Contacts of the helix formed by residues 291 - 296 (chain K) in PDB entry 5ANC
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 PRO 291 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146C ILE* 3.9 22.7 - - + -
160K GLN* 3.3 31.9 - - - +
163K TYR* 3.4 27.1 - - + +
270K ASP* 3.8 14.1 - - - +
271K TYR 4.0 8.5 - - - +
272K TYR* 3.8 15.7 - - + -
290K LYS* 1.4 91.0 - - + +
292K LEU* 1.3 63.4 + - - +
293K PHE 3.6 0.4 - - - -
294K VAL* 3.7 3.6 - - + +
295K GLN* 3.1 21.3 + - - +
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Residues in contact with LEU 292 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163K TYR* 2.9 13.8 + - - +
252K TYR* 3.9 25.8 + - + +
263K LEU* 6.3 0.2 - - + -
266K THR* 3.7 38.1 - - - +
267K LEU* 3.4 33.2 - - + -
271K TYR* 3.2 28.9 - - + +
273K ILE* 4.2 19.7 - - + -
291K PRO* 1.3 70.9 - - - +
293K PHE* 1.3 58.2 + - - +
295K GLN* 3.2 12.9 + - - +
296K LEU* 2.8 36.5 + - - +
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Residues in contact with PHE 293 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159K PRO* 4.0 8.1 - - - +
162K ALA* 4.0 20.2 - - + -
163K TYR* 3.4 46.0 + + + -
166K LEU* 5.2 4.5 - - + -
234K PHE* 4.7 19.1 - + - -
248K PHE* 4.2 22.0 - + - -
267K LEU* 3.4 54.3 - - + -
291K PRO 3.6 0.6 - - - -
292K LEU* 1.3 75.8 - - - +
294K VAL* 1.3 57.8 + - - +
296K LEU 2.8 18.3 - - - +
297K ILE* 5.6 2.5 - - + -
298K LEU* 3.5 25.0 + - + +
299K GLU 3.2 17.7 + - - -
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Residues in contact with VAL 294 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158K THR* 3.4 26.7 - - + +
159K PRO* 4.0 8.4 - - + +
160K GLN* 3.4 40.6 - - + +
163K TYR* 4.9 1.2 - - - -
290K LYS* 4.1 30.6 + - + +
291K PRO 3.7 10.3 - - - +
293K PHE* 1.3 76.7 - - - +
295K GLN* 1.3 67.2 + - - +
299K GLU* 3.3 22.8 - - + +
302K TRP* 5.3 3.8 - - + -
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Residues in contact with GLN 295 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252K TYR* 4.8 3.9 + - - +
273K ILE* 3.0 25.3 + - - +
274K ASN 4.8 1.4 - - - +
275K MET* 3.2 40.2 - - + +
289K LYS* 5.0 2.8 - - - +
290K LYS* 2.6 53.5 + - + +
291K PRO 3.1 13.9 + - - +
292K LEU* 3.2 18.7 + - - +
294K VAL* 1.3 81.1 - - - +
296K LEU* 1.3 72.5 + - + +
299K GLU* 3.4 19.3 - - - +
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Residues in contact with LEU 296 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252K TYR* 3.7 29.2 - - + +
255K LYS* 3.8 40.8 - - + +
275K MET* 4.4 12.3 - - - -
278K LYS* 4.3 13.5 - - - +
292K LEU 2.8 13.7 + - - +
293K PHE* 2.8 20.5 - - - +
295K GLN* 1.3 83.2 - - + +
297K ILE* 1.3 70.7 + - + +
298K LEU 3.4 0.4 - - - -
299K GLU* 4.2 7.4 - - - +
300K ASN* 4.2 13.2 - - - +
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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