Contacts of the strand formed by residues 298 - 304 (chain B) in PDB entry 1QQJ
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 298 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296B ASP* 4.4 8.5 + - - +
297B ILE* 1.3 73.2 - - - +
299B LEU* 1.3 59.6 + - - +
317B SER 3.8 5.9 - - - +
318B ASN* 3.7 13.7 + - - +
394B GLY* 3.0 6.2 - - - -
395B HIS* 2.9 74.6 + - + +
396B CYS* 4.4 0.8 - - - +
397B GLN* 4.2 16.0 - - - +
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Residues in contact with LEU 299 (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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200B LEU* 4.1 27.4 - - + -
202B MET* 3.9 14.8 - - + -
230B LEU* 3.6 31.0 - - + -
297B ILE* 3.7 8.1 - - + +
298B ASN* 1.3 82.2 - - - +
300B SER* 1.3 61.7 + - - +
316B ARG* 3.4 4.7 - - - +
317B SER* 2.8 38.6 + - - +
318B ASN* 4.0 3.1 - - - -
319B PHE* 3.7 18.8 - - - +
351B ILE* 3.6 32.8 - - + -
393B THR 3.5 5.8 - - - +
394B GLY* 4.0 2.9 - - - -
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Residues in contact with SER 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU* 1.3 77.5 - - - +
301B VAL* 1.3 68.2 + - - +
313B THR* 3.3 24.9 + - - +
315B CYS 3.3 5.2 + - - -
316B ARG* 4.2 6.6 + - - +
391B ILE 3.8 0.8 - - - +
392B ILE* 3.4 5.0 - - - +
393B THR* 2.9 46.7 + - - +
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Residues in contact with VAL 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198B MET* 4.0 17.9 - - + -
200B LEU* 4.1 31.6 - - + -
300B SER* 1.3 80.8 - - - +
302B SER* 1.3 63.7 + - - +
313B THR* 3.5 4.2 - - - -
314B ILE* 2.8 33.2 + - + +
315B CYS* 2.9 33.5 + - + -
390B VAL* 3.5 30.5 - - + -
391B ILE 3.4 4.5 - - - +
392B ILE* 4.2 8.3 - - + -
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Residues in contact with SER 302 (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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301B VAL* 1.3 77.6 - - - +
303B LEU* 1.3 61.6 + - - +
311B ALA* 3.9 22.0 - - - +
312B ALA 3.1 14.8 - - - -
313B THR* 4.4 6.5 - - - -
314B ILE* 4.8 0.9 - - - -
389B GLU 3.6 0.7 + - - +
390B VAL* 3.3 9.2 - - - +
391B ILE* 2.9 54.1 + - - +
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Residues in contact with LEU 303 (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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302B SER* 1.3 76.3 - - - +
304B LYS* 1.3 65.4 + - - +
305B GLY 3.8 14.6 - - - +
308B MET* 4.2 2.6 - - - +
311B ALA* 3.5 1.1 - - - -
312B ALA* 2.8 33.4 + - - +
314B ILE* 4.3 22.8 - - + +
362B MET* 3.7 32.8 - - + -
375B VAL* 4.1 20.6 - - + -
381B ARG* 4.0 16.4 - - + +
384B LEU* 3.9 16.8 - - + -
388B ASP* 4.0 17.7 - - + +
389B GLU 3.4 7.0 - - - +
390B VAL* 4.8 2.7 - - + -
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Residues in contact with LYS 304 (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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303B LEU* 1.3 79.5 - - - +
305B GLY* 1.3 71.4 + - - +
308B MET* 3.4 29.2 - - + +
309B SER* 3.8 21.3 + - - +
310B GLN 4.3 0.2 - - - +
311B ALA* 3.8 26.2 - - + +
387B GLY 3.9 1.2 - - - +
388B ASP* 3.5 0.3 - - - -
389B GLU* 2.9 54.6 + - + +
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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