Contacts of the strand formed by residues 350 - 360 (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 GLY 350 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36B ARG* 5.9 0.2 - - - -
348B GLU 3.6 2.2 + - - -
349B THR* 1.3 75.0 + - - +
351B TYR* 1.3 69.7 + - - -
352B PHE* 3.4 11.4 - - - -
411B LYS* 3.5 9.9 - - - +
412B LEU 3.0 32.9 + - - +
442B LYS* 4.4 8.5 - - - -
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Residues in contact with TYR 351 (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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9B VAL* 3.9 22.0 - - + -
34B LEU* 4.3 18.3 - - + +
35B ARG 3.4 18.5 + - - -
36B ARG* 3.4 51.1 - - + +
350B GLY* 1.3 75.9 - - - -
352B PHE* 1.3 63.0 + - - +
409B ILE* 4.1 13.0 - - + -
410B ALA 3.8 1.1 - - - -
411B LYS* 3.6 41.8 + - + +
442B LYS* 3.8 3.7 - - - +
443B LEU* 2.8 43.8 + - + +
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Residues in contact with PHE 352 (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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336B ALA* 4.3 4.9 - - + -
337B LEU* 3.7 35.7 - - + -
346B VAL* 3.9 18.2 - - + -
348B GLU 3.6 25.4 - - - -
350B GLY 3.4 26.0 - - - -
351B TYR* 1.3 74.9 - - - +
353B PHE* 1.3 61.3 + - - +
354B ILE* 3.7 17.9 - - + +
409B ILE* 3.2 4.2 - - - +
410B ALA 2.8 37.2 + - - +
412B LEU* 4.0 17.5 - - + -
440B ALA* 4.6 1.8 - - + -
441B LEU 3.4 7.6 - - - +
442B LYS* 3.8 39.7 - - + -
443B LEU* 4.0 5.4 - - - -
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Residues in contact with PHE 353 (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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56B LEU* 4.3 22.4 - - + -
58B TYR* 3.8 28.7 - + + -
104B TYR* 3.8 8.1 - - - -
140B VAL* 5.0 2.2 - - + -
202B PHE* 4.1 27.6 - + - -
352B PHE* 1.3 72.3 - - - +
354B ILE* 1.3 57.6 + - - +
355B TYR* 4.2 17.2 + + + -
405B TYR* 4.5 2.0 - - - -
407B ALA* 3.5 25.6 - - + -
408B GLY 3.5 22.7 - - - -
409B ILE* 4.3 6.3 - - + +
439B GLY 4.2 0.3 - - - +
440B ALA* 3.4 3.3 - - - -
441B LEU* 2.8 49.8 + - + +
443B LEU* 3.9 20.2 - - + +
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Residues in contact with ILE 354 (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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352B PHE* 3.7 23.3 - - + +
353B PHE* 1.3 75.5 - - - +
355B TYR* 1.3 62.8 + - - +
371B ILE* 3.7 26.9 - - + +
388B LEU* 4.7 3.1 - - + -
389B PHE* 4.2 10.2 - - + -
407B ALA* 3.0 5.4 - - - +
408B GLY 3.0 33.4 + - - +
410B ALA* 3.4 33.4 - - + +
412B LEU* 3.9 8.7 - - + -
418B LEU* 3.7 22.4 - - + -
438B PHE* 3.8 15.9 - - + -
439B GLY 3.5 11.7 - - - +
440B ALA* 4.5 4.0 - - + -
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Residues in contact with TYR 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
202B PHE* 5.2 4.7 - + - -
256B ALA 4.4 3.6 - - - -
257B GLY* 4.4 7.4 - - - -
258B ILE* 3.7 30.8 - - + +
306B LEU 4.3 1.4 + - - -
307B GLN* 3.0 42.1 + - + +
353B PHE* 4.2 19.7 - + + -
354B ILE* 1.3 75.5 - - - +
356B GLY* 1.3 58.9 + - - +
371B ILE* 4.1 5.4 - - - -
405B TYR* 3.3 24.9 - - + +
406B SER 3.4 6.7 - - - -
407B ALA* 3.7 6.1 - - + -
437B PHE* 4.1 26.9 - + - -
438B PHE* 3.3 9.4 - - - -
439B GLY* 3.1 54.3 + - - -
440B ALA* 4.1 4.9 - - - -
441B LEU* 5.1 0.9 - - + -
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Residues in contact with GLY 356 (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 TYR* 1.3 80.1 - - - +
357B GLN* 1.3 61.1 + - - -
369B HIS* 3.4 12.3 + - - -
371B ILE* 3.9 4.2 - - - +
405B TYR* 3.4 6.6 - - - -
406B SER 3.1 31.0 + - - +
420B LEU* 4.1 13.9 - - - -
437B PHE 3.3 11.2 - - - -
438B PHE* 4.3 0.2 - - - -
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Residues in contact with GLN 357 (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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239B ARG 2.8 25.8 + - - -
240B CYS* 5.1 0.2 - - - -
254B TYR 4.1 1.7 - - - +
255B SER* 2.8 28.4 + - - -
327B TRP* 4.8 0.2 - - - -
356B GLY* 1.3 75.6 - - - +
358B VAL* 1.3 70.5 + - - +
403B SER* 3.9 19.6 + - - -
404B CYS 3.1 15.3 - - - +
405B TYR* 3.6 17.2 - - + +
420B LEU* 4.6 0.2 - - - +
435B VAL* 3.1 21.3 + - - +
436B THR* 3.3 4.0 - - - +
437B PHE* 3.0 55.7 + - + +
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Residues in contact with VAL 358 (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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325B VAL* 4.6 0.9 - - + -
327B TRP* 5.3 0.4 - - + -
357B GLN* 1.3 79.5 - - - +
359B LEU* 1.3 62.6 + - - +
360B TYR* 3.5 38.6 - - + +
369B HIS* 3.6 10.5 - - + +
403B SER* 3.4 1.8 - - - -
404B CYS 3.0 29.8 + - - -
420B LEU* 3.4 34.8 - - + -
422B ILE* 4.5 4.0 - - + -
429B ILE* 3.8 28.9 - - + -
435B VAL 4.0 2.5 - - - -
436B THR* 3.7 13.5 - - + +
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Residues in contact with LEU 359 (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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239B ARG* 3.8 13.9 - - - +
241B ILE* 3.7 15.3 - - + -
358B VAL* 1.3 71.5 - - - +
360B TYR* 1.3 67.2 + - - +
361B THR* 5.8 1.3 - - - -
401B ASN* 3.7 23.3 - - - +
402B ASN 3.4 36.3 - - - +
403B SER* 3.8 2.9 - - - +
429B ILE* 3.4 9.4 - - - +
430B SER* 3.1 43.7 + - - -
435B VAL* 3.5 42.2 + - + -
436B THR* 3.2 9.1 + - - -
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Residues in contact with TYR 360 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358B VAL* 3.5 34.5 - - + +
359B LEU* 1.3 73.9 - - - +
361B THR* 1.3 60.2 + - - +
362B ASP 3.5 3.8 - - - +
367B MET* 3.6 33.7 - - + -
368B GLY* 3.0 35.9 + - - -
369B HIS* 3.1 18.7 + - - +
393B GLN* 3.4 17.0 - - - +
395B MET* 3.6 18.9 - - + +
401B ASN* 3.5 6.6 - - - -
402B ASN 2.9 35.4 + - - +
404B CYS* 3.6 18.2 - - + -
422B ILE* 3.6 9.6 - - + +
428B GLN 3.9 1.6 - - - -
429B ILE* 3.6 17.7 - - + -
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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