Contacts of the helix formed by residues 380 - 384 (chain B) in PDB entry 1QXP
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 380 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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372B GLY* 2.6 36.4 + - - +
377B TYR* 2.6 8.8 + - - +
379B ALA* 1.3 93.4 - - + +
381B PHE* 1.4 66.3 + - - +
382B TRP* 3.0 6.7 - - - +
383B VAL* 2.6 25.5 + - + +
492B PRO* 3.9 11.9 - - - +
493B ASN* 5.1 1.8 - - - +
627B TYR* 4.2 37.2 - - + -
628B GLU* 6.1 0.4 - - - +
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Residues in contact with PHE 381 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372B GLY 3.4 6.5 + - - -
373B GLY 3.8 4.3 - - - -
374B CYS* 3.0 34.5 - - + +
375B ARG* 3.1 28.7 - - + +
377B TYR 2.8 14.9 + - - +
378B PRO* 4.2 6.3 - - + -
379B ALA 4.0 1.0 - - - +
380B THR* 1.4 71.9 - - - +
382B TRP* 1.3 66.4 + - - +
383B VAL 2.6 2.1 + - - -
384B ASN* 3.2 19.2 + - - +
386B GLN* 4.7 0.3 + - - -
434B ALA* 4.2 12.1 - - + -
436B TYR* 3.3 41.5 - + - -
454B PHE* 3.6 32.5 - + + -
486B VAL* 3.8 27.7 - - + +
488B SER* 4.5 2.7 - - - -
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Residues in contact with TRP 382 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B PRO 4.7 1.1 + - - -
379B ALA 3.1 27.4 + - - -
380B THR* 3.0 4.8 - - - +
381B PHE* 1.3 82.7 - - - +
383B VAL* 1.3 65.6 + - + +
384B ASN 3.3 0.2 - - - +
386B GLN* 2.8 12.1 + - - -
448B HIS* 2.8 35.1 - - - -
449B LEU 4.4 3.6 - - - -
450B LYS* 3.5 55.0 - - + -
451B ARG* 3.5 25.4 - - + +
454B PHE* 3.9 13.2 - - + +
627B TYR 3.6 17.7 - - - -
628B GLU* 4.3 0.9 + - - -
630B ARG* 3.4 33.0 - - + -
631B MET* 3.1 52.4 - - + +
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Residues in contact with VAL 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
369B SER 2.4 32.7 - - - +
370B THR* 3.1 23.8 - - - +
371B ALA 4.0 0.7 - - - +
372B GLY* 4.5 1.6 - - - +
380B THR* 2.6 20.0 + - - +
381B PHE 2.6 6.5 + - - -
382B TRP* 1.3 99.6 - - + +
384B ASN* 1.4 65.8 - - - +
448B HIS* 3.9 8.7 + - - -
627B TYR* 4.2 27.1 - - + +
630B ARG* 5.4 6.2 + - + +
642B CYS* 5.0 1.9 - - - -
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Residues in contact with ASN 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
365B TRP* 2.9 30.5 + - - -
370B THR 3.3 8.8 - - - +
372B GLY 3.8 6.2 + - - -
373B GLY 3.3 27.9 + - - +
380B THR 3.9 0.2 + - - -
381B PHE* 3.2 22.0 + - - +
382B TRP 3.3 1.7 - - - +
383B VAL* 1.4 76.1 - - - +
385B PRO* 1.3 71.2 - - + +
386B GLN* 3.4 3.6 - - - +
448B HIS* 2.6 33.8 + - - -
486B VAL* 4.1 12.5 - - + +
487B PRO 3.8 5.6 - - - +
488B SER* 3.1 15.9 - - - -
489B THR* 5.7 0.2 + - - -
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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
------------------------------------------------------------
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