Contacts of the helix formed by residues 302 - 307 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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294H GLU 4.7 4.5 - - - -
297H TYR* 5.3 5.8 - - - -
298H SER 3.3 23.1 + - - +
299H PHE* 3.9 3.6 + - - +
300H GLU 3.7 1.0 - - - -
301H MET* 1.3 74.0 - - - +
303H LEU* 1.3 66.5 + - - +
304H LYS* 5.3 4.9 - - - -
305H CYS* 3.2 12.5 + - + +
306H ILE* 3.3 18.5 + - - +
313H HIS* 3.9 11.0 - - - +
317H HIS* 3.9 9.9 - - - -
700H ZN 2.8 34.3 - - - -
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Residues in contact with LEU 303 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301H MET 3.7 12.3 - - - +
302H CYS* 1.3 73.6 - - - +
304H LYS* 1.3 64.6 + - + +
306H ILE* 3.2 6.6 + - + +
307H LYS* 2.8 55.5 + - + +
309H GLU* 5.0 0.7 - - - +
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Residues in contact with LYS 304 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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347G LYS* 5.6 5.4 - - - +
354G GLN* 3.9 21.8 - - - +
294H GLU* 3.9 22.6 + - - +
302H CYS* 3.3 5.3 - - - -
303H LEU* 1.3 81.3 - - + +
305H CYS* 1.3 59.2 + - - +
307H LYS 4.2 0.7 - - - -
308H LYS 3.5 12.1 + - - -
309H GLU* 3.4 38.1 + - + +
310H GLN* 4.7 1.4 + - + +
313H HIS* 3.4 30.7 - - + +
314H TYR* 3.8 8.3 - - - -
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Residues in contact with CYS 305 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299H PHE* 4.5 19.5 - - - +
302H CYS* 3.2 10.6 + - + +
303H LEU 3.1 0.6 - - - -
304H LYS* 1.3 79.7 - - - +
306H ILE* 1.3 64.6 + - + +
308H LYS* 3.6 18.9 + - - +
313H HIS* 3.8 0.8 - - - -
314H TYR* 3.5 37.8 - - + +
317H HIS* 5.4 1.6 - - - -
318H GLU* 5.1 8.5 - - - -
700H ZN 2.9 28.5 - - - -
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Residues in contact with ILE 306 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299H PHE 5.7 2.2 - - - +
300H GLU 5.1 3.8 - - - +
301H MET* 4.5 14.6 - - - +
302H CYS 3.3 19.3 - - - +
303H LEU* 3.2 7.2 + - + +
305H CYS* 1.3 79.2 - - + +
307H LYS* 1.3 77.1 + - + +
308H LYS* 3.1 18.6 + - - +
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Residues in contact with LYS 307 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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303H LEU* 2.8 40.7 + - + +
306H ILE* 1.3 93.3 - - + +
308H LYS* 1.3 72.5 + - - +
309H GLU* 3.8 23.4 - - + +
379H 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