Contacts of the strand formed by residues 382 - 394 (chain B) in PDB entry 4ZCH
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 GLU 382 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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375B LYS 4.5 0.7 - - - -
376B VAL* 3.3 14.0 - - - +
377B HIS* 3.1 58.2 + - + -
380B GLY* 3.5 21.9 - - - +
381B ASP* 1.3 75.9 - - - +
383B LEU* 1.3 61.2 + - - +
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Residues in contact with LEU 383 (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 LYS* 3.7 30.1 - - + -
375B LYS 3.6 1.3 - - - -
376B VAL* 3.8 11.7 - - + -
377B HIS* 6.3 0.2 - - - -
381B ASP 3.9 3.2 + - - +
382B GLU* 1.3 76.3 - - - +
384B SER* 1.3 78.3 + - - +
385B LEU* 4.1 22.2 - - + +
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Residues in contact with SER 384 (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 ARG 4.5 1.1 - - - -
374B LYS* 3.4 6.5 - - - +
375B LYS* 2.9 62.5 + - - +
377B HIS* 6.2 1.8 - - - -
383B LEU* 1.3 76.1 - - - +
385B LEU* 1.3 61.5 + - - +
386B VAL* 4.4 9.6 - - - +
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Residues in contact with LEU 385 (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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322B TYR* 5.9 4.7 - - + +
372B GLN* 3.5 48.9 - - + +
373B ARG 3.5 2.9 - - - +
374B LYS* 3.8 26.9 - - + -
383B LEU* 4.1 22.9 - - + +
384B SER* 1.3 75.8 + - - +
386B VAL* 1.3 62.1 + - - +
387B THR 4.4 0.3 + - - -
419B GLN* 3.7 15.5 - - - +
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Residues in contact with VAL 386 (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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372B GLN* 3.4 7.0 - - - +
373B ARG* 3.1 40.2 + - + +
375B LYS* 5.4 5.4 - - - +
384B SER* 4.7 11.0 - - - +
385B LEU* 1.3 79.0 - - - +
387B THR* 1.3 75.3 + - - +
388B LEU* 3.4 13.1 + - + +
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Residues in contact with THR 387 (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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133B HIS* 3.7 46.8 - - + +
370B LEU* 3.5 32.0 - - + +
371B ILE 3.8 3.8 - - - -
372B GLN* 3.5 21.2 + - - -
385B LEU 4.4 0.4 + - - -
386B VAL* 1.3 81.2 - - - +
388B LEU* 1.3 63.0 + - - +
389B PHE 3.9 11.7 - - - +
390B ARG* 4.2 0.2 - - + -
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Residues in contact with LEU 388 (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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11B HIS* 5.7 0.3 + - - -
132B PRO 4.6 1.9 - - - +
133B HIS* 3.4 16.6 - - - +
354B ILE* 4.7 1.6 - - + -
371B ILE* 2.8 25.3 + - + +
373B ARG* 3.9 36.8 - - + +
386B VAL* 4.4 10.1 - - + +
387B THR* 1.3 73.4 - - - +
389B PHE* 1.3 89.2 + - + +
410B ALA* 4.2 25.4 - - + -
412B LEU* 4.3 1.3 - - + -
418B LEU* 3.6 30.1 - - + -
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Residues in contact with PHE 389 (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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11B HIS* 4.2 14.8 - + - -
133B HIS 3.6 4.5 - - - -
136B PHE* 3.8 25.4 - + + -
354B ILE* 4.2 14.8 - - + -
369B HIS* 4.4 0.3 - - - +
370B LEU* 3.8 2.6 - - - -
371B ILE* 3.0 48.5 + - + +
387B THR* 3.9 4.6 - - - +
388B LEU* 1.3 111.6 - - + +
390B ARG* 1.3 60.4 + - - +
406B SER* 3.4 23.3 - - - +
407B ALA 4.4 2.9 - - - -
408B GLY* 3.4 45.5 - - - -
409B ILE 3.7 15.3 - - - -
410B ALA* 4.4 3.8 - - + -
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Residues in contact with ARG 390 (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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60B GLN* 3.1 26.0 + - - +
62B LEU* 5.2 8.3 - - + -
102B SER* 4.4 1.8 + - - -
133B HIS* 2.8 39.4 + - + +
134B GLY* 5.2 4.3 - - - -
367B MET 4.8 0.4 - - - -
368B GLY* 3.9 10.7 - - - +
369B HIS 3.4 19.0 + - - +
370B LEU* 3.3 36.9 - - + +
387B THR* 4.2 0.4 - - + -
389B PHE* 1.3 75.6 - - - +
391B CYS* 1.3 78.5 + - - +
392B ILE* 3.5 37.8 - - + +
406B SER* 3.5 6.5 + - - -
423B PRO* 3.7 18.2 - - - +
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Residues in contact with CYS 391 (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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102B SER* 3.9 6.3 - - - -
368B GLY* 2.8 26.9 - - - -
369B HIS* 2.9 36.8 + - + +
390B ARG* 1.3 84.1 + - - +
392B ILE* 1.4 54.1 + - - +
404B CYS* 2.1 59.9 - - - -
405B TYR 3.5 17.0 - - - -
406B SER* 4.3 3.6 - - - -
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Residues in contact with ILE 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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62B LEU* 3.3 35.2 - - + -
100B TYR* 3.7 39.0 - - + +
102B SER* 3.0 32.9 + - - +
366B ALA* 4.3 17.0 - - + -
367B MET 3.5 9.9 - - - +
390B ARG* 3.5 27.8 - - + +
391B CYS* 1.4 73.2 - - - +
393B GLN* 1.4 66.6 + - - +
404B CYS* 3.6 4.0 - - - -
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Residues in contact with GLN 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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90B ARG* 5.7 5.4 - - - +
100B TYR 3.6 5.2 - - - -
101B ASN* 3.4 12.6 - - + +
102B SER 5.8 0.4 - - - +
242B GLN* 4.8 2.8 + - - -
360B TYR* 3.4 14.2 - - - -
366B ALA* 3.2 2.7 - - - -
367B MET 2.9 36.5 + - - +
392B ILE* 1.4 77.7 - - - +
394B ASN* 1.4 60.7 + - - +
395B MET* 3.3 19.8 + - - +
402B ASN* 3.4 42.3 + - - +
403B SER 3.3 25.9 + - - -
404B CYS* 3.5 17.3 - - - +
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Residues in contact with ASN 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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93B PRO* 3.7 22.7 - - + +
96B PRO* 5.8 0.4 - - - +
98B ARG 2.9 28.5 + - - -
99B ALA* 3.4 4.6 - - - +
100B TYR 3.0 17.4 + - - +
101B ASN* 2.8 38.7 + - - +
243B ASN* 5.9 0.2 - - - +
365B TYR* 3.2 15.5 + - - +
366B ALA* 4.7 3.5 - - - +
393B GLN* 1.4 72.8 - - - +
395B MET* 1.3 61.3 + - - +
396B PRO* 4.5 0.7 - - - +
402B ASN* 3.6 17.3 + - - -
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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