Contacts of the helix formed by residues 830 - 833 (chain C) in PDB entry 3ZNS
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 LEU 830 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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702C LEU* 3.8 11.7 - - + -
783C MET* 4.0 14.8 - - + -
786C ALA* 3.6 26.0 - - + +
787C ARG* 3.7 44.2 - - + +
790C SER* 5.8 0.4 - - - -
791C PRO* 4.5 7.9 - - + -
794C VAL* 4.1 10.1 - - + -
827C LEU* 3.1 42.2 + - + +
828C MET 3.3 2.4 - - - +
829C ASN* 1.3 76.1 - - - +
831C ALA* 1.3 59.6 + - - +
832C GLY 3.1 3.4 - - - -
833C GLY* 2.8 28.2 + - - -
834C ALA 3.9 0.7 + - - -
835C VAL* 4.7 0.5 - - - +
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Residues in contact with ALA 831 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
791C PRO* 3.5 20.8 + - - +
792C ASP* 3.1 32.9 - - - +
793C LEU* 3.7 3.1 - - - +
794C VAL* 4.0 9.6 - - + -
829C ASN 4.2 0.2 + - - -
830C LEU* 1.3 74.4 - - + +
832C GLY* 1.3 59.9 + - - +
833C GLY 3.1 1.1 + - - -
834C ALA* 3.3 31.2 + - - +
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Residues in contact with GLY 832 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
829C ASN 4.4 5.1 + - - -
830C LEU 2.9 2.0 + - - -
831C ALA* 1.3 75.4 - - - +
833C GLY* 1.3 58.4 + - - +
834C ALA* 3.5 0.4 - - - -
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Residues in contact with GLY 833 (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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658C LYS* 3.2 25.3 - - - +
659C ASN* 4.0 10.7 + - - +
828C MET* 3.2 25.7 + - - +
830C LEU 2.8 8.5 + - - -
832C GLY* 1.3 75.5 - - - +
834C ALA* 1.3 57.5 + - - +
835C VAL* 3.0 14.3 + - - +
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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
------------------------------------------------------------
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