Contacts of the helix formed by residues 290 - 294 (chain B) in PDB entry 4RQO
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 THR 290 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B SER* 3.5 14.5 + - - -
150B GLY* 4.4 7.1 + - - -
287B THR* 3.8 4.2 - - - -
288B ALA 3.0 14.4 + - - +
289B PRO* 1.3 79.3 + - - +
291B ASN* 1.3 62.5 + - - +
292B GLY 3.2 5.4 - - - +
293B ALA* 3.3 21.6 + - + +
294B ALA* 3.5 5.5 + - - +
346B GLU* 3.7 21.1 + - + -
456B PRO* 5.7 0.7 - - - +
458B CYS* 3.1 49.4 + - - -
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Residues in contact with ASN 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12B GLY* 5.8 0.5 - - - -
13B ILE 2.8 30.8 + - - -
14B GLY* 3.8 0.6 - - - -
15B PRO 3.7 8.5 - - - +
16B SER 3.5 7.5 + - - +
17B SER* 3.1 29.4 + - - +
21B VAL* 3.9 5.6 - - - +
276B ASN* 4.3 1.6 + - - -
279B ASN* 3.3 27.5 + - - +
285B ILE* 3.6 19.0 - - - +
287B THR* 3.1 22.2 + - - +
290B THR* 1.3 73.7 - - - +
292B GLY* 1.3 62.6 + - - +
294B ALA* 3.2 21.2 + - - +
458B CYS 3.5 4.2 + - - +
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Residues in contact with GLY 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276B ASN* 3.0 7.2 + - - -
290B THR* 3.2 6.2 - - - +
291B ASN* 1.3 80.5 - - - +
293B ALA* 1.3 49.0 + - - +
294B ALA 3.3 0.7 - - - -
392B VAL* 3.8 14.1 - - - -
396B CYS* 4.7 0.7 - - - +
400B ASN* 2.8 28.6 + - - -
458B CYS* 3.3 29.3 - - - +
501B SF4 4.0 13.0 - - - -
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Residues in contact with ALA 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B ALA* 3.6 11.0 - - - +
289B PRO* 4.0 7.6 - - + -
290B THR* 3.3 15.6 + - + +
291B ASN 3.3 0.4 - - - -
292B GLY* 1.3 74.9 - - - +
294B ALA* 1.3 59.9 + - - +
296B ILE* 3.6 5.5 + - - +
297B ILE 4.8 0.3 + - - -
346B GLU* 3.4 36.1 - - + +
347B VAL* 3.6 9.2 - - - +
350B ALA* 3.7 11.1 - - + +
400B ASN* 3.0 19.6 - - - +
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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
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275B VAL* 3.7 12.2 - - + +
276B ASN* 4.2 0.9 + - - +
279B ASN* 5.5 0.7 - - + -
285B ILE* 3.8 14.6 - - + -
286B VAL 3.5 24.5 - - - +
288B ALA* 4.4 6.6 - - - +
290B THR 3.5 7.8 + - - +
291B ASN 3.2 18.1 + - - +
292B GLY 3.3 3.2 - - - -
293B ALA* 1.3 79.6 - - - +
295B GLY* 1.3 58.0 + - - +
296B ILE 3.3 0.2 - - - -
297B ILE 4.8 0.2 - - - -
298B PRO* 3.0 29.3 - - - +
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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