Contacts of the strand formed by residues 444 - 454 (chain B) 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 LEU 444 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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100B ILE* 4.6 12.6 - - + -
104B ILE* 4.4 19.5 - - + -
129B GLU* 3.8 20.2 - - + +
132B VAL* 4.0 14.8 - - + -
133B ILE* 3.7 31.0 - - + -
136B ILE* 5.6 1.3 - - + -
322B ILE* 3.4 31.9 - - + +
325B PHE* 3.5 8.2 - - - +
429B ILE* 4.5 11.0 - - + -
430B GLY 3.9 1.3 - - - +
431B SER* 3.8 21.3 - - - +
433B LEU* 5.0 2.9 - - + -
442B CYS* 3.5 10.3 - - - -
443B ARG* 1.3 79.1 - - + +
445B ALA* 1.3 62.7 + - - +
446B PHE 3.7 1.1 - - - -
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Residues in contact with ALA 445 (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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321B LYS* 3.6 10.9 - - - +
322B ILE* 3.2 17.5 + - - +
325B PHE* 3.6 25.4 - - + +
329B LEU* 3.9 11.8 - - + +
335B PHE* 3.6 30.1 - - + -
430B GLY 2.8 18.4 + - - +
431B SER* 4.4 3.1 - - - -
443B ARG 3.7 1.4 + - - -
444B LEU* 1.3 73.5 - - - +
446B PHE* 1.3 64.4 + - + +
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Residues in contact with PHE 446 (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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317B ILE* 4.4 18.6 - - + -
319B VAL* 4.1 17.3 - - + -
320B GLU 3.2 17.7 - - - +
322B ILE* 3.7 10.5 - - - +
329B LEU* 3.9 20.6 - - + -
335B PHE* 3.4 32.8 - + + -
337B ILE* 4.9 4.9 - - + -
348B LEU* 3.3 34.1 - - + -
350B PHE* 5.1 0.9 - + - -
414B VAL* 5.8 0.4 - - + -
428B VAL* 5.0 2.9 - - + -
429B ILE* 3.6 10.3 - - - +
430B GLY* 3.2 41.7 + - - -
444B LEU 3.7 1.0 - - - -
445B ALA* 1.3 87.4 - - + +
447B HIS* 1.3 72.6 + - - +
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Residues in contact with HIS 447 (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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136B ILE* 3.2 55.4 - - + +
318B SER 4.3 0.9 - - - -
319B VAL* 3.7 0.7 - - - -
320B GLU* 2.9 71.1 + - + +
321B LYS 4.9 2.6 + - - -
322B ILE* 4.2 10.3 - - + -
427B LEU* 5.8 0.2 - - - +
428B VAL 3.3 13.2 - - - +
429B ILE* 4.1 3.8 - - + -
446B PHE* 1.3 83.9 - - - +
448B GLY* 1.3 64.5 + - - +
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Residues in contact with GLY 448 (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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317B ILE* 5.0 0.4 - - - -
318B SER* 3.1 21.3 - - - -
320B GLU* 5.5 2.0 - - - -
427B LEU* 3.7 8.3 - - - +
428B VAL* 2.9 34.9 + - - +
446B PHE* 5.1 0.6 - - - -
447B HIS* 1.3 83.5 + - - +
449B ILE* 1.3 66.3 + - - +
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Residues in contact with ILE 449 (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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317B ILE* 2.8 26.3 - - - +
318B SER* 2.9 20.3 + - - +
364B LEU* 4.1 37.9 - - + +
425B LEU* 3.7 20.4 - - + +
426B CYS 3.4 11.9 - - - +
427B LEU* 5.0 5.4 - - + -
428B VAL* 4.4 0.4 - - - -
448B GLY* 1.3 78.5 - - - +
450B LEU* 1.3 72.9 + - - +
451B LEU* 3.2 7.2 + - + +
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Residues in contact with LEU 450 (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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310B HIS* 4.0 24.0 - - + +
312B VAL* 4.8 4.9 - - + -
315B ALA* 3.7 21.8 - - + -
317B ILE* 2.8 18.3 - - + +
339B VAL* 4.4 8.1 - - + -
416B PHE* 5.3 5.2 - - + -
420B VAL* 6.0 0.2 - - + -
422B CYS* 4.0 22.0 - - - -
423B PRO 4.3 9.9 - - - +
424B ARG* 4.9 0.2 - - - -
425B LEU* 3.1 30.2 + - - +
426B CYS* 2.8 30.0 + - - +
428B VAL* 3.9 6.8 - - + +
449B ILE* 1.3 69.5 - - - +
451B LEU* 1.3 58.3 + - - +
452B HIS* 4.2 0.7 - - - +
453B GLY* 4.0 17.5 - - - +
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Residues in contact with LEU 451 (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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316B LEU* 2.7 17.2 + - + +
317B ILE 4.3 0.9 - - - -
318B SER* 3.5 28.0 - - - +
363B ILE 4.6 3.4 - - - +
364B LEU* 3.4 35.7 - - - +
365B ASP 4.0 9.3 - - - +
366B SER* 3.7 15.0 - - - +
367B PHE* 4.3 23.8 + - + +
411B TRP* 3.7 25.4 - - + +
425B LEU* 4.2 9.8 - - + +
449B ILE* 3.7 15.9 - - + +
450B LEU* 1.3 74.3 - - - +
452B HIS* 1.3 64.9 + - - +
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Residues in contact with HIS 452 (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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315B ALA* 3.1 5.9 - - - -
316B LEU* 2.9 47.1 + - + +
367B PHE* 5.1 8.5 - - + -
369B PHE* 4.3 19.0 - + + -
450B LEU* 3.7 3.8 - - - -
451B LEU* 1.3 81.9 - - + +
453B GLY* 1.3 74.0 + - - +
454B LEU* 4.6 4.3 - - + +
463B PHE* 3.4 39.2 - + + -
466B ARG* 5.1 2.2 + - - -
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Residues in contact with GLY 453 (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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310B HIS* 3.8 13.0 + - - -
312B VAL* 3.6 19.5 - - - -
314B ALA 3.9 2.5 - - - -
315B ALA* 4.4 0.7 - - - -
450B LEU* 4.0 10.2 - - - +
452B HIS* 1.3 86.8 + - - +
454B LEU* 1.3 61.6 + - - +
455B GLU* 3.5 11.4 + - - +
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Residues in contact with LEU 454 (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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312B VAL* 3.7 3.9 - - - +
313B HIS* 3.0 23.6 + - - -
314B ALA* 2.8 44.7 + - + +
315B ALA* 3.8 9.6 - - - +
316B LEU* 4.9 5.2 - - + +
413B LEU* 4.6 13.0 - - + -
452B HIS* 4.6 4.5 - - - +
453B GLY* 1.3 73.3 - - - +
455B GLU* 1.3 63.5 + - - +
456B ASP* 3.2 6.3 + - + +
459B TYR* 3.8 26.2 - - + -
463B PHE* 3.4 50.0 - - + -
464B LEU* 4.6 4.3 - - + -
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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