Contacts of the helix formed by residues 288 - 295 (chain A) in PDB entry 3QKJ
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 288 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237A SER* 3.6 19.1 + - - +
238A TRP 5.6 0.7 - - - +
286A HIS 3.3 4.4 + - - +
287A PHE* 1.3 73.4 - - - +
289A LEU* 1.4 58.4 + - - +
290A ALA* 3.2 13.5 + - - +
291A THR* 3.0 37.0 + - - +
292A PHE* 3.0 27.5 + - - +
298A TYR* 3.0 17.0 + - - +
337B HIS* 5.3 0.2 - - - -
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Residues in contact with LEU 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A PHE* 3.9 30.7 + - + -
288A ASN* 1.4 69.0 + - - +
290A ALA* 1.4 60.3 + - - +
292A PHE* 3.3 6.7 + - + +
293A ASN* 3.0 51.3 + - - +
287B PHE* 5.7 4.7 - - + -
289B LEU* 6.1 5.4 - - + -
333B LEU* 4.0 48.9 - - + +
334B GLU* 4.1 7.4 - - + +
337B HIS* 4.2 26.4 + - + +
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Residues in contact with ALA 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A ASN* 3.2 9.5 + - - +
289A LEU* 1.4 77.0 - - - +
291A THR* 1.4 56.8 + - - +
293A ASN* 3.4 3.6 + - - +
294A LYS* 3.0 30.5 + - - +
334B GLU* 3.6 38.0 + - + +
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Residues in contact with THR 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A SER* 2.7 29.7 + - - +
239A TRP* 4.7 2.7 - - + -
288A ASN* 3.0 24.5 + - - -
290A ALA* 1.4 75.3 - - - +
292A PHE* 1.3 54.8 + - - +
294A LYS* 4.4 6.3 - - + -
295A LEU* 2.8 58.1 + - + +
298A TYR* 3.6 23.9 - - + +
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Residues in contact with PHE 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A PHE* 3.7 29.6 - + + -
288A ASN 3.0 17.0 + - - +
289A LEU* 3.5 10.5 - - + +
290A ALA 3.3 0.2 - - - -
291A THR* 1.3 77.7 - - - +
293A ASN* 1.4 70.9 + - - +
294A LYS 3.6 0.2 + - - -
295A LEU 3.8 1.2 - - - +
298A TYR* 3.5 18.7 - + + -
299A ARG* 3.1 64.8 + - + +
302A MET* 4.1 7.2 - - + -
329A LEU* 3.7 22.7 - - + -
333A LEU* 3.5 29.2 - - + -
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Residues in contact with ASN 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289A LEU* 3.0 34.2 + - - +
290A ALA 3.8 0.7 - - - +
292A PHE* 1.4 89.2 - - - +
294A LYS* 1.3 59.9 + - - +
299A ARG* 4.0 12.7 + - - +
330B LYS* 3.8 23.3 + - + +
334B GLU* 2.9 32.2 + - - +
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Residues in contact with LYS 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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290A ALA 3.0 18.3 + - - +
291A THR* 3.9 5.4 - - + +
293A ASN* 1.3 78.2 - - - +
295A LEU* 1.3 77.8 - - + +
296A VAL 4.2 0.9 + - - -
299A ARG* 4.5 4.5 + - - -
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239A TRP* 4.7 10.3 - - + -
291A THR* 2.8 38.6 + - + +
292A PHE 3.8 1.0 - - - +
293A ASN 3.7 0.8 - - - -
294A LYS* 1.3 94.9 - - + +
296A VAL* 1.3 64.4 + - - +
297A SER* 3.8 21.1 - - - +
298A TYR* 3.2 13.9 + - + +
299A ARG* 3.2 18.9 + - - +
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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