Contacts of the helix formed by residues 848 - 855 (chain C) in PDB entry 6ZGI
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 ASP 848 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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835C LYS* 4.1 9.9 + - - +
844C ILE* 3.1 24.8 + - + +
846C ALA 4.3 0.9 + - - -
847C ARG* 1.3 86.6 + - - +
849C LEU* 1.3 69.1 + - - +
850C ILE* 3.5 17.8 + - - +
851C CYS* 3.5 30.0 + - + +
852C ALA* 3.2 20.3 + - - +
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Residues in contact with LEU 849 (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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846C ALA 5.8 0.9 - - - +
847C ARG 3.6 15.5 - - - +
848C ASP* 1.3 75.1 + - - +
850C ILE* 1.3 64.8 + - + +
852C ALA* 3.4 8.1 + - + +
853C GLN* 3.0 36.2 + - - +
960C ASN* 3.6 37.4 - - - +
964C LYS* 5.9 3.6 - - - +
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Residues in contact with ILE 850 (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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829C ALA* 5.0 12.8 - - + +
830C ASP* 4.2 31.9 - - + +
835C LYS* 3.7 23.6 - - + -
848C ASP* 3.3 15.6 + - - +
849C LEU* 1.3 81.1 - - + +
851C CYS* 1.3 58.0 + - - +
853C GLN* 3.2 25.1 + - - +
854C LYS* 2.9 44.7 + - + +
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Residues in contact with CYS 851 (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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592B PHE* 5.1 2.5 - - - -
835C LYS* 3.4 24.9 - - - -
840C CYS* 2.0 52.9 - - + -
845C ALA* 4.5 7.6 - - - -
848C ASP* 3.5 17.2 + - + +
849C LEU 3.4 0.4 - - - -
850C ILE* 1.3 74.3 - - - +
852C ALA* 1.3 61.7 + - - +
854C LYS* 3.7 6.4 - - - +
855C PHE* 2.9 43.5 + - + -
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Residues in contact with ALA 852 (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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569B ILE* 5.8 5.4 - - + -
846C ALA* 4.3 21.8 - - - +
848C ASP 3.2 12.3 + - - +
849C LEU* 3.6 12.6 - - + +
851C CYS* 1.3 80.8 - - - +
853C GLN* 1.3 60.2 + - + +
855C PHE* 3.8 7.1 + - - +
856C ASN* 2.8 27.1 - - - +
963C VAL* 4.4 16.5 - - + +
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Residues in contact with GLN 853 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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849C LEU* 3.0 20.9 + - - +
850C ILE* 3.4 29.2 - - - +
852C ALA* 1.3 77.5 - - + +
854C LYS* 1.3 57.9 + - + +
856C ASN* 3.1 16.6 + - - -
857C GLY 3.6 0.3 + - - -
858C LEU* 3.3 36.1 + - + +
860C VAL* 5.4 3.5 - - - +
956C ALA* 4.5 3.4 + - - +
959C LEU* 3.3 39.8 - - + +
960C ASN* 3.3 25.8 + - - +
963C VAL* 4.0 21.8 - - + -
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Residues in contact with LYS 854 (chain C).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317B ASN* 4.5 8.8 + - - -
591B SER 5.2 0.7 - - - +
592B PHE* 3.6 44.1 - - + -
593B GLY* 5.2 3.5 + - - +
594B GLY 5.5 0.2 - - - +
614B ASP* 3.5 32.6 + - - -
740C MET* 5.4 0.7 - - - +
835C LYS* 4.5 13.9 - - + -
850C ILE* 2.9 37.3 + - + +
851C CYS* 3.2 2.9 + - - +
853C GLN* 1.3 73.3 - - + +
855C PHE* 1.3 60.3 + - - +
856C ASN 3.1 5.9 + - - -
857C GLY* 3.6 9.1 + - - -
858C LEU 4.0 13.7 - - - +
859C THR* 3.9 27.0 - - - +
860C VAL 5.3 1.4 - - - +
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Residues in contact with PHE 855 (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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588B THR* 3.9 18.6 - - + -
589B PRO* 3.9 47.8 - - + +
591B SER 4.3 9.1 - - - +
592B PHE* 3.6 27.1 - + + -
740C MET* 4.0 14.7 - - - +
837C TYR* 4.0 10.5 - + - -
840C CYS* 4.0 22.4 - - - -
845C ALA* 3.6 28.7 - - + -
846C ALA 5.5 0.7 - - - -
851C CYS* 2.9 28.3 + - + +
852C ALA* 4.3 6.5 - - - +
853C GLN 3.3 0.4 - - - -
854C LYS* 1.3 75.8 - - - +
856C ASN* 1.3 66.3 + - - +
857C GLY 3.6 0.7 - - - -
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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