Contacts of the helix formed by residues 252 - 261 (chain E) in PDB entry 1SMK
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 ASN 252 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222E GLY* 4.6 8.7 - - - -
223E VAL* 5.9 3.1 - - - +
248E ASP* 2.9 40.4 + - - +
249E ARG* 3.2 5.4 - - - +
251E GLN* 1.3 85.4 + - - +
253E GLY* 1.3 64.1 + - - +
254E GLY 3.1 2.9 - - - +
255E THR* 3.1 30.3 + - - +
256E GLU* 3.3 9.2 + - - +
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Residues in contact with GLY 253 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E ARG* 3.8 25.1 - - - +
200E PHE* 4.9 2.9 - - - -
249E ARG 2.7 18.9 + - - -
250E ILE 3.6 2.8 + - - -
251E GLN 3.5 3.4 - - - -
252E ASN* 1.3 73.7 - - - +
254E GLY* 1.3 65.7 + - - +
256E GLU* 3.2 19.3 + - - +
257E VAL* 3.5 1.0 + - - +
90F HIS* 3.3 17.2 - - - -
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Residues in contact with GLY 254 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E ARG* 5.7 1.1 - - - -
196E ARG* 3.5 24.2 - - - +
251E GLN 5.2 0.8 + - - -
252E ASN* 3.1 1.8 - - - +
253E GLY* 1.3 74.2 - - - +
255E THR* 1.3 63.7 + - - +
257E VAL* 2.9 16.8 + - - +
258E VAL* 3.1 17.2 + - - +
267E ALA* 5.5 1.8 + - - -
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Residues in contact with THR 255 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E ARG* 6.2 0.7 - - - +
252E ASN* 3.1 25.8 + - + +
254E GLY* 1.3 74.5 - - - +
256E GLU* 1.3 56.6 + - - +
258E VAL* 3.9 14.1 - - + +
259E GLU* 2.7 46.4 + - - +
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Residues in contact with GLU 256 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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200E PHE* 4.6 0.3 - - - -
249E ARG* 2.9 50.2 + - - +
252E ASN 3.3 8.2 + - - +
253E GLY* 3.2 12.2 + - - +
254E GLY 3.1 0.4 + - - -
255E THR* 1.3 81.4 + - - +
257E VAL* 1.3 58.7 + - + +
259E GLU* 3.5 6.9 - - - +
260E ALA* 3.1 24.9 + - - +
86F ALA* 5.1 6.3 - - + +
89F SER* 4.5 2.4 + - - -
90F HIS* 2.7 28.2 + - + +
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Residues in contact with VAL 257 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196E ARG* 4.9 0.9 - - - +
253E GLY 3.8 2.9 - - - +
254E GLY 2.9 6.3 + - - +
256E GLU* 1.3 76.0 - - - +
258E VAL* 1.3 67.3 + - - +
259E GLU 3.1 1.1 - - - -
260E ALA* 3.1 5.9 + - - +
261E LYS* 2.9 32.6 + - - +
267E ALA* 4.0 29.4 - - + +
83F GLY 4.2 2.7 - - - +
86F ALA* 3.9 14.4 - - + +
87F ASP* 3.9 28.5 - - + +
90F HIS* 3.3 36.1 - - + +
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Residues in contact with VAL 258 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E ARG* 2.9 49.1 - - - +
254E GLY 3.1 16.2 + - - +
255E THR* 3.7 16.4 - - + +
257E VAL* 1.3 76.8 - - - +
259E GLU* 1.3 65.1 + - - +
261E LYS* 3.3 5.9 + - - -
262E ALA 3.7 0.2 + - - -
263E GLY* 3.4 28.1 + - - +
265E GLY 3.4 17.7 - - - +
266E SER* 3.9 11.2 - - - -
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Residues in contact with GLU 259 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255E THR* 2.7 30.5 + - - +
256E GLU* 3.5 7.9 - - - +
258E VAL* 1.3 75.0 - - - +
260E ALA* 1.3 57.0 + - - +
262E ALA* 2.9 23.4 + - - -
263E GLY 4.1 2.5 + - - +
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Residues in contact with ALA 260 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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256E GLU 3.1 14.6 + - - +
257E VAL 3.1 3.7 + - - +
259E GLU* 1.3 78.5 - - - +
261E LYS* 1.3 58.0 + - - +
262E ALA* 3.2 4.9 + - - +
82F PRO* 4.0 15.0 - - + +
83F GLY* 3.6 13.8 + - - -
86F ALA* 3.5 28.5 - - + -
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Residues in contact with LYS 261 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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257E VAL* 2.9 17.5 + - - +
258E VAL 3.8 0.7 - - - +
259E GLU 3.1 0.8 + - - -
260E ALA* 1.3 74.5 - - - +
262E ALA* 1.3 72.4 + - - +
263E GLY 3.5 0.9 - - - -
264E ALA* 3.6 16.0 - - - +
265E GLY* 3.5 35.5 - - - +
266E SER 2.6 26.9 + - - +
268E THR* 3.6 13.5 + - - +
58F GLN* 5.1 6.8 + - - -
80F ASN* 5.0 8.5 - - - +
83F GLY* 3.4 34.5 - - - -
84F VAL* 4.5 5.6 - - - +
87F ASP* 3.6 18.0 + - - -
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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