Contacts of the helix formed by residues 793 - 801 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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789B THR* 3.5 17.7 - - - +
790B SER* 3.1 18.3 + - - +
792B ALA* 1.3 83.0 - - - +
794B VAL* 1.3 62.0 + - - +
795B GLU 3.4 2.7 - - - -
796B SER* 2.8 25.3 + - - +
797B ILE* 3.2 20.6 + - + +
806B LEU* 3.5 28.7 - - + +
833B TYR* 3.5 14.6 - + - -
793D TYR* 3.4 39.0 - + - -
796D SER* 3.6 16.8 + - - -
803D ASP* 2.6 40.4 + - - +
806D LEU* 4.1 6.8 - - - +
901D GOL 3.9 14.1 - - - -
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Residues in contact with VAL 794 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
728B TYR* 5.8 0.2 - - - +
730B LEU* 3.9 28.3 - - + -
790B SER 3.9 0.4 + - - +
791B ARG* 3.2 23.8 + - + +
792B ALA 3.5 0.2 - - - -
793B TYR* 1.3 76.8 - - - +
795B GLU* 1.3 65.1 + - - +
797B ILE* 3.3 2.1 + - - +
798B CYS* 3.0 34.8 + - - -
839B VAL* 3.6 33.4 - - + -
841B PHE* 3.8 16.1 - - + -
890B VAL* 4.2 10.3 - - + -
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Residues in contact with GLU 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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726B LYS* 3.6 26.1 + - - -
728B TYR* 3.4 28.7 + - + +
791B ARG 5.0 0.4 + - - -
792B ALA 4.9 3.3 + - - +
793B TYR 3.4 0.6 - - - -
794B VAL* 1.3 79.3 - - - +
796B SER* 1.3 62.2 + - - +
798B CYS* 3.4 1.4 + - - +
799B SER* 3.0 30.6 + - - +
795D GLU* 5.6 1.9 - - - +
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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
----------------------------------------------------------
792B ALA 5.3 1.3 + - - -
793B TYR* 2.8 26.7 + - - +
795B GLU* 1.3 77.7 - - - +
797B ILE* 1.3 60.0 + - - +
799B SER* 4.2 3.1 - - - -
800B ASN* 2.8 41.0 + - - +
801B ASN 3.9 2.3 + - - +
806B LEU* 5.9 0.2 - - - +
792D ALA* 3.8 31.0 + - - -
793D TYR* 3.7 26.7 + - - -
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Residues in contact with ILE 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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787B TYR* 3.9 19.1 - - + +
789B THR* 3.8 17.0 - - + -
793B TYR* 3.2 21.5 + - + +
794B VAL 3.8 0.9 - - - +
796B SER* 1.3 78.1 + - - +
798B CYS* 1.3 64.1 + - - +
801B ASN* 2.9 34.9 + - - +
802B PHE* 3.6 34.8 - - + +
803B ASP* 5.2 2.9 - - + +
806B LEU* 5.4 3.1 - - + -
841B PHE* 3.5 44.4 - - + -
887B PRO* 3.7 11.3 - - + +
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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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728B TYR* 3.4 39.7 - - + +
730B LEU* 4.2 9.4 - - - -
762B ILE* 3.8 41.2 - - + +
764B ASN* 2.8 23.6 + - - +
767B LEU* 3.8 2.6 - - - +
794B VAL* 3.0 32.3 + - - +
795B GLU 3.4 0.8 + - - +
797B ILE* 1.3 76.4 - - - +
799B SER* 1.3 57.3 + - - +
841B PHE* 4.1 6.7 - - - -
887B PRO* 4.8 2.0 - - - -
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Residues in contact with SER 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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727B LYS* 3.7 30.6 + - - +
728B TYR* 3.7 19.1 - - - -
764B ASN* 3.2 18.2 + - - +
766B GLU* 4.8 1.4 - - - +
767B LEU* 4.2 5.4 - - - +
795B GLU* 3.0 20.7 + - - +
796B SER* 3.7 2.9 + - - -
798B CYS* 1.3 78.5 - - - +
800B ASN* 1.4 74.9 + - - +
801B ASN 3.8 0.9 - - - -
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Residues in contact with ASN 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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727B LYS* 3.2 26.0 + - - +
767B LEU* 4.2 6.2 - - - +
796B SER* 2.8 22.2 + - - +
799B SER* 1.4 83.9 + - - +
801B ASN* 1.3 65.7 + - - +
882B LYS* 2.8 37.8 + - - +
790D SER* 5.3 1.2 + - - -
792D ALA* 4.1 23.2 - - - +
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Residues in contact with ASN 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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767B LEU* 3.7 25.4 + - + +
796B SER 3.9 2.6 - - - +
797B ILE* 2.9 31.0 + - - +
800B ASN* 1.3 84.5 - - - +
802B PHE* 1.3 87.9 + - - +
803B ASP* 3.8 2.9 + - - +
818B ILE* 6.3 0.4 - - - -
882B LYS* 3.1 35.8 + - + +
883B ASP* 5.2 0.4 - - - +
885B VAL* 3.0 29.9 + - - +
887B PRO* 3.7 14.1 - - - +
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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