Contacts of the helix formed by residues 247 - 256 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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239I TRP* 3.0 47.1 + - + +
242I VAL* 3.8 36.8 - - + -
245I PHE* 3.4 3.5 + - + +
246I ASP* 1.3 79.1 - - - +
248I THR* 1.3 65.2 + - - +
249I CYS* 3.1 3.4 - - - +
250I ILE* 3.0 14.7 + - + +
251I ARG 3.3 7.4 + - - -
90J LEU* 4.6 2.9 - - + -
122J THR* 4.4 19.7 - - + -
124J ILE* 4.2 10.8 - - + -
127J MET* 4.0 25.4 - - + -
152J ILE* 4.0 33.2 - - + +
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Residues in contact with THR 248 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239I TRP 3.9 1.1 + - - -
240I GLU* 3.9 18.8 - - + -
246I ASP* 3.1 33.0 + - - +
247I MET* 1.3 76.3 - - - +
249I CYS* 1.3 59.0 + - - +
251I ARG* 3.1 39.8 + - - +
252I ASP* 2.9 34.7 + - - +
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Residues in contact with CYS 249 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246I ASP* 4.9 0.4 + - - -
247I MET* 3.1 2.1 - - - -
248I THR* 1.3 82.4 + - - +
250I ILE* 1.3 63.9 + - - +
252I ASP* 3.9 10.7 - - - +
253I VAL* 3.7 20.3 + - - +
148J TYR* 3.9 23.8 - - + -
151J LYS* 4.0 29.4 - - + -
152J ILE* 3.8 30.5 - - - -
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Residues in contact with ILE 250 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239I TRP* 3.6 41.5 - - + -
247I MET* 3.0 9.8 + - - +
249I CYS* 1.3 78.9 - - - +
251I ARG* 1.3 58.2 + - - +
252I ASP 3.1 1.6 - - - -
253I VAL* 2.7 27.1 + - + +
254I ALA* 2.8 12.5 + - + +
83J PHE* 3.8 25.8 - - + -
86J HIS* 6.3 0.2 - - + -
122J THR* 4.2 13.2 - - + -
145J ILE* 4.8 8.3 - - + -
148J TYR* 4.1 28.0 - - + -
152J ILE* 3.8 22.7 - - + -
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Residues in contact with ARG 251 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236I ILE* 3.1 38.5 - - + +
237I HIS* 4.9 2.7 + - - -
239I TRP* 3.6 25.7 - - + +
240I GLU* 3.6 28.9 + - + +
247I MET 3.3 3.6 + - - -
248I THR* 3.1 36.9 + - - +
250I ILE* 1.3 77.5 - - - +
252I ASP* 1.3 90.4 + - - +
254I ALA* 3.2 3.8 + - - +
255I MET* 3.1 36.7 + - - +
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Residues in contact with ASP 252 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248I THR* 2.9 21.9 + - - +
249I CYS* 3.9 10.3 - - - +
251I ARG* 1.3 105.8 + - - +
253I VAL* 1.3 60.0 - - + +
255I MET* 3.8 10.1 - - - +
256I LYS* 3.5 23.0 + - - +
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Residues in contact with VAL 253 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249I CYS 3.7 13.7 + - - +
250I ILE* 2.7 16.6 + - + +
252I ASP* 1.3 72.7 - - + +
254I ALA* 1.3 64.7 + - - +
256I LYS* 3.1 20.5 + - + +
257I GLU* 3.6 9.3 + - - +
83J PHE* 4.5 17.0 - - + -
148J TYR* 3.3 32.8 - - + +
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Residues in contact with ALA 254 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235I LYS 4.9 5.6 - - - +
236I ILE* 5.0 5.6 - - + -
239I TRP* 4.3 18.4 - - + +
250I ILE 2.8 14.8 + - - +
251I ARG* 3.7 7.6 - - - +
253I VAL* 1.3 73.8 - - - +
255I MET* 1.3 54.0 + - - +
257I GLU* 2.8 35.5 + - - +
259I LEU* 5.3 2.8 - - - +
341I TYR* 6.1 0.2 - - - -
83J PHE* 4.0 33.4 - - + -
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Residues in contact with MET 255 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232I LYS* 3.8 5.4 - - - +
236I ILE* 3.8 36.2 - - + +
237I HIS* 5.4 2.0 - - + -
251I ARG* 3.1 28.0 + - - +
252I ASP* 3.8 10.8 - - - +
254I ALA* 1.3 74.7 - - - +
256I LYS* 1.3 68.4 + - - +
257I GLU 3.2 6.1 + - - +
341I TYR* 3.9 34.0 + - - +
342I LEU 3.5 23.1 - - - +
343I GLU* 3.8 23.8 - - + +
391I TYR* 3.4 21.5 - - - -
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Residues in contact with LYS 256 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252I ASP 3.5 18.3 + - - +
253I VAL* 3.1 11.8 + - + +
254I ALA 3.1 1.4 - - - -
255I MET* 1.3 86.5 - - - +
257I GLU* 1.3 57.8 + - - +
343I GLU* 5.5 14.2 + - - -
389I ASN* 5.3 7.8 - - - +
390I ASP* 2.9 39.2 + - + +
391I TYR* 3.0 11.0 - - + +
392I LYS* 2.8 33.0 + - + +
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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