Contacts of the strand formed by residues 388 - 395 (chain B) in PDB entry 4Z8M
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 LYS 388 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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379B GLY* 4.2 13.8 - - - -
380B PHE 3.3 14.1 - - - +
381B TYR* 3.8 38.7 + - + +
386B GLY 3.9 0.8 + - - -
387B TYR* 1.3 75.1 - - - +
389B LEU* 1.3 57.4 + - - +
413B THR* 3.5 6.5 - - - +
414B MET* 2.6 76.6 + - + +
415B GLN 3.4 21.4 + - - +
416B GLY* 4.1 4.5 - - - -
419B ASP* 5.1 3.0 + - - -
424B TRP* 6.0 0.4 - - - -
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Residues in contact with LEU 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
379B GLY* 3.5 1.7 - - - -
380B PHE* 2.8 52.1 + - + +
382B THR* 3.5 29.6 - - + -
387B TYR* 4.7 6.1 - - + -
388B LYS* 1.3 81.9 - - - +
390B CYS* 1.3 63.2 + - - +
411B VAL* 4.2 17.7 - - + -
412B HIS 3.1 16.6 - - - +
413B THR* 3.8 18.4 - - + +
414B MET* 4.1 3.5 - - - +
426B PHE* 5.5 8.3 - - + -
430B ILE* 4.8 5.4 - - + -
459B PHE* 6.0 3.6 - - + -
499B VAL* 3.6 25.8 - - + -
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Residues in contact with CYS 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
376B HIS* 6.2 2.5 - - - -
377B SER* 3.6 11.2 - - - +
378B PRO 3.8 13.9 - - - +
379B GLY* 4.1 0.2 - - - -
380B PHE* 3.7 5.8 - - - -
389B LEU* 1.3 77.3 - - - +
391B MET* 1.3 67.8 + - - +
411B VAL* 3.5 5.4 - - - +
412B HIS* 2.8 54.2 + - - -
414B MET* 3.8 28.0 - - - -
466B ARG* 5.0 7.0 - - - -
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Residues in contact with MET 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
353B TYR* 4.1 5.4 - - + -
355B TRP* 3.7 41.9 - - + -
376B HIS* 3.5 4.7 - - - +
377B SER* 2.7 42.7 + - - +
380B PHE* 4.0 18.4 - - + -
390B CYS* 1.3 82.2 - - - +
392B ARG* 1.3 59.7 + - - +
409B LEU* 4.7 4.9 - - + -
410B PHE 3.2 9.6 - - - +
411B VAL* 4.3 10.3 - - + -
412B HIS* 5.0 0.4 - - - -
432B LEU* 3.8 17.0 - - + -
495B VAL* 3.9 21.3 - - - +
497B CYS* 3.5 31.4 - - + -
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Residues in contact with ARG 392 (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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374B VAL* 4.6 2.0 - - + -
375B ILE 3.6 4.0 - - - +
376B HIS* 3.8 24.0 - - + +
391B MET* 1.3 72.3 - - - +
393B LEU* 1.3 62.1 + - - +
394B HIS* 3.1 26.6 + - - +
409B LEU* 3.4 6.1 - - - +
410B PHE* 2.8 70.4 + - + +
412B HIS* 2.7 54.4 + - + +
606D ASN* 2.8 36.4 + - - -
608D TYR* 3.7 35.5 - - - +
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Residues in contact with LEU 393 (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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355B TRP* 3.8 17.4 - - + -
357B ILE* 3.9 20.6 - - + -
360B PHE* 4.9 4.5 - - + -
374B VAL* 3.5 3.3 - - - +
375B ILE* 2.9 56.7 + - + +
392B ARG* 1.3 75.0 - - - +
394B HIS* 1.3 76.7 + - - +
395B LEU* 4.2 15.5 - - + +
407B ILE* 3.9 16.8 - - + -
408B SER 3.5 9.4 - - - +
409B LEU* 4.1 8.3 - - + -
434B ILE* 5.4 1.3 - - + -
493B LEU* 4.5 10.3 - - + -
495B VAL* 4.2 14.4 - - + -
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Residues in contact with HIS 394 (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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373B VAL 3.4 4.0 + - - +
374B VAL* 3.3 35.6 - - + +
392B ARG* 3.1 40.2 + - + -
393B LEU* 1.3 82.1 - - - +
395B LEU* 1.3 72.5 + - - +
396B GLN* 3.9 18.2 + - - +
407B ILE* 3.6 0.7 - - - -
408B SER* 3.1 40.9 + - - +
410B PHE* 4.3 12.1 - + - -
608D TYR* 4.5 11.0 - + - -
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Residues in contact with LEU 395 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
360B PHE* 4.2 12.1 - - + -
363B HIS* 3.9 23.3 - - + +
364B LEU* 3.8 27.4 - - + -
367B GLN* 3.8 16.7 - - + +
373B VAL* 3.1 42.7 + - + +
393B LEU* 4.2 12.3 - - + -
394B HIS* 1.3 84.1 - - - +
396B GLN* 1.3 66.8 + - - +
397B LEU* 3.4 6.2 + - - +
406B TYR 4.0 1.1 - - - +
407B ILE* 3.6 29.6 - - + -
479B LEU* 4.1 9.6 - - + -
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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