Contacts of the strand formed by residues 357 - 364 (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 ASN 357 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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344B THR* 5.0 0.7 - - - -
355B ASN* 5.0 2.8 + - - +
356B TRP* 1.3 74.8 + - - +
358B THR* 1.3 61.4 + - - +
502B PHE 3.6 3.6 - - - +
503B PHE* 3.6 0.5 - - - -
504B SER* 2.8 46.9 + - - +
505B GLU 3.4 2.4 - - - +
506B LYS* 2.8 30.1 - - - -
507B LYS* 3.0 32.8 + - - +
508B ALA 5.1 1.6 - - - +
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Residues in contact with THR 358 (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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343B LEU* 4.2 14.3 - - + +
344B THR* 4.2 25.0 + - + +
345B PRO* 5.7 0.7 - - - +
356B TRP* 3.8 3.9 + - + +
357B ASN* 1.3 77.4 - - - +
359B THR* 1.3 79.1 + - - +
360B PHE* 5.7 3.1 - - - -
502B PHE 3.4 5.8 - - - -
503B PHE* 3.8 35.4 - - + -
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Residues in contact with THR 359 (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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358B THR* 1.3 86.9 - - - +
360B PHE* 1.3 70.7 - - - +
361B TYR* 4.3 11.4 - - - +
501B ARG* 3.4 2.1 - - - +
502B PHE* 2.9 44.9 + - - +
503B PHE* 5.1 0.9 - - - -
510B THR* 2.7 34.7 + - + +
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Residues in contact with PHE 360 (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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147B GLY* 4.6 13.2 - - - -
358B THR* 5.7 2.9 - - - -
359B THR* 1.3 83.9 - - - +
361B TYR* 1.4 79.9 + - - +
362B GLU* 4.8 11.4 - - + -
499B LEU* 3.9 24.2 - - + -
500B LEU 3.3 9.9 - - - +
501B ARG* 4.1 14.8 - - + -
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Residues in contact with TYR 361 (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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359B THR* 4.3 7.8 - - - +
360B PHE* 1.4 83.1 - - - +
362B GLU* 1.4 58.4 + - - +
363B GLY 3.9 0.9 + - - -
387B PHE* 3.1 49.1 - + + -
498B PHE* 3.7 1.0 - - - +
499B LEU* 2.7 15.3 - - - +
500B LEU* 2.4 53.9 + - + +
502B PHE* 4.2 15.3 - + - -
510B THR* 2.9 45.7 + - - -
511B GLN* 3.4 14.7 - - - -
512B GLU* 3.7 20.0 + - + -
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Residues in contact with GLU 362 (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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146B PHE 3.9 5.6 - - - +
147B GLY 5.2 3.1 - - - +
148B GLU* 5.1 6.2 - - - +
360B PHE* 4.8 12.2 - - + -
361B TYR* 1.4 74.4 - - - +
363B GLY* 1.4 60.9 + - - +
387B PHE* 5.2 3.0 - - - -
416B LYS* 3.0 44.6 + - - +
498B PHE* 3.1 7.0 - - - +
499B LEU* 3.9 20.9 - - + +
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Residues in contact with GLY 363 (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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362B GLU* 1.4 77.3 - - - +
364B THR* 1.3 65.6 + - - +
385B PRO* 5.6 2.5 - - - -
387B PHE* 5.5 2.2 - - - -
497B ASP* 3.4 4.0 - - - +
498B PHE* 2.7 68.2 + - - +
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Residues in contact with THR 364 (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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363B GLY* 1.3 81.3 - - - +
365B TRP* 1.4 65.6 + - - +
366B ARG* 3.4 17.1 + - - +
370B THR* 3.1 13.9 + - - +
385B PRO* 3.9 12.1 - - - +
496B GLY 3.2 10.5 - - - -
497B ASP* 3.9 12.3 - - - +
498B PHE* 3.9 1.9 - - - -
646B GLN* 1.9 49.5 + - - +
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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