Contacts of the helix formed by residues 290 - 301 (chain B) in PDB entry 4EG8
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 GLY 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250B TYR* 3.8 3.1 - - - -
289B HIS* 1.3 75.2 - - - +
291B GLN* 1.3 67.0 + - - -
292B LYS 3.3 3.4 + - - -
293B VAL 3.4 2.6 + - - -
294B ALA* 3.4 16.3 + - - +
456B LEU* 4.3 6.7 - - - -
459B TRP* 2.8 25.2 + - - -
812B 0P6 3.5 23.3 - - - -
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Residues in contact with GLN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B TYR* 4.5 0.4 + - - -
290B GLY* 1.3 71.4 - - - -
292B LYS* 1.3 68.9 + - + +
294B ALA* 3.3 3.5 + - - +
295B GLU* 2.9 46.8 + - - +
363B TYR* 4.6 0.5 + - - -
365B ILE* 2.9 36.8 + - - +
366B SER* 4.7 1.8 + - - +
368B GLU* 3.4 32.2 + - - +
455B THR* 3.4 34.4 + - - +
456B LEU* 3.8 23.4 + - - +
457B HIS* 3.6 17.2 - - + -
472B TYR* 5.6 0.2 - - - -
812B 0P6 4.8 1.4 - - - -
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Residues in contact with LYS 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B TYR* 3.9 20.5 + - + +
252B ASN* 4.1 24.4 - - + +
290B GLY 3.3 1.0 - - - -
291B GLN* 1.3 85.4 - - + +
293B VAL* 1.3 61.1 + - - +
295B GLU* 3.6 15.3 + - - +
296B ALA* 2.9 28.8 + - - +
366B SER* 3.1 29.5 + - - +
368B GLU* 3.1 22.9 + - - +
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Residues in contact with VAL 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B TYR* 3.8 27.8 + - + +
251B VAL* 3.6 22.4 - - + -
252B ASN* 4.7 6.3 - - + +
288B GLU 3.5 14.4 - - - +
289B HIS 4.1 0.9 - - - +
290B GLY 3.4 7.1 + - - +
291B GLN 3.3 0.2 - - - -
292B LYS* 1.3 75.1 - - - +
294B ALA* 1.3 66.8 + - - +
296B ALA* 3.1 8.0 + - - +
297B ALA* 2.9 22.7 + - - +
304B PRO* 4.8 3.1 - - + +
307B PHE* 4.1 11.6 - - + -
308B THR* 3.4 31.6 - - + -
459B TRP* 3.6 7.6 - - + +
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290B GLY 3.4 8.9 + - - +
291B GLN 3.3 9.1 + - - +
293B VAL* 1.3 79.9 - - - +
295B GLU* 1.3 57.5 + - - +
297B ALA* 3.5 8.0 - - - +
298B LYS* 3.0 27.4 + - - +
304B PRO* 4.6 12.9 - - + +
457B HIS* 3.8 30.3 - - + +
459B TRP* 4.1 14.0 - - + -
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Residues in contact with GLU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B GLN* 2.9 35.0 + - - +
292B LYS* 3.6 21.8 + - - +
294B ALA* 1.3 75.0 - - - +
296B ALA* 1.3 65.6 + - - +
298B LYS* 3.1 9.2 + - + +
299B GLN* 3.0 30.5 + - + +
457B HIS* 2.7 32.5 + - + +
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Residues in contact with ALA 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B ASN* 5.2 9.0 - - + +
292B LYS 2.9 18.0 + - - +
293B VAL* 3.5 4.5 - - - +
295B GLU* 1.3 74.7 - - - +
297B ALA* 1.3 63.6 + - - +
299B GLN* 3.3 8.7 + - - +
300B LYS* 3.1 26.2 + - - +
307B PHE* 3.4 29.8 - - + -
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Residues in contact with ALA 297 (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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293B VAL 2.9 11.1 + - - +
294B ALA 3.5 9.9 - - - +
296B ALA* 1.3 77.0 - - - +
298B LYS* 1.3 56.4 + - - +
300B LYS 3.3 1.7 + - - -
301B GLN 2.9 23.0 + - - -
302B VAL* 3.1 26.8 + - - +
304B PRO* 3.7 28.3 - - + -
307B PHE* 3.7 21.8 - - + -
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Residues in contact with LYS 298 (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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294B ALA 3.0 15.8 + - - +
295B GLU* 3.1 13.4 + - - +
297B ALA* 1.3 77.2 - - - +
299B GLN* 1.3 69.2 + - - +
301B GLN* 3.1 21.3 + - - +
302B VAL 4.8 1.3 - - - -
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Residues in contact with GLN 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLU* 3.0 20.3 + - + +
296B ALA* 3.3 9.1 + - - +
298B LYS* 1.3 83.5 - - - +
300B LYS* 1.3 63.9 + - + +
301B GLN* 3.2 10.0 + - - +
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Residues in contact with LYS 300 (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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296B ALA 3.1 16.5 + - - +
297B ALA 3.9 3.4 - - - +
298B LYS 3.2 0.2 - - - -
299B GLN* 1.3 78.1 + - + +
301B GLN* 1.3 70.0 + - - +
302B VAL* 3.3 22.8 + - + +
307B PHE* 4.1 17.7 - - + -
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Residues in contact with GLN 301 (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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297B ALA 2.9 5.0 + - - -
298B LYS* 3.1 15.2 + - - +
299B GLN 3.6 12.1 + - - +
300B LYS* 1.3 81.4 - - - +
302B VAL* 1.3 60.0 + - - +
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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
------------------------------------------------------------
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