Contacts of the strand formed by residues 431 - 437 (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 ILE 431 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B TRP* 4.3 24.7 - - + -
413B LEU* 4.1 21.5 - - + +
414B MET 4.7 1.3 - - - -
415B GLN* 3.6 31.2 - - + +
429B GLU* 3.7 16.2 - - + +
430B THR* 1.4 83.0 - - - +
432B GLY* 1.4 59.2 + - - +
466B PHE* 3.4 22.8 + - - +
467B ILE 4.1 0.3 - - - +
468B ASN* 4.0 5.6 - - - +
469B LEU 3.7 10.8 - - - +
470B ARG 4.1 5.4 - - - +
472B VAL* 3.2 31.2 - - + +
488B SER 3.3 5.8 - - - +
489B THR* 4.5 3.8 - - + -
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Residues in contact with GLY 432 (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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413B LEU* 3.7 6.3 - - - +
431B ILE* 1.4 76.9 - - - +
433B PHE* 1.3 63.4 - - - +
463B SER* 3.0 17.7 - - - -
466B PHE* 3.9 12.2 - - - -
472B VAL* 4.2 5.3 - - - +
487B PRO* 3.6 0.7 - - - +
488B SER* 2.6 38.2 + - - +
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Residues in contact with PHE 433 (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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411B LEU* 3.8 49.8 - - + -
412B ALA 4.6 0.4 - - - -
413B LEU* 4.6 14.4 - - + -
432B GLY* 1.3 80.8 - - - +
434B ALA* 1.4 60.8 + - - +
435B VAL* 4.3 3.4 - - + -
462B GLN* 3.0 17.4 - - - +
463B SER* 2.7 64.2 + - - +
466B PHE* 4.5 10.7 - - - -
472B VAL* 4.1 13.7 - - + -
473B SER* 4.4 0.7 - - - -
474B ASN* 3.8 24.0 - - + -
476B ILE* 4.6 5.6 - - + -
485B VAL* 4.5 6.1 - - + -
486B VAL 3.4 14.8 - - - +
487B PRO* 3.9 8.3 - - + -
488B SER* 5.5 0.7 - - - -
500B LEU* 5.0 1.8 - - + -
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Residues in contact with ALA 434 (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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375B ARG* 4.7 12.3 - - + -
381B PHE* 4.2 13.7 - - + -
433B PHE* 1.4 75.9 - - - +
435B VAL* 1.3 64.7 + - - +
436B TYR* 3.8 29.4 + - + -
459B SER* 4.7 3.8 - - - -
462B GLN* 3.7 9.4 - - + -
484B ILE 3.4 1.7 - - - +
485B VAL* 3.5 0.7 - - - -
486B VAL* 3.1 30.2 + - - +
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Residues in contact with VAL 435 (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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389B ILE* 4.8 4.7 - - + -
409B PHE* 5.0 2.5 - - + -
411B LEU* 3.6 30.7 - - + -
433B PHE* 4.3 7.0 - - + -
434B ALA* 1.3 78.4 - - - +
436B TYR* 1.4 57.5 + - - +
459B SER* 4.0 1.4 - - - -
460B ARG* 2.8 25.0 + - - +
461B ALA* 2.6 31.6 + - + +
462B GLN* 4.6 0.7 - - - +
476B ILE* 4.9 5.2 - - + -
478B LEU* 4.1 15.0 - - + -
483B TYR* 3.8 24.9 - - + -
484B ILE 2.9 14.1 - - - +
485B VAL* 4.2 7.9 - - + +
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Residues in contact with TYR 436 (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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375B ARG* 3.6 23.4 - - - +
381B PHE* 3.3 38.6 - + - -
434B ALA* 3.8 22.9 - - + -
435B VAL* 1.4 74.5 - - - +
437B GLN* 1.3 62.6 + - - +
453B PHE* 4.1 17.0 - + + -
454B PHE* 3.6 27.5 + + - -
457B ASN* 3.5 30.8 + - + -
458B ALA* 3.6 5.1 - - - -
459B SER* 3.1 31.7 + - - +
460B ARG* 4.2 4.0 - - - +
483B TYR* 3.5 8.8 - - - +
484B ILE* 2.8 31.9 + - + +
486B VAL* 5.0 2.7 - - + -
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Residues in contact with GLN 437 (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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436B TYR* 1.3 76.5 - - - +
438B VAL* 1.3 72.7 + - - +
439B PRO* 3.8 0.7 - - - +
453B PHE* 3.0 24.1 - - - -
457B ASN* 4.3 3.4 + - - +
460B ARG* 3.1 51.9 + - + +
480B PRO 5.0 1.4 - - - +
481B GLY* 4.8 7.8 - - - -
482B GLU 3.6 14.3 + - - +
483B TYR* 4.3 9.8 + - + -
484B ILE* 4.6 0.9 - - - -
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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