Contacts of the strand formed by residues 452 - 458 (chain B) in PDB entry 1JQO
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 LYS 452 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B ASP* 5.7 1.3 - - - +
284B ARG* 4.9 22.0 - - + +
285B PHE 3.5 7.0 + - - +
286B SER* 3.5 16.5 - - - +
287B SER* 2.8 27.5 + - - +
449B SER* 4.7 3.1 - - - +
451B VAL* 1.3 77.2 - - - +
453B LEU* 1.3 59.4 + - - +
526B PRO 4.7 0.8 + - - -
527B ASP* 3.2 32.0 + - - +
528B SER 4.2 4.7 - - - -
529B PHE 3.6 16.1 + - - +
530B GLY* 4.2 13.9 - - - +
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Residues in contact with LEU 453 (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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287B SER* 3.4 27.4 - - - +
288B TRP 3.9 4.0 - - - -
289B MET 4.1 7.6 - - - +
290B GLY 4.1 4.7 - - - -
291B GLY* 3.6 31.6 - - - +
304B THR* 4.2 20.9 - - + +
307B VAL* 4.5 13.7 - - + -
308B CYS* 4.9 7.0 - - + -
451B VAL* 5.2 1.8 - - + +
452B LYS* 1.3 74.8 - - - +
454B ASP* 1.3 70.1 + - - +
455B ILE* 4.1 3.2 + - + +
528B SER 3.4 17.7 + - - +
529B PHE* 3.3 17.4 - - + +
530B GLY* 2.3 30.4 + - - +
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Residues in contact with ASP 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B VAL* 4.8 0.2 - - - -
286B SER* 4.4 2.6 - - - -
287B SER 3.1 7.9 + - - +
288B TRP* 2.7 42.0 + - + +
291B GLY* 3.0 26.5 - - - -
292B ASP* 3.8 1.3 + - - -
452B LYS 4.6 0.3 - - - +
453B LEU* 1.3 77.6 - - - +
455B ILE* 1.3 62.2 + - - +
456B ARG* 6.2 0.2 - - + -
530B GLY* 3.6 2.9 - - - -
531B PRO* 3.0 30.4 - - + +
533B ILE* 3.7 6.5 - - + +
638B PHE* 3.2 12.1 - - - -
669B ARG* 3.1 27.3 + - - -
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Residues in contact with ILE 455 (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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291B GLY* 3.2 20.4 - - - +
293B ARG* 4.2 22.0 - - - +
304B THR* 4.4 8.5 - - + -
453B LEU* 4.4 4.9 - - + +
454B ASP* 1.3 83.4 - - - +
456B ARG* 1.3 59.2 + - - +
517B ALA* 5.9 2.0 - - + -
521B LEU* 3.9 24.2 - - + -
529B PHE* 4.4 7.4 - - + -
531B PRO 2.9 11.1 + - - +
532B TYR* 3.2 36.9 - - + +
533B ILE* 2.5 35.3 + - - +
559B LEU* 4.0 20.9 - - + -
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Residues in contact with ARG 456 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B HIS* 5.2 3.2 + - - -
288B TRP* 3.8 27.7 - - + -
291B GLY 3.0 8.5 + - - -
292B ASP* 2.8 50.0 + - + +
293B ARG* 2.9 32.8 + - - +
294B ASP* 3.2 21.2 + - - +
454B ASP 5.7 0.2 - - - -
455B ILE* 1.3 73.2 - - - +
457B GLN* 1.3 59.3 + - - +
533B ILE* 3.1 40.6 - - + +
535B SER* 3.1 35.6 + - - +
564B LEU* 4.1 12.3 - - - +
566B GLU* 4.7 4.2 + - - -
598B MET* 5.7 0.6 - - - +
759B ARG* 4.2 13.1 - - - +
773B ARG* 4.8 2.8 - - - +
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Residues in contact with GLN 457 (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 ARG* 3.1 36.6 + - + +
294B ASP* 4.1 9.6 - - - -
456B ARG* 1.3 74.4 - - - +
458B GLU* 1.3 95.6 + - - +
461B ARG* 3.6 32.6 + - + +
462B HIS* 3.3 21.2 + - + +
513B ASP* 5.3 2.8 + - - +
514B VAL* 5.0 12.4 - - + +
532B TYR* 3.1 24.6 + - + +
533B ILE 3.1 5.9 + - - -
534B ILE* 3.4 10.6 - - - +
535B SER* 3.1 19.1 + - - -
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Residues in contact with GLU 458 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B ASP* 3.8 19.6 - - - +
295B GLY* 4.1 14.1 + - - -
457B GLN* 1.3 89.6 + - - +
459B SER* 1.3 67.8 + - - +
460B GLU* 4.5 8.3 - - + +
461B ARG* 3.3 36.6 + - + +
462B HIS* 3.6 7.3 - - - -
535B SER* 3.8 15.5 - - - +
536B MET* 5.0 9.8 - - + +
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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