Contacts of the helix formed by residues 291 - 299 (chain I) in PDB entry 1DZG
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 SER 291 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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72I ASP* 5.4 1.6 + - - -
286I PRO* 4.6 0.4 - - - -
289I GLU 3.6 2.4 + - - -
290I LYS* 1.3 88.7 - - - +
292I LEU* 1.3 65.5 + - - +
293I ALA* 3.4 19.4 + - - +
294I LYS* 3.2 33.0 + - - +
295I VAL* 3.5 6.2 + - - +
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Residues in contact with LEU 292 (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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284I ILE* 4.6 1.6 - - + +
286I PRO* 4.1 21.2 - - + +
290I LYS 3.9 1.6 + - - -
291I SER* 1.3 70.7 + - - +
293I ALA* 1.3 55.2 + - - +
295I VAL* 2.8 35.3 + - + +
296I GLU* 2.8 25.4 + - + +
407I PRO* 3.7 33.9 - - + +
408I PHE* 3.8 6.1 - - - +
409I LEU* 3.7 32.3 - - + +
425I ARG* 3.5 37.2 - - + -
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Residues in contact with ALA 293 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72I ASP* 4.8 19.7 - - - +
291I SER* 3.4 15.4 + - - +
292I LEU* 1.3 75.0 - - - +
294I LYS* 1.3 57.5 + - + +
296I GLU* 3.4 15.5 + - - +
297I LYS* 3.0 46.4 + - - +
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Residues in contact with LYS 294 (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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265I GLU* 5.5 2.2 - - - +
290I LYS* 3.9 19.1 - - + +
291I SER* 3.2 30.4 + - - +
293I ALA* 1.3 77.4 - - + +
295I VAL* 1.3 57.6 + - - +
297I LYS* 3.7 14.7 + - + +
298I GLU* 2.8 42.5 + - - +
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Residues in contact with VAL 295 (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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267I THR* 4.3 5.4 - - + +
284I ILE* 4.2 15.3 - - + -
286I PRO* 3.7 23.1 - - + -
290I LYS* 3.5 19.3 - - - +
291I SER 3.5 15.0 - - - +
292I LEU* 2.8 19.9 + - + +
294I LYS* 1.3 69.6 - - - +
296I GLU* 1.3 58.0 + - - +
298I GLU* 3.1 6.9 + - + +
299I LEU* 2.9 29.7 + - + +
307I TRP* 3.8 30.3 - - + -
409I LEU* 4.8 7.6 - - + -
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Residues in contact with GLU 296 (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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63I TYR* 2.6 40.1 + - + -
64I GLN* 3.0 20.6 + - - +
67I ALA* 3.8 8.9 - - + +
72I ASP* 5.5 1.9 - - - +
292I LEU* 2.8 32.2 + - + +
293I ALA* 3.8 18.6 + - - +
295I VAL* 1.3 69.6 - - - +
297I LYS* 1.3 64.4 + - + +
299I LEU* 3.2 21.9 + - - +
409I LEU* 4.2 10.1 - - + -
425I ARG* 2.8 39.1 + - - -
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Residues in contact with LYS 297 (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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64I GLN* 2.9 21.7 + - - +
68I ASP* 5.2 11.2 - - - +
293I ALA* 3.0 30.2 + - - +
294I LYS* 3.8 14.1 - - + +
296I GLU* 1.3 77.3 - - + +
298I GLU* 1.3 58.7 + - + +
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Residues in contact with GLU 298 (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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265I GLU* 4.6 2.0 - - - +
290I LYS* 2.9 28.5 + - - -
294I LYS* 2.8 30.0 + - - +
295I VAL* 3.1 5.5 + - + +
297I LYS* 1.3 76.3 - - + +
299I LEU* 1.3 64.4 + - - +
300I THR* 3.2 12.6 + - - -
303I VAL* 3.6 16.3 - - + +
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Residues in contact with LEU 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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60I THR* 3.4 26.0 - - + +
63I TYR* 4.6 11.4 - - + -
64I GLN* 3.4 18.3 + - + +
295I VAL* 2.9 13.0 + - + +
296I GLU* 3.2 14.6 + - - +
297I LYS 4.4 0.2 - - - +
298I GLU* 1.3 74.0 - - - +
300I THR* 1.3 62.7 + - - +
303I VAL* 4.4 5.8 - - + -
304I LEU* 4.1 32.3 - - + -
307I TRP* 4.4 18.2 - - + -
409I LEU* 4.0 25.8 - - + -
411I PHE* 4.1 15.7 - - + -
423I MET* 4.5 11.4 - - + -
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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