Contacts of the strand formed by residues 431 - 437 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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365A TRP* 4.2 21.3 - - + -
413A LEU* 3.6 33.4 - - + +
414A MET 4.3 0.2 - - - -
415A GLN* 3.9 35.9 - - + +
429A GLU* 3.9 11.7 - - + +
430A THR* 1.3 78.1 - - - +
432A GLY* 1.3 63.5 - - - +
466A PHE* 3.4 6.4 - - - -
467A ILE 2.7 36.9 + - - +
469A LEU 4.5 4.9 - - - +
471A GLU* 4.3 7.9 - - - +
472A VAL* 3.8 13.5 - - + +
488A SER 3.5 13.5 - - - +
489A THR* 4.2 4.7 - - + -
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Residues in contact with GLY 432 (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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413A LEU* 3.5 4.6 - - - +
431A ILE* 1.3 84.0 - - - +
433A PHE* 1.3 69.0 + - - +
463A SER* 3.4 11.0 - - - -
466A PHE* 3.3 20.1 - - - -
472A VAL* 4.3 8.1 - - - -
488A SER 3.0 21.8 + - - +
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Residues in contact with PHE 433 (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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381A PHE* 6.5 0.2 - - - -
411A LEU* 3.4 47.8 - - + -
413A LEU* 4.0 9.6 - - + -
432A GLY* 1.3 78.0 - - - +
434A ALA* 1.3 73.9 - - - +
435A VAL* 5.4 2.0 - - + -
462A GLN* 3.7 6.7 - - - +
463A SER* 2.7 61.7 + - - -
466A PHE* 3.3 13.2 - - - -
472A VAL* 3.5 27.4 - - + -
474A ASN* 3.9 22.7 - - + -
476A ILE* 4.3 11.0 - - + -
485A VAL* 4.7 2.5 - - + -
486A VAL 3.7 12.8 - - - +
487A PRO* 3.9 11.4 - - + -
488A SER* 4.7 0.7 - - - +
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Residues in contact with ALA 434 (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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375A ARG* 6.1 2.7 - - + -
381A PHE* 4.9 8.5 - - + -
433A PHE* 1.3 86.4 - - - +
435A VAL* 1.3 61.3 + - - +
436A TYR* 3.9 17.6 - - + +
459A SER* 4.4 6.7 - - - +
461A ALA 4.2 4.5 - - - -
462A GLN* 4.3 8.7 - - + +
466A PHE* 5.8 1.3 - - + -
485A VAL* 4.8 0.4 - - - -
486A VAL* 2.8 33.5 + - - +
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Residues in contact with VAL 435 (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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389A ILE* 4.7 6.5 - - + -
409A PHE* 5.1 2.2 - - + -
411A LEU* 5.6 2.5 - - + -
433A PHE* 5.4 2.5 - - + -
434A ALA* 1.3 75.9 - - - +
436A TYR* 1.3 67.0 + - - +
459A SER* 3.9 0.9 + - - -
460A ARG* 2.3 41.9 + - - +
461A ALA* 2.7 45.8 + - + +
462A GLN* 4.6 0.9 - - - -
476A ILE* 4.7 7.2 - - + -
478A LEU* 4.3 12.1 - - + -
483A TYR* 4.1 16.2 - - + -
484A ILE 3.2 20.6 - - - +
485A VAL* 4.3 13.2 - - + +
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Residues in contact with TYR 436 (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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375A ARG* 4.2 12.8 - - - +
381A PHE* 3.6 28.5 - + - -
434A ALA* 3.9 22.4 - - + +
435A VAL* 1.3 75.6 - - - +
437A GLN* 1.3 61.1 - - - +
453A PHE* 4.1 20.9 - + + -
454A PHE* 3.9 28.3 + + - +
457A ASN* 4.3 10.8 - - + -
458A ALA* 3.7 23.3 - - - +
459A SER* 3.9 25.3 + - - -
460A ARG* 4.5 2.0 - - - +
483A TYR* 3.3 7.5 - - - +
484A ILE* 2.5 54.2 + - + +
486A VAL* 4.6 3.6 - - + -
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Residues in contact with GLN 437 (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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436A TYR* 1.3 61.2 - - - +
438A VAL* 1.4 76.8 + - - +
439A PRO* 3.5 1.4 - - - +
453A PHE* 3.8 15.6 - - - -
457A ASN* 4.4 7.9 + - - +
458A ALA 4.8 2.6 + - - -
460A ARG* 2.8 50.3 + - + +
481A GLY* 4.7 10.3 - - - -
482A GLU 4.0 6.9 + - - +
483A TYR* 3.5 31.3 + - + -
484A ILE* 4.8 1.1 - - - -
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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