Contacts of the helix formed by residues 247 - 256 (chain H) in PDB entry 5DST
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 MET 247 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90G LEU* 4.3 2.7 - - + -
122G THR* 4.1 26.0 - - + +
124G ILE* 4.2 19.1 - - + -
127G MET* 4.3 14.8 - - + -
152G ILE* 3.9 28.5 - - + -
239H TRP* 2.9 46.8 + - + +
242H VAL* 3.6 38.8 - - + -
245H PHE* 3.5 3.6 + - + +
246H ASP* 1.3 78.8 - - - +
248H THR* 1.3 63.6 + - - +
249H CYS* 3.1 3.4 - - - -
250H ILE* 3.0 15.1 + - + +
251H ARG 3.2 8.0 + - - -
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Residues in contact with THR 248 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239H TRP 4.6 0.4 - - - -
240H GLU* 3.9 27.4 - - + -
246H ASP* 3.2 32.1 + - - +
247H MET* 1.3 77.2 - - - +
249H CYS* 1.3 59.0 + - - +
250H ILE 3.2 0.2 - - - -
251H ARG* 3.6 28.7 - - - +
252H ASP* 2.9 35.7 + - - +
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Residues in contact with CYS 249 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148G TYR* 3.7 41.0 - - + -
151G LYS* 4.1 24.9 - - + -
152G ILE* 3.6 31.4 - - - -
246H ASP* 4.9 0.2 + - - -
247H MET 3.1 2.0 + - - -
248H THR* 1.3 81.3 + - - +
250H ILE* 1.3 64.0 + - - +
252H ASP* 3.9 9.2 + - - +
253H VAL* 3.7 11.4 + - - +
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Residues in contact with ILE 250 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83G PHE* 3.5 26.9 - - + -
86G HIS* 6.0 0.2 - - + -
122G THR* 4.0 15.3 - - + -
145G ILE* 4.4 9.9 - - + -
148G TYR* 4.0 27.8 - - + -
152G ILE* 3.9 21.5 - - + -
239H TRP* 3.5 42.4 - - + +
247H MET* 3.0 9.2 + - - +
249H CYS* 1.3 78.6 - - - +
251H ARG* 1.3 58.2 + - - +
252H ASP 3.1 1.1 - - - -
253H VAL* 2.6 29.9 + - - +
254H ALA* 2.9 10.6 + - + -
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Residues in contact with ARG 251 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236H ILE* 3.3 36.7 - - + +
237H HIS* 4.8 3.9 + - - -
239H TRP* 3.6 27.5 - - + -
240H GLU* 3.2 35.8 + - + +
247H MET 3.2 2.8 + - - -
248H THR* 3.2 30.5 - - + +
250H ILE* 1.3 77.8 - - - +
252H ASP* 1.3 95.3 + - - +
254H ALA* 3.2 2.5 + - - +
255H MET* 3.0 37.6 + - - +
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Residues in contact with ASP 252 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248H THR* 2.9 17.9 + - - +
249H CYS* 4.0 9.4 - - - +
250H ILE 3.0 0.4 + - - -
251H ARG* 1.3 109.3 + - - +
253H VAL* 1.3 62.3 + - + +
255H MET* 3.7 10.7 - - - +
256H LYS* 3.4 23.2 + - - +
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Residues in contact with VAL 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G PHE* 4.3 18.4 - - + -
148G TYR* 3.1 34.8 - - + +
249H CYS 3.7 13.5 - - - +
250H ILE* 2.6 17.1 + - + +
252H ASP* 1.3 72.7 - - + +
254H ALA* 1.3 59.4 + - - +
256H LYS* 3.1 26.6 + - + +
257H GLU* 3.6 8.0 + - - +
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Residues in contact with ALA 254 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83G PHE* 3.6 37.8 - - + -
235H LYS 4.9 4.9 - - - +
236H ILE* 5.0 5.4 - - + -
239H TRP* 4.2 17.5 - - + +
250H ILE 2.9 9.9 + - - +
251H ARG* 3.6 8.3 - - - +
253H VAL* 1.3 73.2 - - - +
255H MET* 1.3 66.7 + - - +
257H GLU* 3.0 23.4 + - - +
259H LEU* 5.3 3.5 - - - +
341H TYR* 5.9 0.9 - - - -
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Residues in contact with MET 255 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232H LYS* 3.9 4.7 - - - -
236H ILE* 3.7 38.0 - - + +
237H HIS* 5.5 1.6 - - + -
251H ARG* 3.0 30.2 + - - +
252H ASP* 3.7 10.5 - - - +
254H ALA* 1.3 76.4 - - - +
256H LYS* 1.3 67.3 + - - +
257H GLU 3.2 7.6 + - - +
341H TYR* 3.8 33.3 + - - +
342H LEU 3.6 21.8 - - - +
343H GLU* 3.8 23.8 - - + +
391H TYR* 3.5 20.5 - - - -
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Residues in contact with LYS 256 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252H ASP* 3.4 19.0 + - - +
253H VAL* 3.1 13.9 + - - +
255H MET* 1.3 82.6 - - - +
257H GLU* 1.3 58.6 + - - +
343H GLU* 5.6 12.9 - - - -
389H ASN* 5.4 7.7 - - - +
390H ASP* 3.0 39.0 - - + +
391H TYR* 3.0 9.4 - - + +
392H LYS* 2.8 34.4 + - + +
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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