Contacts of the helix formed by residues 290 - 294 (chain D) in PDB entry 6O81
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 ALA 290 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A ARG 3.3 14.1 - - - +
317A TRP 4.3 4.0 - - - +
319A TYR* 3.6 22.3 - - + +
289D VAL* 1.3 82.4 - - - +
291D PRO* 1.3 65.5 - - + +
292D GLU* 3.2 22.0 - - + +
293D GLU* 2.9 29.6 + - - +
310D CYS* 4.3 3.5 - - - +
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Residues in contact with PRO 291 (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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315A ARG 3.9 6.7 - - - +
316A ARG* 3.3 20.0 - - + +
317A TRP* 3.6 37.2 - - + +
289D VAL 3.6 5.4 - - - +
290D ALA* 1.3 81.4 - - + +
292D GLU* 1.3 58.0 + - - +
293D GLU 3.2 2.7 - - - -
294D VAL 3.2 3.8 + - - +
295D LEU* 2.8 33.2 + - - +
308D VAL* 3.7 37.9 - - + +
309D HIS 5.4 0.4 - - - -
310D CYS* 4.6 9.6 - - + -
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Residues in contact with GLU 292 (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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158A ASN* 5.2 1.6 + - - -
186A LYS* 2.7 32.9 + - - +
293A ALA 4.8 3.8 - - - +
294A LYS* 3.7 26.5 - - - +
295A GLU* 3.2 12.3 + - - -
296A TYR* 3.5 4.9 + - - -
317A TRP* 3.3 47.7 - - + +
290D ALA* 3.2 12.8 - - + +
291D PRO* 1.3 79.3 - - - +
293D GLU* 1.3 65.3 + - - +
294D VAL 3.5 0.3 + - - -
295D LEU 3.5 11.5 - - - +
296D PRO* 3.8 13.4 - - + +
297D PHE* 4.7 8.5 - - + +
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Residues in contact with GLU 293 (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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294A LYS* 4.5 16.8 - - + +
195D ALA 4.6 2.3 - - - +
196D PRO* 3.3 38.6 - - + +
197D PHE* 4.7 13.0 - - + -
289D VAL* 4.8 6.1 - - + +
290D ALA* 2.9 32.8 + - - +
291D PRO 3.2 0.6 - - - -
292D GLU* 1.3 81.2 + - - +
294D VAL* 1.3 62.0 + - + +
310D CYS* 5.4 1.8 - - - -
467E ARG* 4.2 16.8 + - - +
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Residues in contact with VAL 294 (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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196D PRO* 4.6 3.8 - - + -
291D PRO 3.2 6.5 + - - +
293D GLU* 1.3 81.4 - - - +
295D LEU* 1.3 52.5 + - - +
296D PRO* 4.1 1.0 - - - +
308D VAL* 3.9 15.9 - - + -
309D HIS 4.6 5.2 - - - +
310D CYS* 3.7 37.2 - - + -
370E ARG* 2.7 30.5 + - - -
385E TYR* 3.6 25.8 + - + +
386E LEU 5.0 1.6 - - - -
387E LEU* 3.8 37.5 - - + +
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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