Contacts of the helix formed by residues 794 - 802 (chain B) in PDB entry 1E3K
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 PHE 794 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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714B LEU* 3.1 37.9 - - + -
715B LEU* 3.4 28.0 - - + -
718B LEU* 3.7 23.6 - - + -
778B PHE* 5.6 2.2 - + - -
784B LEU* 5.0 2.2 - - + -
792B SER* 3.4 13.9 + - - -
793B SER* 1.3 97.6 - - - +
795B TYR* 1.3 58.0 + - - +
796B SER* 3.0 4.5 - - - +
797B LEU* 2.7 22.3 + - + +
798B CYS* 2.5 56.1 + - - -
801B MET* 4.2 9.6 - - + -
890B TYR* 3.1 22.4 - - + +
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Residues in contact with TYR 795 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786B GLU* 2.7 40.0 + - + -
789B MET* 3.8 24.0 - - + -
790B LYS* 3.9 26.7 - - - +
792B SER* 3.3 9.8 + - - +
793B SER 5.7 0.4 - - - +
794B PHE* 1.3 77.0 - - - +
796B SER* 1.3 53.8 + - - +
798B CYS* 4.0 4.7 - - - -
799B LEU* 2.7 73.2 + - + +
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Residues in contact with SER 796 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794B PHE* 2.8 2.2 + - - +
795B TYR* 1.3 77.4 - - - +
797B LEU* 1.4 63.8 - - - +
799B LEU* 4.0 10.9 + - - +
800B THR* 3.1 21.7 + - - -
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Residues in contact with LEU 797 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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794B PHE* 2.7 21.4 + - + +
796B SER* 1.4 78.6 - - - +
798B CYS* 1.3 56.4 + - - +
800B THR* 2.6 31.9 + - - +
801B MET* 3.1 39.0 + - + +
886B GLN* 4.3 10.8 - - + +
887B LEU* 3.9 22.9 - - + +
890B TYR* 3.8 54.1 - - + -
1000B R18 4.4 10.1 - - + -
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Residues in contact with CYS 798 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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776B LEU* 3.8 8.7 - - + +
778B PHE* 5.7 1.3 - - - -
784B LEU* 4.3 9.2 - - - -
789B MET* 3.7 37.0 - - + -
792B SER* 4.6 2.7 - - - -
794B PHE* 2.5 48.8 + - - -
795B TYR* 3.5 9.0 - - - +
797B LEU* 1.3 72.0 - - - +
799B LEU* 1.3 61.0 + - - +
801B MET* 3.4 14.7 - - - +
802B TRP* 3.1 24.8 + - - +
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Residues in contact with LEU 799 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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786B GLU* 4.1 0.7 - - - +
795B TYR* 2.7 72.2 + - + +
796B SER* 4.3 8.3 - - - +
798B CYS* 1.3 69.4 - - - +
800B THR* 1.3 61.7 + - - +
802B TRP* 3.1 42.0 + - + +
803B GLN* 3.5 12.5 + - - +
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Residues in contact with THR 800 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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796B SER 3.1 15.1 + - - -
797B LEU* 2.6 18.9 + - + +
799B LEU* 1.3 69.0 - - - +
801B MET* 1.3 65.8 + - - +
803B GLN* 2.9 42.0 + - - +
883B LEU* 3.9 30.2 - - + +
886B GLN* 3.4 27.5 + - + +
887B LEU* 4.7 10.3 - - + -
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Residues in contact with MET 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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718B LEU* 5.9 1.6 - - + -
760B VAL* 4.7 6.1 - - + -
763B LEU* 4.4 14.9 - - + +
776B LEU* 4.6 5.8 - - + -
778B PHE* 4.5 15.5 - - + -
794B PHE* 4.2 7.4 - - + -
797B LEU* 3.2 34.8 - - + +
798B CYS* 3.4 37.0 - - - +
800B THR* 1.3 72.0 - - - +
802B TRP* 1.3 57.2 + - - +
803B GLN 2.9 6.9 + - - -
804B ILE* 3.0 26.1 + - - +
805B PRO* 3.2 5.6 - - - +
883B LEU* 4.7 4.0 - - - -
887B LEU* 3.7 28.9 - - + -
1000B R18 4.2 23.1 - - + -
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Residues in contact with TRP 802 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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773B GLY 2.9 21.9 + - - -
774B GLN* 3.7 29.8 - - - -
775B MET 4.1 6.2 + - - +
776B LEU* 3.6 20.9 - - + +
786B GLU* 3.4 43.7 - - + -
789B MET* 4.2 22.7 - - + -
798B CYS 3.1 10.3 + - - +
799B LEU* 3.1 36.8 - - + +
801B MET* 1.3 77.0 - - - +
803B GLN* 1.3 60.0 + - - -
804B ILE 3.3 0.2 - - - -
805B PRO* 3.3 15.1 - - + +
806B GLN* 3.0 39.6 + - + +
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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