Contacts of the strand formed by residues 432 - 442 (chain A) in PDB entry 4LT6
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 TYR 432 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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379A SER* 3.2 7.2 + - - -
380A ALA 2.9 34.0 + - - +
381A SER 3.8 11.2 - - - -
382A THR* 3.2 26.0 - - - -
383A GLU* 3.1 46.9 + - + +
386A HIS* 3.6 25.5 + + + -
431A ASN* 1.3 94.4 + - - +
433A VAL* 1.3 60.3 + - - +
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Residues in contact with VAL 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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377A THR* 3.5 24.9 - - + -
378A ALA 3.2 18.8 - - - +
379A SER* 3.2 16.6 - - - +
386A HIS* 3.3 6.4 + - - -
421A PRO* 4.1 11.8 - - - +
422A GLY* 3.4 34.1 - - - +
431A ASN* 4.3 3.7 + - - +
432A TYR* 1.3 74.1 - - - +
434A SER* 1.3 73.5 + - - +
435A MET* 5.1 4.7 - - - -
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Residues in contact with SER 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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376A LEU 3.7 0.5 - - - +
377A THR* 3.5 1.9 - - - +
378A ALA* 2.8 31.9 + - - +
386A HIS* 2.8 17.3 + - - -
390A VAL* 3.5 21.2 - - - +
419A SER* 4.6 9.8 + - - -
420A PHE 3.2 11.7 + - - -
421A PRO* 5.4 0.2 - - - +
433A VAL* 1.3 83.3 + - - +
435A MET* 1.3 65.3 + - - +
436A TRP* 4.2 11.1 - - - -
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Residues in contact with MET 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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375A VAL* 3.8 22.4 - - + -
376A LEU 3.2 8.5 - - - +
377A THR* 4.3 15.5 - - - +
418A GLN 4.1 0.7 - - - +
419A SER* 3.2 7.3 - - - -
420A PHE* 2.9 40.4 + - + +
421A PRO 4.3 14.6 - - - +
422A GLY* 4.7 9.6 - - - -
433A VAL* 5.1 2.5 - - + -
434A SER* 1.3 79.2 - - - +
436A TRP* 1.3 65.9 + - - +
437A PHE* 3.4 24.9 - - + -
495A TYR* 3.2 35.2 - - + +
497A PRO* 4.9 2.7 - - + -
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Residues in contact with TRP 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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240A LEU* 4.9 5.8 - - + +
374A ILE 3.6 0.5 - - - +
375A VAL* 3.6 4.3 - - - +
376A LEU* 2.9 59.9 + - + -
378A ALA* 3.8 17.0 - - + -
390A VAL* 4.2 33.2 - - + -
393A VAL* 3.7 26.5 - - + -
394A GLU* 4.0 29.5 + - + +
397A ILE* 3.6 23.0 - - + +
415A VAL* 4.8 7.0 - - + -
416A ASN 4.1 15.0 - - - +
417A PRO 4.9 3.7 + - - -
418A GLN 4.3 3.3 - - - -
419A SER* 3.4 35.2 - - - +
434A SER* 4.2 7.9 - - - -
435A MET* 1.3 74.9 - - - +
437A PHE* 1.3 69.0 + - - +
438A LEU* 5.4 0.9 - - + -
482A ILE* 6.2 0.2 - - + -
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Residues in contact with PHE 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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366A PHE* 3.4 22.2 - - + -
367A PHE* 3.7 16.8 - + - -
373A TYR* 4.6 5.4 - + + -
374A ILE 3.2 5.4 - - - +
375A VAL* 4.1 20.4 - - + -
415A VAL* 3.7 2.8 - - - +
416A ASN* 3.0 30.3 + - + +
418A GLN 5.2 0.6 + - - -
420A PHE* 3.8 29.8 - + - -
435A MET* 3.4 38.1 - - + -
436A TRP* 1.3 83.0 - - - +
438A LEU* 1.3 63.6 + - - +
492A LEU* 4.2 22.7 - - + -
495A TYR* 4.1 10.8 - - + -
496A LEU* 4.3 6.5 - - + -
497A PRO* 4.3 11.2 - - + -
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Residues in contact with LEU 438 (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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366A PHE* 4.1 0.2 - - - -
373A TYR* 2.9 12.7 - - - +
374A ILE* 2.8 47.6 + - + +
376A LEU* 4.9 11.2 - - + -
397A ILE* 4.6 7.2 - - + -
400A LEU* 3.6 23.8 - - + -
401A VAL* 3.8 20.9 - - + -
404A LEU* 3.7 29.4 - - + -
413A ALA* 4.4 9.2 - - + -
414A HIS 3.2 2.9 - - - -
415A VAL* 3.7 30.1 - - + +
436A TRP* 5.4 0.4 - - + -
437A PHE* 1.3 74.6 - - - +
439A GLY* 1.3 61.8 + - - +
440A ILE* 4.6 1.8 - - + -
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Residues in contact with GLY 439 (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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366A PHE* 3.8 2.0 - - - -
370A TYR* 3.4 30.7 - - - -
372A HIS 3.5 5.8 - - - -
373A TYR* 3.8 4.9 - - - -
412A LEU* 3.6 2.3 - - - +
414A HIS* 2.9 35.6 + - - +
438A LEU* 1.3 72.7 - - - +
440A ILE* 1.3 67.2 + - - +
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Residues in contact with ILE 440 (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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370A TYR* 4.1 7.3 - - - +
371A ARG* 4.2 3.8 + - - +
372A HIS* 2.8 41.9 + - + +
373A TYR 4.8 2.0 - - - +
374A ILE* 3.5 39.7 - - + -
404A LEU* 4.3 11.7 - - + -
410A ILE* 3.6 27.4 - - + -
412A LEU 3.4 9.6 - - - +
413A ALA* 5.0 1.6 - - - -
438A LEU* 4.6 3.8 - - + +
439A GLY* 1.3 82.7 - - - +
441A ILE* 1.3 74.0 + - - +
442A PHE* 4.2 10.5 - - + -
455A LEU* 3.9 17.0 - - + -
486A HIS* 5.6 0.4 - - + -
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Residues in contact with ILE 441 (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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369A LYS 5.8 0.4 - - - +
370A TYR* 3.9 20.4 - - + -
372A HIS* 5.7 0.2 - - - -
410A ILE* 3.5 6.2 - - - +
411A THR* 2.8 51.8 + - + -
412A LEU* 3.1 37.9 + - + -
440A ILE* 1.3 81.8 - - - +
442A PHE* 1.3 70.2 + - - +
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Residues in contact with PHE 442 (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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372A HIS* 3.4 52.6 - + + -
407A ASN* 5.7 1.6 - - - -
409A PHE* 3.3 26.9 - - + -
410A ILE* 3.5 24.5 - - + -
411A THR* 4.5 3.1 + - - -
440A ILE* 4.3 6.3 - - + -
441A ILE* 1.3 88.7 - - - +
443A ARG* 1.3 66.9 + - - +
454A ASP 5.6 6.5 - - - -
455A LEU* 3.5 29.6 - - + -
486A HIS* 4.7 7.2 - + - -
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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
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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