Contacts of the helix formed by residues 799 - 804 (chain B) in PDB entry 1MZC
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 CYS 799 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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797B ASP* 3.0 9.7 + - - -
798B GLY* 1.3 70.7 - - - +
800B TYR* 1.3 70.8 + - - +
801B SER 2.9 9.9 + - - -
802B PHE 3.0 12.1 + - - -
803B TRP* 3.4 13.4 + - - +
861B TYR* 3.3 34.8 - - + +
862B HIS* 3.6 9.0 - - + -
865B TYR* 3.7 25.4 - - + +
866B CYS 4.7 0.7 - - - +
1001B ZN 2.4 34.3 - - - -
1003B BNE 3.4 6.5 - - - -
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Residues in contact with TYR 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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748B HIS* 3.2 26.7 + + - -
750B GLY 4.8 1.3 - - - -
788B PHE* 3.6 22.8 - - + +
789B GLN* 3.5 3.4 - - - -
790B GLY* 3.3 32.3 - - - -
795B LEU 4.5 1.1 - - - -
797B ASP* 3.0 37.0 + - + +
799B CYS* 1.3 80.4 - - - +
801B SER* 1.3 60.6 + - - +
802B PHE 2.9 5.8 - - - -
803B TRP* 3.8 27.4 - + + +
804B GLN* 3.0 33.4 + - + +
805B ALA 3.5 1.9 + - - -
1002B FPP 2.6 35.4 + - + -
1003B BNE 3.5 21.0 - + - -
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Residues in contact with SER 801 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
788B PHE* 4.8 2.6 + - - +
797B ASP 4.0 1.5 + - - -
798B GLY* 2.6 25.1 + - - -
799B CYS 2.9 0.6 - - - -
800B TYR* 1.3 76.9 - - - +
802B PHE* 1.3 58.1 + - - +
805B ALA* 3.0 24.1 - - - +
806B GLY 4.1 0.7 + - - -
835B LEU* 3.5 22.9 - - - +
838B TYR* 4.9 1.7 - - - -
839B ILE* 3.4 34.7 - - - +
865B TYR 4.2 3.6 - - - -
866B CYS 4.5 0.4 - - - -
869B GLY* 3.3 19.5 - - - -
872B ILE* 5.1 0.7 - - - +
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Residues in contact with PHE 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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654B TYR* 6.0 0.4 - - - -
753B PHE* 3.4 42.0 - + - -
799B CYS 3.0 7.1 + - - +
800B TYR 2.9 0.8 - - - -
801B SER* 1.3 80.1 - - - +
803B TRP* 1.3 83.1 + + - +
804B GLN 3.2 2.0 - - - -
806B GLY* 2.7 31.9 + - - +
865B TYR* 3.5 42.3 + + + +
868B SER* 3.8 14.8 - - - -
869B GLY* 4.2 1.1 - - - -
872B ILE* 3.6 28.3 - - + -
897B THR* 5.0 0.4 - - + -
898B HIS 4.9 2.2 - - - -
899B PRO 4.1 6.3 - - - -
902B ASN* 3.5 36.3 - - + -
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Residues in contact with TRP 803 (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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654B TYR* 5.8 3.6 - - - -
705B TYR* 5.5 0.9 - + - -
749B GLY 3.7 17.0 - - - +
750B GLY 4.6 0.4 - - - -
753B PHE* 3.4 56.1 - + + +
799B CYS 3.4 22.0 + - - -
800B TYR* 3.8 21.1 - + + -
802B PHE* 1.3 89.9 - + - +
804B GLN* 1.3 60.8 + - - +
807B LEU* 3.6 10.7 + - - +
861B TYR* 2.9 23.1 + - - -
865B TYR* 3.3 42.6 - + - -
1002B FPP 3.5 62.9 - - + +
1003B BNE 4.0 8.7 - + - -
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Residues in contact with GLN 804 (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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749B GLY* 3.4 22.2 - - - -
776B TRP* 3.4 25.5 - - - -
777B VAL* 3.4 13.2 - - + +
780B ARG* 3.6 14.1 - - - +
788B PHE* 3.4 19.3 - - + -
789B GLN 2.9 28.4 + - - +
790B GLY 3.3 19.6 + - - -
800B TYR* 3.0 23.9 + - + +
803B TRP* 1.3 75.6 - - - +
805B ALA* 1.3 61.6 + - - +
806B GLY 3.0 1.3 - - - -
807B LEU* 2.8 36.1 + - - +
808B LEU 4.1 0.5 + - - -
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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