Contacts of the helix formed by residues 302 - 307 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294G GLU 4.7 3.8 - - - -
297G TYR* 5.3 5.8 - - - -
298G SER 3.3 23.6 + - - +
299G PHE* 3.8 3.2 + - - -
300G GLU 3.7 1.4 - - - -
301G MET* 1.3 74.2 - - - +
303G LEU* 1.3 67.3 + - - +
304G LYS* 5.3 5.6 - - - -
305G CYS* 3.2 15.4 + - + +
306G ILE* 3.3 18.2 + - - +
313G HIS* 3.9 10.3 - - - +
317G HIS* 3.9 8.7 - - - -
700G ZN 3.3 31.6 - - - -
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Residues in contact with LEU 303 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301G MET 3.7 12.1 - - - +
302G CYS* 1.3 73.6 - - - +
304G LYS* 1.3 64.4 + - + +
306G ILE* 3.2 7.3 + - + +
307G LYS* 2.8 66.0 + - + +
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Residues in contact with LYS 304 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294G GLU* 3.9 21.3 + - - +
302G CYS* 3.3 4.9 - - - -
303G LEU* 1.3 82.4 - - + +
305G CYS* 1.3 59.1 + - - +
307G LYS 4.2 0.7 - - - -
308G LYS 3.5 12.5 + - - -
309G GLU* 3.4 38.4 + - + +
310G GLN* 4.7 1.0 + - + +
313G HIS* 3.4 29.9 - - + +
314G TYR* 3.8 8.0 - - - -
347L LYS* 6.0 1.4 - - - +
354L GLN* 4.1 19.5 - - - +
355L LEU* 6.2 3.6 - - - -
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Residues in contact with CYS 305 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299G PHE* 4.5 19.3 - - - +
302G CYS* 3.2 13.1 + - + +
303G LEU 3.1 0.6 - - - -
304G LYS* 1.3 79.6 - - - +
306G ILE* 1.3 64.2 + - + +
308G LYS* 3.6 18.7 + - - +
313G HIS* 3.8 1.7 - - - -
314G TYR* 3.5 38.2 - - + +
317G HIS* 5.4 1.3 - - - -
318G GLU* 5.1 8.7 - - - -
700G ZN 3.3 24.0 - - - -
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Residues in contact with ILE 306 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299G PHE 5.7 2.2 - - - +
300G GLU 5.1 4.0 - - - +
301G MET* 4.5 14.6 - - - +
302G CYS 3.3 19.1 - - - +
303G LEU* 3.2 7.7 + - + +
305G CYS* 1.3 78.1 - - + +
307G LYS* 1.3 63.5 + - + +
308G LYS* 3.1 17.6 + - - +
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Residues in contact with LYS 307 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303G LEU* 2.8 50.4 + - + +
306G ILE* 1.3 76.8 - - + +
308G LYS* 1.3 72.5 + - - +
309G GLU* 3.8 30.8 + - + +
379G THR* 5.9 0.3 - - - -
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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