Contacts of the helix formed by residues 280 - 287 (chain E) in PDB entry 4HY0
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 ASN 280 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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278E SER 3.5 4.5 + - - -
279E VAL* 1.3 74.3 - - - +
281E LYS* 1.3 65.7 + - - +
282E GLU* 3.0 29.0 + - - +
283E GLN* 2.7 50.7 + - + +
284E LEU* 3.1 26.3 + - - +
286E ARG* 4.9 0.2 + - - -
316E PRO* 4.9 0.3 - - - +
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Residues in contact with LYS 281 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269E ILE* 3.9 14.2 + - + +
272E PHE* 3.9 45.1 + - + +
275E TRP* 3.9 25.2 - - + +
279E VAL 3.5 1.8 + - - -
280E ASN* 1.3 73.7 - - - +
282E GLU* 1.3 84.6 + - + +
284E LEU* 3.3 13.0 + - - +
285E ALA* 3.0 28.6 + - - +
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Residues in contact with GLU 282 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E TYR* 3.8 9.3 + - - +
269E ILE* 3.6 21.5 - - + +
280E ASN* 3.0 23.5 + - - +
281E LYS* 1.3 100.5 + - - +
283E GLN* 1.3 63.6 + - - +
285E ALA* 3.2 3.5 + - - +
286E ARG* 3.1 49.9 + - - +
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Residues in contact with GLN 283 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280E ASN* 2.7 38.3 + - + +
281E LYS 3.3 0.2 - - - -
282E GLU* 1.3 72.2 - - - +
284E LEU* 1.3 61.0 + - - +
286E ARG* 3.4 22.5 + - - +
287E ALA* 3.1 23.0 + - - +
315E ASP* 4.3 6.1 - - - +
316E PRO* 3.8 27.6 - - + +
317E TRP* 5.3 4.0 + - - -
259H ASN* 5.7 1.9 + - - -
260H PRO* 4.4 30.1 - - - +
261H SER* 4.8 9.8 + - - +
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Residues in contact with LEU 284 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272E PHE* 3.9 17.9 - - + -
275E TRP* 3.8 36.3 - - + +
279E VAL* 3.8 16.6 - - + -
280E ASN 3.1 20.0 + - - +
281E LYS* 3.4 8.7 - - - +
283E GLN* 1.3 77.2 - - - +
285E ALA* 1.3 58.8 + - - +
287E ALA 3.3 6.6 + - - -
288E GLY 3.4 0.2 + - - -
289E PHE* 3.1 45.2 + - + +
298E VAL* 4.7 4.7 - - + -
310E TRP* 3.9 35.2 - - + -
316E PRO* 3.9 12.8 - - + +
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Residues in contact with ALA 285 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E TYR* 3.6 22.4 - - + -
268E ARG* 2.7 41.1 + - + +
269E ILE* 3.6 38.8 - - + +
272E PHE* 4.4 2.4 - - + -
281E LYS 3.0 8.0 + - - +
282E GLU 3.7 0.9 - - - +
284E LEU* 1.3 76.3 - - - +
286E ARG* 1.3 56.6 + - - +
288E GLY 3.3 1.4 + - - -
289E PHE 3.7 10.7 + - - -
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Residues in contact with ARG 286 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265E TYR* 3.7 24.1 + - + -
268E ARG* 4.6 0.2 - - - +
280E ASN* 4.9 0.2 + - - -
282E GLU* 3.1 31.7 + - - +
283E GLN* 3.7 41.6 - - - +
284E LEU 3.3 0.2 - - - -
285E ALA* 1.3 72.1 - - - +
287E ALA* 1.3 56.7 + - - +
288E GLY 3.1 5.4 - - - -
317E TRP* 3.1 22.5 - - + +
329E TYR* 2.7 25.5 + - - -
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Residues in contact with ALA 287 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283E GLN 3.1 8.4 + - - +
284E LEU 3.3 0.6 + - - -
286E ARG* 1.3 75.7 - - - +
288E GLY* 1.3 56.6 + - - +
289E PHE* 3.5 17.4 - - + -
316E PRO* 3.5 32.8 - - + -
317E TRP* 3.7 27.5 - - + +
320E HIS* 2.8 32.2 + - - -
329E TYR* 3.7 6.3 - - - -
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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