Contacts of the helix formed by residues 930 - 934 (chain D) in PDB entry 3LZB
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 930 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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928D MET* 3.2 6.6 - - + +
929D ILE* 1.3 76.2 - - - +
931D ALA* 1.3 69.9 + - - +
932D ASP* 3.3 18.5 + - - +
933D SER* 2.9 42.8 + - - +
934D ARG 3.6 2.8 + - - -
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Residues in contact with ALA 931 (chain D).
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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860D GLU* 3.9 10.5 - - + +
868D THR* 5.3 1.1 - - - +
870D GLN* 3.1 31.8 + - + +
929D ILE 3.2 7.1 + - - -
930D ASP* 1.3 71.7 + - - +
932D ASP* 1.3 62.4 + - - +
934D ARG* 3.0 48.3 + - - +
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Residues in contact with ASP 932 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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851C LYS* 5.5 8.5 - - - -
870D GLN* 4.2 11.4 - - - +
930D ASP* 3.1 13.5 + - - +
931D ALA* 1.3 82.3 - - - +
933D SER* 1.3 58.9 + - - +
934D ARG 3.3 5.4 + - - +
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Residues in contact with SER 933 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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925D LYS* 3.3 24.5 + - - +
928D MET* 3.3 32.7 - - - +
930D ASP* 2.9 35.2 + - - +
932D ASP* 1.3 76.6 - - - +
934D ARG* 1.3 63.3 + - - +
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Residues in contact with ARG 934 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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858D ALA* 4.0 0.8 - - - +
859D LEU* 4.8 0.6 - - - +
860D GLU* 2.8 41.4 + - - -
870D GLN* 3.1 44.6 + - - +
871D SER* 3.9 3.0 - - - +
873D VAL* 4.1 4.7 - - + -
874D TRP* 3.4 24.2 - - - +
925D LYS* 3.4 11.8 + - - +
926D CYS 3.2 22.7 - - - +
928D MET* 2.6 29.1 + - + +
929D ILE* 3.4 12.7 + - - +
930D ASP 3.6 1.3 + - - +
931D ALA* 3.0 28.8 + - - +
932D ASP 4.2 4.3 - - - +
933D SER* 1.3 82.4 + - - +
935D PRO* 1.3 72.1 - - + +
936D LYS* 3.7 3.3 + - - +
939D GLU* 4.8 0.9 - - - +
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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