Contacts of the helix formed by residues 273 - 284 (chain B) in PDB entry 5IJ7
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 GLN 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272B VAL* 1.4 79.6 - - - +
274B ARG* 1.4 65.2 + - - +
275B GLU* 3.5 12.4 - - + +
276B GLN* 3.6 31.0 - - + +
277B SER* 3.7 18.5 + - - -
438B SER 4.4 1.7 - - - +
441B ARG* 3.9 15.0 - - - +
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Residues in contact with ARG 274 (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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273B GLN* 1.4 73.5 - - - +
275B GLU* 1.4 72.5 + - + +
276B GLN 3.5 0.2 + - - -
277B SER 3.5 1.9 + - - -
278B LEU* 3.2 43.6 + - - +
282B HIS* 4.6 2.8 - - - -
306B TYR 5.6 0.2 + - - -
441B ARG* 3.4 27.5 - - + +
442B VAL* 2.8 34.3 + - - +
445B GLY* 3.4 13.6 + - - -
446B THR* 2.8 37.6 + - - +
661T VAL* 3.9 4.9 - - - +
665T ASP* 3.0 33.9 + - - -
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Residues in contact with GLU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273B GLN* 3.5 9.2 - - - +
274B ARG* 1.4 84.3 - - + +
276B GLN* 1.3 55.0 + - - +
278B LEU* 4.5 2.0 - - - -
279B HIS* 2.8 52.5 + - + +
282B HIS* 3.3 36.1 + - - +
283B THR* 5.9 0.5 - - - +
306B TYR* 4.3 14.5 + - - -
307B LYS* 5.2 3.3 + - - -
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Residues in contact with GLN 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B THR* 4.0 32.5 + - - +
272B VAL* 3.5 44.5 - - + +
273B GLN* 3.6 34.6 + - + +
274B ARG 3.4 0.8 - - - -
275B GLU* 1.3 78.8 - - - +
277B SER* 1.3 59.3 + - - +
278B LEU 3.7 0.2 + - - -
279B HIS* 3.8 13.8 - - - +
280B SER 5.1 0.5 + - - -
610T GLU* 5.2 2.4 - - - +
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Residues in contact with SER 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B THR* 5.2 4.7 - - - +
264B ILE* 4.6 6.1 - - - +
272B VAL* 3.7 17.9 - - - +
273B GLN 3.7 5.5 + - - -
274B ARG 3.5 1.0 + - - -
275B GLU 3.4 0.2 - - - -
276B GLN* 1.3 78.4 - - - +
278B LEU* 1.4 59.0 + - - +
281B PHE* 3.9 2.4 - - - -
438B SER* 3.7 17.2 - - - -
442B VAL* 3.8 24.5 - - - -
610T GLU* 3.6 17.1 - - - +
658T LEU* 3.5 28.5 - - - +
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Residues in contact with LEU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B ARG* 3.2 58.7 + - - +
275B GLU* 4.2 1.6 - - - +
277B SER* 1.4 76.5 - - - +
279B HIS* 1.3 53.3 + - - +
280B SER 3.3 2.5 - - - -
281B PHE* 2.9 11.3 + - + +
282B HIS* 2.8 47.6 + - + +
442B VAL* 4.2 7.0 - - + -
658T LEU* 3.3 41.5 - - + +
661T VAL* 3.8 14.4 - - + -
662T SER* 4.3 9.6 - - - -
665T ASP* 3.5 11.4 - - - +
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Residues in contact with HIS 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 GLU* 2.8 37.5 + - + +
276B GLN* 3.8 12.6 - - - +
277B SER 3.7 1.0 - - - -
278B LEU* 1.3 71.2 - - - +
280B SER* 1.3 64.5 + - - +
282B HIS* 3.3 1.3 + - - -
283B THR* 2.9 66.2 + - + +
605T ASP* 6.2 1.6 - - + -
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Residues in contact with SER 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 GLN 5.1 0.6 + - - -
278B LEU 3.2 1.4 + - - -
279B HIS* 1.3 83.4 - - - +
281B PHE* 1.3 61.5 + - - +
283B THR* 3.8 4.6 + - - -
284B LEU* 3.1 31.6 + - - +
605T ASP 4.1 7.8 + - - -
606T VAL* 3.8 20.8 - - - +
610T GLU* 2.9 38.4 + - - -
614T MET* 3.6 11.9 - - - -
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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
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277B SER 3.9 11.2 - - - -
278B LEU* 2.9 13.1 + - - +
280B SER* 1.3 76.1 - - - +
282B HIS* 1.3 59.9 + - - +
285B PHE* 3.1 32.9 + - - +
292B TYR* 3.3 26.2 - + - +
610T GLU* 3.6 40.8 - - + -
613T VAL* 4.3 11.0 - - + -
614T MET* 3.8 15.3 - - + -
655T ASN* 3.3 29.8 - - + -
658T LEU* 3.8 20.2 - - + -
659T HIS* 3.7 18.2 - - + -
662T SER* 3.6 23.4 + - - +
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Residues in contact with HIS 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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274B ARG* 4.6 2.5 - - - -
275B GLU* 3.3 34.7 + - - +
278B LEU* 2.8 39.0 + - + +
279B HIS 3.8 3.6 - - - +
281B PHE* 1.3 78.8 - - - +
283B THR* 1.3 62.1 + - + +
285B PHE 4.3 3.3 + - - +
301B ALA* 4.9 4.0 + - - +
306B TYR* 3.4 49.4 - + + -
662T SER* 3.5 20.5 + - - -
665T ASP* 2.8 33.4 + - - +
666T PHE* 3.5 20.1 - + - -
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Residues in contact with THR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B GLU* 5.9 0.2 - - - +
279B HIS* 2.9 53.4 + - + +
280B SER* 3.8 5.0 + - - -
282B HIS* 1.3 77.7 - - + +
284B LEU* 1.3 71.2 + - - +
285B PHE 3.6 1.7 - - - +
300B HIS* 3.2 40.9 + - + +
301B ALA 5.4 1.8 + - - +
306B TYR* 4.8 12.1 - - + +
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Residues in contact with LEU 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280B SER* 3.1 15.8 + - - +
283B THR* 1.3 89.4 - - - +
285B PHE* 1.3 62.2 + - - +
286B CYS* 3.6 1.2 + - - +
292B TYR* 3.3 12.6 - - + -
293B ASP* 2.8 43.6 + - + +
294B CYS 4.7 0.3 + - - -
300B HIS* 5.5 7.0 - - + -
600T ILE* 5.1 3.1 - - + -
603T PHE* 4.2 35.2 - - + -
606T VAL* 3.9 24.7 - - + -
614T MET* 3.7 23.6 - - + -
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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