Contacts of the helix formed by residues 356 - 367 (chain B) in PDB entry 1Z3S
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 356 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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309B ILE* 5.2 0.4 - - - -
342B TYR 3.7 7.4 - - - -
343B LYS 3.5 12.3 - - - -
345B GLY 3.8 4.5 - - - -
354B TRP* 2.7 21.1 + - - -
355B LEU* 1.3 76.3 - - - +
357B ASN* 1.3 63.3 + - - -
358B GLU 3.4 2.7 - - - -
359B PHE* 3.6 4.4 + - - +
360B VAL* 3.0 32.0 + - - +
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Residues in contact with ASN 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339B TRP* 5.6 0.8 + - - -
342B TYR* 2.9 27.0 + - - +
343B LYS* 3.3 1.0 + - - -
354B TRP* 3.2 23.1 - - - +
356B GLY* 1.3 68.0 - - - -
358B GLU* 1.3 56.4 + - - +
360B VAL* 3.9 0.9 - - - +
361B SER* 2.7 38.3 + - - -
392B LEU* 3.7 17.7 - - + +
399B TYR* 3.4 41.1 - - + -
423B PHE* 3.6 36.9 - - - -
446B TRP* 4.5 0.7 - - - -
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Residues in contact with GLU 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 4.0 17.3 - - + -
343B LYS* 3.3 32.8 + - + +
344B VAL* 5.7 0.2 - - - -
357B ASN* 1.3 77.5 - - - +
359B PHE* 1.3 57.6 + - - +
361B SER* 3.1 2.8 + - - -
362B GLN* 2.8 61.8 + - - +
395B GLU* 4.5 7.1 + - - +
399B TYR* 2.8 38.5 + - - +
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Residues in contact with PHE 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ARG 3.5 22.0 - - - -
300B LEU* 3.8 22.9 - - + -
301B THR 3.5 23.1 - - - -
302B PHE* 3.6 39.9 - + + -
303B PRO* 4.6 0.7 - - + -
309B ILE* 3.6 34.8 - - + -
323B THR* 5.0 1.3 - - + -
343B LYS 4.7 0.8 + - - -
355B LEU* 3.9 24.9 - - + -
356B GLY* 3.6 7.0 + - - +
357B ASN 3.4 0.2 - - - -
358B GLU* 1.3 77.9 - - - +
360B VAL* 1.3 59.9 + - + +
362B GLN* 3.4 2.4 + - - +
363B LEU* 3.0 56.0 + - + +
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Residues in contact with VAL 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325B ILE* 4.0 33.2 - - + -
354B TRP* 5.3 2.0 - - + +
355B LEU* 4.1 15.5 - - + -
356B GLY 3.0 21.5 + - - +
357B ASN* 3.9 3.4 - - - +
359B PHE* 1.3 76.1 - - + +
361B SER* 1.3 62.8 + - - +
363B LEU* 4.5 4.3 - - - +
364B THR* 2.7 41.1 + - + +
390B PHE* 4.2 13.5 - - + -
392B LEU* 3.6 23.1 - - + -
491B ILE* 4.8 4.9 - - + -
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Residues in contact with SER 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B ASN 2.7 22.1 + - - -
358B GLU* 3.6 5.2 - - - -
360B VAL* 1.3 73.8 - - - +
362B GLN* 1.3 65.9 + - - +
364B THR* 3.4 2.6 + - - -
365B ASN* 2.8 32.1 + - - +
392B LEU* 2.9 17.7 + - - -
393B SER 2.8 31.2 + - - -
394B SER* 3.7 6.6 + - - -
399B TYR* 3.8 11.9 - - - -
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Residues in contact with GLN 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B PHE* 3.9 17.9 - - - +
303B PRO* 2.9 54.2 + - + +
305B SER* 5.0 3.0 - - - -
358B GLU* 2.8 43.6 + - - +
359B PHE 3.8 4.0 - - - +
361B SER* 1.3 78.9 - - - +
363B LEU* 1.3 60.7 + - - +
365B ASN* 3.6 4.4 + - - +
366B GLN* 3.4 20.1 + - - +
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Residues in contact with LEU 363 (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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282B ARG* 3.6 26.0 - - + +
283B ASP* 4.0 14.4 - - + -
303B PRO* 3.8 22.9 - - + -
323B THR* 5.2 2.7 - - + -
359B PHE* 3.0 48.9 + - + +
360B VAL* 4.2 4.5 - - - +
361B SER 3.3 0.2 - - - -
362B GLN* 1.3 73.4 - - - +
364B THR* 1.3 60.6 + - + +
365B ASN 3.0 9.9 + - - -
366B GLN* 3.0 29.6 + - - +
367B GLN 3.6 0.9 + - - -
369B TYR* 3.3 27.9 - - + +
491B ILE* 4.5 16.2 - - + -
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Residues in contact with THR 364 (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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360B VAL* 2.7 25.3 + - + +
361B SER* 3.4 6.1 + - - -
363B LEU* 1.3 75.9 - - - +
365B ASN* 1.3 58.0 + - - +
367B GLN 3.1 14.2 - - - +
369B TYR* 3.9 19.5 - - + -
389B HIS* 5.4 2.1 - - - -
390B PHE* 3.6 37.8 - - + +
391B TYR* 3.3 27.3 - - - +
392B LEU 3.1 19.8 + - - -
491B ILE* 4.4 6.5 - - + -
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Residues in contact with ASN 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361B SER* 2.8 26.2 + - - +
362B GLN* 4.1 4.5 - - - +
363B LEU 3.0 1.0 - - - -
364B THR* 1.3 78.2 - - - +
366B GLN* 1.3 66.1 + - - +
367B GLN* 3.1 3.8 + - - +
391B TYR* 3.9 22.2 - - - -
392B LEU 3.0 18.1 + - - +
393B SER* 4.6 4.6 - - - +
394B SER 4.9 0.9 + - - -
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Residues in contact with GLN 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ARG* 4.1 26.6 + - - +
303B PRO* 3.6 30.6 - - + +
362B GLN 3.4 10.8 + - - +
363B LEU* 3.0 25.0 + - - +
365B ASN* 1.3 80.0 - - - +
367B GLN* 1.3 68.1 + - + +
369B TYR* 5.2 0.2 + - - -
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Residues in contact with GLN 367 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282B ARG* 3.7 25.3 - - - +
283B ASP* 4.7 1.4 + - - -
363B LEU 3.6 1.2 + - - +
364B THR 3.1 23.9 - - - +
365B ASN 3.1 2.7 - - - -
366B GLN* 1.3 86.1 - - + +
368B ARG* 1.3 66.2 + - - +
369B TYR* 3.4 38.3 + - + -
389B HIS* 5.1 0.7 - - - -
493B PRO* 3.7 19.8 - - - +
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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