Contacts of the helix formed by residues 793 - 801 (chain C) in PDB entry 4X52
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 793 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792A ALA 5.7 0.2 - - - -
793A TYR* 3.5 36.3 - + - -
796A SER* 3.6 17.5 + - - -
803A ASP* 2.6 31.6 + - - +
806A LEU* 4.2 6.5 - - + +
901A GOL 3.7 13.8 - - - -
789C THR* 3.6 17.3 - - - +
790C SER* 3.0 17.4 + - - +
792C ALA* 1.3 82.8 - - - +
794C VAL* 1.4 62.3 + - - +
795C GLU 3.3 3.1 - - - -
796C SER* 2.8 25.3 + - - +
797C ILE* 3.2 20.6 + - + +
806C LEU* 3.5 28.4 - - + +
833C TYR* 3.5 25.4 - + - -
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Residues in contact with VAL 794 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728C TYR* 5.4 1.8 - - - +
730C LEU* 4.4 17.0 - - + -
790C SER 3.8 1.0 + - - +
791C ARG* 3.2 20.9 + - + +
792C ALA 3.5 0.2 - - - -
793C TYR* 1.4 76.8 - - - +
795C GLU* 1.3 59.0 + - - +
797C ILE* 3.3 1.7 + - - +
798C CYS* 3.0 44.4 + - - -
839C VAL* 3.5 33.9 - - + -
841C PHE* 3.8 15.7 - - + -
890C VAL* 4.2 10.5 - - + -
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Residues in contact with GLU 795 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792A ALA* 6.0 3.4 - - + +
795A GLU* 5.4 3.8 - - - +
728C TYR* 3.5 33.0 + - + +
791C ARG 4.9 0.4 + - - -
792C ALA 4.9 4.6 + - - +
793C TYR 3.3 0.6 - - - -
794C VAL* 1.3 78.7 - - + +
796C SER* 1.4 61.7 + - - +
798C CYS 3.4 0.3 + - - -
799C SER* 2.9 33.3 + - - +
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Residues in contact with SER 796 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
792A ALA* 3.7 37.3 + - - +
793A TYR* 3.6 28.1 + - - -
792C ALA 5.3 1.0 + - - -
793C TYR* 2.8 26.7 + - - +
795C GLU* 1.4 77.2 - - - +
797C ILE* 1.3 61.0 + - - +
799C SER* 4.2 2.9 - - - -
800C ASN* 2.8 36.2 + - - +
801C ASN 3.8 2.5 + - - +
806C LEU* 5.7 0.5 - - - +
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Residues in contact with ILE 797 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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787C TYR* 3.9 20.0 - - + +
789C THR* 3.7 28.5 - - + +
793C TYR* 3.2 22.1 + - + +
794C VAL 3.8 3.1 - - - +
796C SER* 1.3 83.5 + - - +
798C CYS* 1.3 60.5 + - - +
801C ASN* 2.8 38.1 + - - +
802C PHE* 3.5 34.3 - - + +
803C ASP* 5.3 2.7 - - + +
806C LEU* 5.3 4.0 - - + -
841C PHE* 3.5 28.5 - - + -
887C PRO* 3.7 12.1 - - + +
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Residues in contact with CYS 798 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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728C TYR* 3.4 35.4 - - + +
730C LEU* 4.0 12.6 - - - -
762C ILE* 3.7 41.4 - - + +
764C ASN* 2.8 23.0 + - - +
767C LEU* 3.8 2.8 - - - +
794C VAL* 3.0 30.8 + - - +
797C ILE* 1.3 77.1 - - - +
799C SER* 1.3 58.7 + - - +
841C PHE* 3.9 8.1 - - - -
887C PRO* 4.8 2.0 - - - -
890C VAL* 4.3 0.4 - - - -
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Residues in contact with SER 799 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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792A ALA* 5.7 0.3 - - - +
727C LYS* 3.7 29.4 + - - +
728C TYR* 3.7 18.1 - - - -
764C ASN* 3.2 16.8 + - - +
766C GLU* 4.7 2.3 - - - +
767C LEU* 4.2 5.8 - - - +
795C GLU* 2.9 20.0 + - - +
796C SER* 3.7 2.8 + - - -
798C CYS* 1.3 80.9 - - - +
800C ASN* 1.4 75.7 + - - +
801C ASN 3.8 0.9 - - - -
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Residues in contact with ASN 800 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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790A SER* 4.8 3.0 + - - -
792A ALA* 3.7 26.9 - - - +
837A ASN* 5.7 6.0 + - - -
727C LYS* 3.2 25.6 + - - +
767C LEU* 4.2 6.6 - - - +
796C SER* 2.8 23.5 + - - +
799C SER* 1.4 82.1 + - - +
801C ASN* 1.3 66.8 + - - +
882C LYS* 2.8 32.2 + - - +
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Residues in contact with ASN 801 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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767C LEU* 3.6 23.6 + - + +
796C SER 3.9 2.4 - - - +
797C ILE* 2.8 30.3 + - - +
800C ASN* 1.3 84.3 - - - +
802C PHE* 1.3 90.8 + - - +
803C ASP* 3.8 2.8 + - - +
818C ILE* 5.9 0.3 - - - +
882C LYS* 3.0 47.5 + - + +
883C ASP* 5.2 0.2 - - - +
885C VAL* 3.0 18.9 + - - +
887C PRO* 3.7 14.7 - - - +
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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