Contacts of the helix formed by residues 280 - 287 (chain B) in PDB entry 4HY4
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 GLN 280 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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273B TRP* 5.6 1.8 - - - +
275B SER* 5.5 1.8 + - - +
277B VAL 3.7 14.6 + - - -
278B PRO* 3.1 23.2 + - - +
279B VAL* 1.3 76.2 - - - +
281B PRO* 1.3 80.9 - - + +
282B GLU* 3.3 3.8 - - + +
283B GLN* 3.1 34.6 + - - +
284B LEU* 3.3 14.9 + - - +
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Residues in contact with PRO 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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267B MET* 3.7 15.0 - - + -
270B PHE* 3.6 47.9 - - + +
273B TRP* 3.8 24.5 - - + -
280B GLN* 1.3 95.4 - - + +
282B GLU* 1.3 63.5 + - - +
284B LEU* 3.1 2.8 + - + +
285B ALA* 2.8 27.0 + - - +
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Residues in contact with GLU 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B HIS* 3.3 31.5 + - - -
267B MET* 3.6 21.0 - - + +
280B GLN* 3.2 3.5 + - + +
281B PRO* 1.3 77.9 - - - +
283B GLN* 1.3 77.0 + - - +
286B SER* 2.9 42.5 + - - +
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Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B VAL* 4.8 4.3 - - + -
280B GLN* 3.1 32.0 + - - +
282B GLU* 1.3 94.9 - - - +
284B LEU* 1.3 61.4 + - - +
286B SER* 3.6 6.4 + - - -
287B ALA* 3.4 21.7 + - - +
316B PRO* 3.8 24.5 - - + +
317B TRP* 5.8 0.9 - - - -
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B PHE* 3.8 22.9 - - + -
273B TRP* 3.4 37.7 - - + -
279B VAL* 3.8 12.8 - - + -
280B GLN 3.3 15.2 + - - +
281B PRO 3.1 4.4 + - - +
283B GLN* 1.3 74.7 - - - +
285B ALA* 1.3 64.0 + - - +
287B ALA* 3.1 10.4 + - - -
288B GLY 3.4 0.3 + - - -
289B PHE* 3.0 28.5 + - + +
298B VAL* 4.5 7.6 - - + -
310B TRP* 3.4 42.0 - - + +
316B PRO* 3.7 12.6 - - + -
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Residues in contact with ALA 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B HIS* 3.7 11.2 - - + +
266B ARG* 2.9 44.7 + - + +
267B MET* 3.5 28.3 - - + +
270B PHE* 4.3 3.6 - - + -
281B PRO 2.8 19.3 + - - +
284B LEU* 1.3 73.0 - - - +
286B SER* 1.3 62.2 + - - +
288B GLY 3.1 2.8 + - - -
289B PHE 3.3 11.8 + - - +
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Residues in contact with SER 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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263B HIS* 3.2 20.2 + - - -
266B ARG* 4.7 0.7 + - - -
282B GLU* 2.9 31.3 + - - +
283B GLN* 3.8 7.4 - - - -
284B LEU 3.2 0.2 - - - -
285B ALA* 1.3 76.6 - - - +
287B ALA* 1.3 58.2 + - - +
288B GLY 3.3 1.1 + - - -
317B TRP* 3.2 24.0 + - - -
329B PHE* 4.0 8.5 - - - -
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Residues in contact with ALA 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283B GLN 3.4 10.0 + - - +
284B LEU 3.1 8.7 + - - +
286B SER* 1.3 77.6 - - - +
288B GLY* 1.3 56.6 + - - +
289B PHE* 3.5 10.2 - - + -
316B PRO* 3.7 22.0 - - + -
317B TRP* 3.6 32.7 - - + +
320B HIS* 2.8 32.9 + - - -
329B PHE* 3.8 4.7 - - - -
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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