Contacts of the helix formed by residues 297 - 300 (chain I) in PDB entry 1ZUM
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 ASN 297 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110I ASN* 4.5 1.2 - - - +
112I LYS* 3.1 33.5 + - - +
113I PRO* 5.9 1.6 - - - -
116I ILE* 6.1 1.0 - - - +
169I ASN* 3.0 22.0 + - - +
170I PHE* 3.6 22.5 - - + -
295I PHE 3.2 0.6 + - - -
296I PHE* 1.3 88.8 - - + +
298I GLN* 1.3 81.8 + - - +
300I GLN* 2.9 48.5 + - - +
301I CYS* 5.3 0.4 - - + -
329I ARG* 4.9 2.2 - - - +
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Residues in contact with GLN 298 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110I ASN* 4.7 1.4 + - - -
111I GLY 4.5 0.2 - - - -
112I LYS* 3.8 16.9 - - - +
113I PRO* 3.5 16.1 - - - +
295I PHE 3.0 8.4 + - - -
297I ASN* 1.3 98.1 + - - +
299I GLY* 1.3 59.2 + - - +
300I GLN* 3.1 12.8 + - - +
329I ARG* 4.9 1.0 - - - +
340I GLU 4.4 1.7 - - - +
341I GLN* 3.8 16.9 - - + -
342I GLY* 3.1 36.8 + - - +
343I PRO 3.4 22.7 + - - +
344I GLN* 3.1 34.9 + - - +
402I GLY 3.6 0.7 - - - -
403I PRO* 3.6 15.9 - - - +
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Residues in contact with GLY 299 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294I LEU 3.2 24.5 - - - -
295I PHE* 3.2 6.2 + - - +
296I PHE 3.0 8.9 + - - -
298I GLN* 1.3 76.8 - - - +
300I GLN* 1.3 57.8 + - - +
301I CYS 3.2 7.2 + - - -
304I ALA* 4.0 12.1 - - - +
399I GLU* 4.7 0.2 - - - +
401I PHE* 3.2 23.0 - - - -
402I GLY 3.5 14.1 + - - +
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Residues in contact with GLN 300 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110I ASN* 4.8 8.3 + - - +
168I TRP* 3.4 38.6 - - + -
169I ASN* 3.1 15.4 + - - +
170I PHE* 3.8 0.3 - - - -
296I PHE 3.9 0.2 + - - -
297I ASN* 2.9 40.0 + - - +
298I GLN* 3.6 19.7 - - - +
299I GLY* 1.3 74.0 - - - +
301I CYS* 1.3 57.5 + - - +
343I PRO 4.8 0.2 + - - -
344I GLN* 3.3 17.0 + - - +
345I VAL* 3.0 33.7 + - - +
349I GLN* 4.7 2.6 - - - +
401I PHE* 3.4 26.2 - - - +
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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