.4 - - - -
788A ILE* 3.3 48.7 - - + -
789A LEU* 4.4 13.0 - - + -
798A LEU* 5.7 2.7 - - + -
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Residues in contact with VAL 747 (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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726A VAL* 4.0 35.4 - - + -
728A ILE* 5.0 5.4 - - + -
743A VAL 3.4 8.8 + - - +
744A GLN* 3.0 18.1 + - + +
746A PHE* 1.3 80.8 - - - +
748A THR* 1.3 66.1 + - - +
751A VAL* 3.5 13.8 - - + +
752A GLY* 3.3 16.3 + - - -
798A LEU* 4.7 13.9 - - + -
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Residues in contact with THR 748 (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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56A GLN* 5.4 9.4 - - - +
744A GLN* 2.8 24.6 + - - +
745A LEU* 4.4 2.2 - - - -
747A VAL* 1.3 82.5 - - - +
749A SER* 1.3 61.1 + - - +
752A GLY* 3.0 6.0 - - - -
753A GLY 2.8 20.6 + - - -
754A ALA* 3.3 23.3 + - + -
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Residues in contact with SER 749 (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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203A LEU* 4.7 3.8 - - - -
207A LYS* 6.1 1.0 - - - +
745A LEU* 3.0 29.4 + - - +
748A THR* 1.3 78.4 - - - +
750A ALA* 1.3 65.7 + - - +
751A VAL 3.3 0.9 - - - -
753A GLY 3.1 15.4 + - - +
754A ALA* 4.0 18.1 + - - +
770A LEU* 2.9 33.8 - - - +
771A ARG* 3.2 5.5 - - - -
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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