Contacts of the strand formed by residues 411 - 422 (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 TRP 411 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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316B LEU* 5.8 1.3 - - + -
317B ILE 3.7 9.9 - - - +
318B SER* 4.1 5.2 - - - -
319B VAL* 3.8 7.8 - - - +
350B PHE* 3.8 6.9 - - - +
351B PHE* 3.4 57.3 + + + +
353B PRO* 3.5 30.7 - - + -
363B ILE 4.7 0.6 + - - -
367B PHE* 3.8 21.6 - + + -
371B GLN* 6.0 0.4 - - - -
373B TYR* 3.8 22.2 - + - -
409B GLN* 3.2 60.8 - - + +
410B GLN* 1.3 80.5 - - - +
412B ALA* 1.3 68.6 + - - +
451B LEU* 3.7 25.7 - - + +
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Residues in contact with ALA 412 (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 3.8 0.4 - - - +
316B LEU* 3.6 8.8 - - - +
317B ILE* 3.3 28.9 + - + +
319B VAL* 3.6 18.4 - - + -
348B LEU* 4.5 11.2 - - + -
349B MET 3.4 16.4 - - - +
350B PHE* 3.8 17.3 - - + -
351B PHE* 4.0 7.4 - - - -
411B TRP* 1.3 79.6 - - - +
413B LEU* 1.3 61.8 + - - +
414B VAL* 5.3 0.4 - - + -
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Residues in contact with LEU 413 (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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314B ALA* 4.3 4.9 - - + -
315B ALA 3.5 9.9 - - - +
316B LEU* 3.8 20.2 - - + -
347B ARG 3.5 1.7 - - - +
348B LEU* 3.2 7.1 - - - -
349B MET* 3.1 43.2 + - + +
351B PHE* 5.1 2.2 - - + -
412B ALA* 1.3 76.3 - - - +
414B VAL* 1.3 68.5 + - - +
415B GLU* 3.4 38.2 - - + +
454B LEU* 4.6 6.5 - - + -
459B TYR* 5.0 1.8 - - + -
464B LEU* 3.7 31.2 - - + -
584B TYR* 4.1 13.7 - - + +
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Residues in contact with VAL 414 (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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314B ALA* 3.0 30.8 - - - +
315B ALA* 3.3 9.0 + - + +
317B ILE* 4.2 30.1 - - + -
337B ILE* 4.3 22.0 - - + -
346B GLY* 4.4 4.9 - - - -
347B ARG 3.5 2.9 - - - -
348B LEU* 3.9 21.1 - - + -
412B ALA 5.2 0.4 - - - -
413B LEU* 1.3 77.6 - - - +
415B GLU* 1.3 63.0 + - - +
416B PHE* 2.8 45.8 - - + -
428B VAL* 5.8 0.7 - - + -
446B PHE* 5.8 0.4 - - + -
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Residues in contact with GLU 415 (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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313B HIS 3.9 3.4 - - - -
346B GLY* 3.3 3.9 - - - -
347B ARG* 3.0 43.9 + - + +
348B LEU 5.7 0.9 - - - -
349B MET* 5.3 6.2 - - - +
413B LEU* 3.4 27.8 - - + +
414B VAL* 1.3 72.5 - - - +
416B PHE* 1.3 63.1 + - - +
417B GLU* 3.6 1.9 + - - +
459B TYR* 3.3 29.1 + - + +
464B LEU* 5.8 3.5 - - - +
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Residues in contact with PHE 416 (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* 3.8 26.5 - - + -
313B HIS* 3.1 36.5 + - - +
314B ALA* 3.8 17.5 - - - -
315B ALA* 4.6 9.4 - - + -
337B ILE* 4.2 17.7 - - + -
339B VAL* 4.9 11.0 - - + -
344B VAL* 3.7 18.6 - - + -
345B MET 3.3 8.5 - - - +
346B GLY* 4.8 0.4 - - - -
414B VAL* 2.8 37.0 - - + -
415B GLU* 1.3 70.9 - - - +
417B GLU* 1.3 63.7 + - - +
418B LYS 2.9 23.5 + - - +
420B VAL* 4.7 7.4 - - + -
450B LEU* 5.3 3.8 - - + -
459B TYR* 5.3 0.2 + - - -
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Residues in contact with GLU 417 (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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334B LYS* 5.6 3.7 - - - +
344B VAL* 5.0 1.6 - - + -
345B MET* 3.1 39.7 + - + +
346B GLY* 4.7 2.5 - - - +
347B ARG* 4.6 22.3 + - + +
415B GLU 3.6 3.1 + - - +
416B PHE* 1.3 72.8 - - - +
418B LYS* 1.3 58.2 + - - +
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Residues in contact with LYS 418 (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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313B HIS* 5.3 0.7 - - - -
344B VAL* 3.4 23.4 - - + +
416B PHE* 2.9 23.6 - - - +
417B GLU* 1.3 77.1 - - + +
419B PRO* 1.3 78.1 - - + +
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Residues in contact with PRO 419 (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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311B THR* 5.4 5.4 - - - -
312B VAL 3.5 12.8 - - - +
313B HIS* 3.5 38.8 - - + +
342B GLU* 4.7 0.7 - - - +
344B VAL* 5.2 0.2 - - - +
418B LYS* 1.3 95.7 - - + +
420B VAL* 1.3 64.8 + - - +
421B THR* 5.6 0.2 - - - -
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Residues in contact with VAL 420 (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 3.9 0.5 - - - +
311B THR* 3.2 2.2 - - - -
312B VAL* 2.8 41.3 + - + +
339B VAL* 4.1 22.9 - - + -
342B GLU* 3.4 27.6 - - + +
344B VAL* 3.7 30.7 - - + -
416B PHE* 4.7 7.2 - - + -
419B PRO* 1.3 79.4 - - + +
421B THR* 1.3 65.4 + - - +
422B CYS* 3.9 20.0 - - - -
450B LEU* 6.0 0.2 - - + -
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Residues in contact with THR 421 (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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259B PRO* 4.3 21.0 - - + +
302B LEU* 4.6 9.7 - - - +
309B LEU* 4.0 24.2 - - + +
310B HIS 3.7 7.9 - - - +
311B THR* 3.3 29.7 - - + +
339B VAL 4.8 4.0 - - - +
342B GLU* 3.2 28.4 + - - +
419B PRO 5.6 0.5 - - - -
420B VAL* 1.3 73.3 - - - +
422B CYS* 1.3 67.7 + - - +
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Residues in contact with CYS 422 (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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302B LEU* 5.1 1.3 - - - -
309B LEU* 3.4 10.4 - - - +
310B HIS* 3.1 42.4 + - - +
312B VAL* 4.2 9.4 - - - -
339B VAL* 3.8 22.2 - - + +
420B VAL* 3.9 16.4 - - + -
421B THR* 1.3 81.7 - - - +
423B PRO* 1.3 83.5 - - + +
426B CYS* 4.0 1.3 - - - -
450B LEU* 4.0 23.1 - - - -
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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