Contacts of the helix formed by residues 302 - 307 (chain K) in PDB entry 4E2I
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 CYS 302 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294K GLU 4.7 4.3 - - - -
297K TYR* 5.3 6.3 - - - -
298K SER 3.3 23.0 + - - +
299K PHE* 3.9 3.8 + - - +
300K GLU 3.7 1.0 - - - -
301K MET* 1.3 74.6 - - - +
303K LEU* 1.3 66.7 + - - +
304K LYS* 4.5 5.4 - - - +
305K CYS* 3.2 12.9 + - + +
306K ILE* 3.3 18.4 + - - +
313K HIS* 3.9 11.0 - - - +
317K HIS* 3.9 9.2 - - - -
700K ZN 2.9 33.7 - - - -
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Residues in contact with LEU 303 (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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301K MET 3.7 12.6 - - - +
302K CYS* 1.3 72.6 - - - +
304K LYS* 1.3 63.7 + - + +
306K ILE* 3.2 8.2 + - + +
307K LYS* 2.8 35.8 + - + +
309K GLU* 5.0 0.9 - - - +
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Residues in contact with LYS 304 (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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347J LYS* 5.8 4.1 - - - +
354J GLN* 4.0 20.0 - - - +
355J LEU* 6.6 0.7 - - - -
294K GLU* 3.9 22.2 + - - +
302K CYS* 3.3 5.4 - - - -
303K LEU* 1.3 81.1 - - + +
305K CYS* 1.3 60.5 + - - +
307K LYS 4.2 0.7 - - - -
308K LYS 3.5 12.3 + - - -
309K GLU* 3.4 38.7 + - + +
310K GLN* 4.7 0.7 + - + -
313K HIS* 3.4 31.7 - - + +
314K TYR* 3.8 7.8 - - - -
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Residues in contact with CYS 305 (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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299K PHE* 4.5 18.2 - - - +
302K CYS* 3.2 11.5 + - + +
303K LEU 3.1 0.2 - - - -
304K LYS* 1.3 80.9 - - - +
306K ILE* 1.3 62.4 + - + +
308K LYS* 3.6 18.7 + - - +
313K HIS* 3.8 1.0 - - - -
314K TYR* 3.5 37.9 - - + +
317K HIS* 5.4 1.6 - - - -
318K GLU* 5.1 8.5 - - - -
700K ZN 3.0 26.2 - - - -
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Residues in contact with ILE 306 (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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299K PHE 5.7 2.2 - - - +
300K GLU 5.1 3.8 - - - +
301K MET* 4.5 14.8 - - - +
302K CYS 3.3 19.7 - - - +
303K LEU* 3.2 7.7 + - + +
305K CYS* 1.3 79.1 - - + +
307K LYS* 1.3 60.2 + - - +
308K LYS* 3.1 18.3 + - - +
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Residues in contact with LYS 307 (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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303K LEU* 2.8 18.7 + - + +
306K ILE* 1.3 75.9 - - - +
308K LYS* 1.3 73.2 + - - +
309K GLU* 3.8 26.9 - - + +
379K THR* 5.8 0.5 - - - -
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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