Contacts of the strand formed by residues 389 - 397 (chain A) 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 GLU 389 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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302A SER* 3.6 1.0 + - - +
303A LEU* 3.3 4.9 - - - -
304A LYS* 2.9 61.6 + - + +
387A GLY 3.5 0.9 + - - +
388A ASP* 1.3 74.2 - - - +
390A VAL* 1.3 63.3 + - - +
391A ILE* 4.1 29.8 + - + +
409A ALA* 5.1 6.0 - - - +
410A GLY 3.4 16.3 - - - +
411A LYS* 4.1 23.0 - - + +
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Residues in contact with VAL 390 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A MET* 4.2 11.4 - - + -
232A ASN* 3.8 17.4 + - - +
234A TRP* 3.8 22.6 - - + -
301A VAL* 3.7 25.8 - - + -
302A SER 3.3 4.9 - - - +
303A LEU* 4.7 7.4 - - + -
314A ILE* 5.9 1.1 - - + -
362A MET* 5.6 0.2 - - - -
384A LEU* 3.6 31.9 - - + -
388A ASP 5.2 1.6 - - - +
389A GLU* 1.3 76.4 - - - +
391A ILE* 1.3 65.3 + - - +
392A ILE* 4.7 3.4 - - + -
408A CYS 3.8 1.6 - - - +
409A ALA* 3.4 2.6 - - - -
410A GLY 2.9 31.3 + - - -
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Residues in contact with ILE 391 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
300A SER 3.8 0.9 - - - +
301A VAL* 3.4 3.1 - - - -
302A SER* 2.9 50.5 + - - +
389A GLU* 4.1 26.5 - - + +
390A VAL* 1.3 78.3 - - - +
392A ILE* 1.3 67.6 + - - +
393A THR* 4.1 8.4 + - + -
407A GLN* 3.9 42.6 - - + +
408A CYS 3.7 2.5 - - - +
409A ALA* 3.9 14.6 - - + -
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Residues in contact with ILE 392 (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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198A MET* 5.5 1.3 - - - -
200A LEU* 3.5 36.6 - - + +
230A LEU* 3.7 21.7 - - + +
231A MET 3.4 27.4 - - - +
232A ASN* 3.7 24.7 - - + +
299A LEU* 5.0 0.2 - - + -
300A SER 3.4 6.5 - - - +
301A VAL* 4.2 18.2 - - + -
390A VAL* 4.7 4.5 - - + -
391A ILE* 1.3 75.5 - - - +
393A THR* 1.3 70.0 + - - +
407A GLN* 3.3 5.7 - - - +
408A CYS* 2.9 42.7 + - + +
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Residues in contact with THR 393 (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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230A LEU* 3.9 6.3 - - - -
299A LEU* 3.5 6.6 - - - +
300A SER* 2.9 44.3 + - - +
391A ILE* 4.1 10.1 + - + +
392A ILE* 1.3 80.1 - - - +
394A GLY* 1.3 59.3 + - - +
402A ARG* 6.2 2.5 - - - -
406A GLY 3.6 16.8 - - - +
407A GLN* 4.0 13.5 - - + +
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Residues in contact with GLY 394 (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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11A ASP* 4.6 2.8 - - - +
230A LEU* 3.9 11.5 - - - +
297A ILE* 4.8 0.2 - - - -
298A ASN 3.0 13.9 - - - -
299A LEU* 4.1 9.9 - - - -
393A THR* 1.3 77.8 - - - +
395A HIS* 1.3 67.3 + - - +
402A ARG* 4.7 2.3 + - - +
404A GLY* 3.6 0.5 - - - -
405A PHE* 3.0 30.8 + - - -
406A GLY 4.1 2.5 + - - -
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Residues in contact with HIS 395 (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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297A ILE* 4.1 3.6 - - - +
298A ASN* 2.9 65.4 + - + +
394A GLY* 1.3 78.6 - - - +
396A CYS* 1.3 78.4 + - - +
397A GLN* 3.5 22.9 + - - +
402A ARG* 3.5 45.2 + - + +
403A VAL 3.3 12.3 - - - +
404A GLY* 3.8 6.1 - - - -
405A PHE* 4.4 2.5 - - - -
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Residues in contact with CYS 396 (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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269A LEU* 3.7 30.5 - - - -
272A PHE* 3.5 37.9 - - + -
295A PHE* 5.9 0.2 - - - -
296A ASP 3.5 21.8 - - - +
297A ILE* 3.7 15.3 - - - -
298A ASN* 4.5 0.4 - - - +
395A HIS* 1.3 75.0 - - - +
397A GLN* 1.3 60.2 + - - +
398A GLY 3.8 0.6 + - - -
402A ARG* 3.2 8.0 - - - +
403A VAL* 2.8 36.7 + - + +
405A PHE* 4.8 0.2 - - - -
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Residues in contact with GLN 397 (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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8A GLU 5.9 0.2 + - - -
272A PHE* 3.5 13.6 - - - -
296A ASP 5.1 0.8 + - - -
298A ASN* 4.1 11.6 - - - +
395A HIS* 3.5 27.2 + - - +
396A CYS* 1.3 73.9 - - - +
398A GLY* 1.3 79.8 + - - +
400A GLY 4.7 1.6 - - - +
401A TYR 3.1 20.6 + - - +
402A ARG* 4.3 11.8 + - - +
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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