Contacts of the strand formed by residues 411 - 422 (chain A) in PDB entry 5IZL
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 TRP 411 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316A LEU* 6.0 0.7 - - + -
317A ILE 3.7 7.2 - - - +
318A SER* 4.0 6.1 - - - -
319A VAL* 3.6 10.0 - - - +
350A PHE* 3.6 7.3 - - - +
351A PHE* 3.1 53.8 + + + +
352A SER 4.2 0.2 - - - -
353A PRO* 3.6 28.0 - - + -
360A GLN* 3.6 23.3 - - - -
363A ILE* 4.9 2.4 + - + -
366A SER 5.6 0.4 + - - -
367A PHE* 3.7 22.7 - + - -
373A TYR* 3.5 37.2 - + - -
409A GLN* 3.3 38.7 - - - +
410A GLN* 1.3 82.7 - - - +
412A ALA* 1.3 67.3 + - - +
451A LEU* 3.8 27.3 - - + +
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Residues in contact with ALA 412 (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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316A LEU* 3.6 6.1 - - - +
317A ILE* 3.1 33.1 + - + +
319A VAL* 3.5 16.6 - - + -
348A LEU* 4.1 18.6 - - + -
349A MET 3.3 13.9 - - - +
350A PHE* 4.0 12.8 - - + -
351A PHE* 3.8 9.8 - - - -
411A TRP* 1.3 79.0 - - - +
413A LEU* 1.3 61.5 + - - +
414A VAL 4.0 0.7 - - - -
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Residues in contact with LEU 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ALA* 4.6 2.9 - - + -
315A ALA 3.6 12.8 - - - +
316A LEU* 3.5 27.1 - - + -
347A ARG 3.2 13.5 - - - +
348A LEU* 3.6 1.4 - - - -
349A MET* 3.1 35.7 + - + +
351A PHE* 4.8 1.6 - - + -
412A ALA* 1.3 74.2 - - - +
414A VAL* 1.3 62.9 + - - +
415A GLU* 3.7 29.3 + - + +
454A LEU* 4.3 16.8 - - + -
459A TYR* 5.2 0.4 - - + -
464A LEU* 4.5 15.5 - - + -
467A LEU* 5.3 1.6 - - + -
584A TYR* 3.8 26.9 - - + +
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Residues in contact with VAL 414 (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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314A ALA* 3.1 8.7 - - - +
315A ALA* 3.0 31.5 + - + +
317A ILE* 3.8 31.9 - - + -
337A ILE* 4.2 24.2 - - + -
346A GLY* 4.4 2.9 - - - -
347A ARG 3.6 3.1 - - - -
348A LEU* 3.6 21.3 - - + -
412A ALA* 4.0 0.4 - - + -
413A LEU* 1.3 72.4 - - - +
415A GLU* 1.3 65.2 + - - +
416A PHE* 3.3 40.6 - - + -
428A VAL* 5.4 0.4 - - + -
446A PHE* 5.5 0.2 - - + -
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Residues in contact with GLU 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A HIS 4.1 4.3 - - - -
314A ALA* 4.1 0.2 - - - -
346A GLY* 3.2 18.1 - - - -
347A ARG* 3.1 24.5 + - + +
413A LEU* 3.7 29.4 - - + +
414A VAL* 1.3 75.6 - - - +
416A PHE* 1.3 66.1 + - - +
417A GLU* 3.8 1.4 + - - +
459A TYR* 3.3 32.8 + - + +
460A ALA* 5.9 0.7 - - - +
464A LEU* 4.8 4.3 - - - +
584A TYR* 5.5 1.7 + - - -
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Residues in contact with PHE 416 (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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312A VAL* 3.8 24.5 - - + -
313A HIS* 3.0 37.8 + - - +
314A ALA* 3.7 18.6 - - - -
315A ALA* 4.2 8.7 - - + -
317A ILE* 6.3 0.4 - - + -
337A ILE* 3.9 20.0 - - + -
339A VAL* 5.0 11.7 - - + -
344A VAL* 3.4 22.9 - - + -
345A MET 3.5 5.6 - - - +
346A GLY* 4.3 0.2 - - - -
414A VAL* 3.3 29.4 - - + -
415A GLU* 1.3 74.7 - - - +
417A GLU* 1.3 61.1 + - - +
418A LYS 3.1 24.0 + - - +
420A VAL* 4.6 6.1 - - + -
428A VAL* 6.4 0.7 - - + -
450A LEU* 5.1 4.9 - - + -
459A TYR* 5.7 0.2 + - - -
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Residues in contact with GLU 417 (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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334A LYS* 5.5 2.1 - - - +
344A VAL* 4.9 3.4 - - + -
345A MET* 2.9 51.0 + - + +
346A GLY* 4.7 3.6 + - - +
347A ARG* 4.7 16.9 + - + +
415A GLU 5.1 1.1 - - - +
416A PHE* 1.3 72.6 - - - +
418A LYS* 1.3 60.1 + - + +
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Residues in contact with LYS 418 (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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313A HIS* 5.5 1.3 - - - -
344A VAL* 3.9 16.2 - - + +
416A PHE* 3.1 21.8 + - - +
417A GLU* 1.3 79.5 - - + +
419A PRO* 1.3 80.7 - - + +
420A VAL* 3.8 4.7 - - - +
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Residues in contact with PRO 419 (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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311A THR* 5.0 8.5 - - - +
312A VAL 3.2 16.8 - - - +
313A HIS* 3.7 29.6 - - + +
342A GLU* 4.5 7.8 - - - +
344A VAL* 5.3 0.3 - - - +
418A LYS* 1.3 95.5 - - + +
420A VAL* 1.3 63.0 + - - +
421A THR* 4.3 0.4 - - - -
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Residues in contact with VAL 420 (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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310A HIS 3.6 1.2 - - - +
311A THR* 3.3 2.2 - - - -
312A VAL* 3.0 43.4 + - + +
339A VAL* 3.9 29.8 - - + +
342A GLU* 4.5 20.0 - - + +
344A VAL* 3.5 34.1 - - + -
416A PHE* 4.5 8.3 - - + -
418A LYS 3.8 4.3 - - - +
419A PRO* 1.3 80.9 - - - +
421A THR* 1.3 72.7 + - - +
422A CYS* 3.7 8.6 + - + -
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Residues in contact with THR 421 (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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259A PRO* 4.0 25.0 - - + +
262A LYS* 4.1 8.1 + - - +
302A LEU* 5.4 6.9 - - - +
309A LEU* 3.8 29.8 - - + +
310A HIS 3.5 6.1 - - - +
311A THR* 3.1 29.4 - - + +
339A VAL 5.1 1.2 - - - +
342A GLU* 4.0 15.2 + - - +
420A VAL* 1.3 74.0 - - - +
422A CYS* 1.3 67.2 + - - +
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Residues in contact with CYS 422 (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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302A LEU* 6.2 0.9 - - - -
309A LEU* 4.2 7.2 - - - -
310A HIS* 3.0 41.6 + - - +
312A VAL* 4.3 8.5 - - - -
339A VAL* 4.2 11.7 - - + +
420A VAL* 4.0 21.3 - - + -
421A THR* 1.3 80.4 - - - +
423A PRO* 1.3 71.5 - - + +
426A CYS* 4.2 9.6 - - - -
450A LEU* 3.4 32.8 - - - -
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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