Contacts of the helix formed by residues 270 - 285 (chain B) in PDB entry 5ZR1
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 THR 270 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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268B ASP 3.8 3.5 + - - -
269B VAL* 1.3 77.5 - - - +
271B ARG* 1.3 64.5 + - + +
272B GLU* 3.9 23.1 - - + +
273B GLU* 3.0 26.5 + - - +
274B PHE* 2.9 23.7 + - - +
496B MET* 4.1 0.2 - - - -
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Residues in contact with ARG 271 (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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269B VAL 3.8 1.2 + - - -
270B THR* 1.3 77.6 - - + +
272B GLU* 1.3 58.2 + - - +
274B PHE* 3.3 6.6 + - + +
275B SER* 3.1 30.8 + - - +
494B ASP* 3.0 32.9 + - - -
495B VAL 5.4 1.0 - - - +
496B MET* 3.7 37.4 - - + +
508B GLU* 4.2 1.6 + - - -
511B LYS* 3.5 30.8 - - - +
515B GLN* 5.9 1.3 - - - +
611B LYS* 5.4 9.5 - - - +
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Residues in contact with GLU 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B THR* 3.9 18.0 - - + +
271B ARG* 1.3 79.0 - - - +
273B GLU* 1.3 69.9 + - - +
275B SER* 3.7 6.6 + - - -
276B LEU* 3.2 22.0 + - - +
565C LYS* 4.1 32.7 + - - +
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Residues in contact with GLU 273 (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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268B ASP 4.2 2.1 - - - +
269B VAL* 3.8 7.1 - - + -
270B THR* 3.0 44.7 + - - +
272B GLU* 1.3 86.9 - - - +
274B PHE* 1.3 64.0 + - - +
275B SER 3.3 0.2 - - - -
276B LEU* 3.6 11.4 - - + -
277B VAL* 3.2 19.4 + - - +
569C LEU* 3.5 20.4 - - + +
578C LYS* 2.9 41.6 + - - -
582C ILE* 3.3 12.1 - - + +
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Residues in contact with PHE 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B VAL* 4.2 2.4 - - + +
270B THR 2.9 14.9 + - - +
271B ARG* 3.3 15.2 + - + +
273B GLU* 1.3 77.2 - - - +
275B SER* 1.3 67.5 + - - +
278B SER* 3.0 37.7 + - - -
495B VAL* 3.6 43.1 - - + -
496B MET* 4.0 15.0 - - + -
582C ILE* 3.6 43.9 - - + +
585C MET* 3.6 33.9 - - + -
586C GLN* 4.6 7.4 - - + -
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Residues in contact with SER 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B ARG* 3.1 20.2 + - - +
272B GLU* 3.7 7.6 + - - -
274B PHE* 1.3 81.8 - - - +
276B LEU* 1.3 62.5 + - - +
278B SER* 3.4 7.4 - - - -
279B ASN* 2.8 39.2 + - - +
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Residues in contact with LEU 276 (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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272B GLU* 3.2 19.2 + - - +
273B GLU* 3.8 11.2 - - + +
274B PHE 3.2 0.6 - - - -
275B SER* 1.3 79.2 - - - +
277B VAL* 1.3 62.1 + - - +
279B ASN* 4.1 2.1 - - - +
280B PHE* 3.3 22.1 + - + +
563C ASN* 5.0 12.3 - - - +
565C LYS* 3.5 48.0 - - + +
566C LEU* 3.8 29.6 - - + +
569C LEU* 4.7 11.7 - - + -
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Residues in contact with VAL 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLU 3.2 18.3 + - - +
276B LEU* 1.3 75.3 - - + +
278B SER* 1.3 65.3 + - - +
280B PHE* 3.3 5.7 + - - +
281B PHE* 3.1 46.3 + - + -
557C ILE* 4.7 2.5 - - + -
566C LEU* 4.2 12.8 - - + -
569C LEU* 3.8 22.2 - - + -
579C VAL* 3.9 29.2 - - + +
582C ILE* 3.7 26.2 - - + -
583C LEU* 5.7 1.3 - - + +
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Residues in contact with SER 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B PHE* 3.0 31.1 + - - -
275B SER* 3.3 11.3 + - - -
277B VAL* 1.3 77.8 - - - +
279B ASN* 1.3 62.7 + - - +
280B PHE 3.3 0.2 + - - -
281B PHE* 3.3 3.9 + - - +
282B ASN* 2.8 41.7 + - - +
582C ILE* 4.0 10.0 - - - +
583C LEU* 6.0 1.6 - - - -
586C GLN* 4.0 22.2 - - - +
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Residues in contact with ASN 279 (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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275B SER* 2.8 30.5 + - - +
276B LEU* 4.4 2.0 - - - +
278B SER* 1.3 83.5 + - - +
280B PHE* 1.3 60.7 + - - +
282B ASN* 4.0 8.7 - - - +
283B GLU* 3.3 44.7 + - - +
487B THR* 4.4 18.0 + - - +
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Residues in contact with PHE 280 (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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276B LEU 3.3 16.5 + - - +
277B VAL* 3.3 6.1 + - - +
278B SER 3.2 0.6 - - - -
279B ASN* 1.3 77.2 - - - +
281B PHE* 1.3 61.2 + + - +
283B GLU* 5.2 0.4 - - - -
284B ASN* 3.0 50.7 + - - +
509C LEU* 3.8 18.2 - - + -
556C PHE* 3.4 47.8 - + - -
557C ILE* 3.6 25.1 - - + -
560C ASP* 3.6 36.3 - - + -
563C ASN* 4.6 5.6 - - - +
566C LEU* 3.6 20.0 - - + -
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Residues in contact with PHE 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B VAL* 3.1 35.8 + - + +
278B SER* 4.0 3.1 - - - +
280B PHE* 1.3 78.3 - + - +
282B ASN* 1.3 67.2 + - - +
285B PHE* 3.1 46.9 + + + +
290B ARG* 4.4 2.6 + - - -
513C LEU* 4.3 10.8 - - + -
517C MET* 5.0 2.5 - - + -
520C VAL* 6.3 0.2 - - + -
553C ILE* 4.0 13.2 - - + -
556C PHE* 3.5 34.1 - + - -
557C ILE* 4.0 14.1 - - + -
579C VAL* 3.6 31.2 - - + -
583C LEU* 3.9 39.3 - - + -
586C GLN* 5.4 0.2 - - - +
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Residues in contact with ASN 282 (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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278B SER* 2.8 33.4 + - - +
279B ASN* 4.2 9.0 - - - +
281B PHE* 1.3 78.0 - - - +
283B GLU* 1.3 61.5 + - + +
287B LYS* 4.2 4.0 + - - +
290B ARG* 3.3 25.4 + - - +
485B PRO* 3.3 38.5 - - + +
487B THR* 4.9 10.8 + - + -
586C GLN* 3.6 31.5 + - - -
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Residues in contact with GLU 283 (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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279B ASN* 3.3 36.7 + - - +
280B PHE* 5.2 0.3 - - - -
281B PHE 3.2 0.4 - - - -
282B ASN* 1.3 82.5 - - + +
284B ASN* 1.3 73.7 + - - +
287B LYS* 3.2 26.0 - - - +
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Residues in contact with ASN 284 (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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280B PHE* 3.0 38.8 + - + +
282B ASN 3.6 0.2 - - - -
283B GLU* 1.3 93.4 + - - +
285B PHE* 1.3 61.1 + - - +
286B GLN 3.7 0.7 - - - -
287B LYS* 4.0 9.4 + - - +
508C THR* 5.5 1.4 + - - -
509C LEU* 3.5 29.1 - - + +
510C SER* 2.8 23.0 + - - -
556C PHE* 3.6 15.7 - - + -
560C ASP* 5.3 0.2 - - - +
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Residues in contact with PHE 285 (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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281B PHE* 3.1 41.7 + + + +
284B ASN* 1.3 74.2 - - - +
286B GLN* 1.3 80.4 + - + +
290B ARG* 4.7 0.6 - - - +
510C SER* 2.3 28.2 + - - -
513C LEU* 3.6 29.2 - - + -
514C ASP* 2.8 21.0 - - - +
517C MET* 3.6 41.1 - - + -
518C ALA 3.4 26.7 - - - -
519C PRO* 3.9 9.0 - - + -
520C VAL* 4.9 7.6 - - + -
556C PHE* 4.0 3.3 - - - -
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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