Contacts of the helix formed by residues 252 - 261 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222D GLY* 5.3 4.5 - - - -
248D ASP* 2.7 47.2 + - - +
249D ARG* 3.0 8.2 + - - +
251D GLN* 1.3 87.5 + - - +
253D GLY* 1.3 65.5 + - - +
254D GLY 3.2 3.1 - - - -
255D THR* 3.0 20.5 + - + +
256D GLU* 3.0 21.1 + - - +
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Residues in contact with GLY 253 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90C HIS* 3.4 13.9 - - - -
196D ARG* 3.5 28.5 + - - +
200D PHE* 4.8 2.7 - - - -
249D ARG 2.8 12.7 + - - -
250D ILE 3.3 5.6 + - - -
251D GLN 3.5 0.6 - - - -
252D ASN* 1.3 75.8 - - - +
254D GLY* 1.3 62.3 + - - +
256D GLU* 3.1 18.0 + - - +
257D VAL 3.2 9.4 + - - -
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Residues in contact with GLY 254 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196D ARG* 3.2 25.8 - - - +
251D GLN 5.3 0.6 + - - -
252D ASN 3.2 1.2 - - - -
253D GLY* 1.3 75.5 - - - +
255D THR* 1.3 56.0 + - - +
257D VAL* 3.3 5.0 + - - +
258D VAL* 3.0 32.7 + - - +
266D SER* 5.1 2.0 - - - -
267D ALA* 5.6 1.6 - - - -
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Residues in contact with THR 255 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252D ASN* 3.0 25.0 + - + +
254D GLY* 1.3 73.0 - - - +
256D GLU* 1.3 57.7 + - - +
258D VAL* 4.3 8.3 - - + -
259D GLU* 2.7 57.8 + - + +
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Residues in contact with GLU 256 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86C ALA* 5.1 7.6 - - + +
89C SER* 4.7 2.6 + - - -
90C HIS* 2.9 20.9 + - + +
200D PHE* 4.2 1.2 - - - -
249D ARG* 2.6 57.3 + - - +
252D ASN 3.0 10.8 + - - +
253D GLY* 3.2 10.4 - - - +
255D THR* 1.3 76.6 - - - +
257D VAL* 1.3 60.2 + - + +
259D GLU* 3.9 10.3 - - - +
260D ALA* 3.1 22.5 + - - +
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Residues in contact with VAL 257 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C GLY 5.0 0.7 - - - +
86C ALA* 4.1 2.7 - - + +
87C ASP* 3.9 27.1 - - + +
90C HIS* 3.5 30.5 - - + +
196D ARG* 4.4 5.8 - - - +
253D GLY 3.2 3.6 + - - +
254D GLY 3.7 6.7 - - - +
255D THR 3.1 0.2 - - - -
256D GLU* 1.3 75.4 - - - +
258D VAL* 1.3 66.1 + - - +
260D ALA* 2.9 8.0 + - - +
261D LYS* 2.8 38.0 + - + +
266D SER* 3.7 5.6 - - - -
267D ALA* 3.3 34.1 - - + +
270D SER* 5.5 0.2 - - - +
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Residues in contact with VAL 258 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D MET* 3.9 33.7 - - + +
254D GLY 3.0 21.3 + - - +
255D THR* 3.8 8.3 - - + +
257D VAL* 1.3 75.7 - - - +
259D GLU* 1.3 64.1 + - + +
261D LYS* 3.4 2.4 + - - +
262D ALA* 3.2 17.7 + - - -
263D GLY* 3.8 5.6 + - - +
265D GLY 3.8 12.5 - - - +
266D SER* 3.3 31.9 - - - -
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Residues in contact with GLU 259 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128D MET* 6.0 3.1 - - + -
255D THR* 2.7 45.9 + - + +
256D GLU* 3.9 8.4 - - - +
258D VAL* 1.3 75.7 - - + +
260D ALA* 1.3 59.9 + - - +
262D ALA* 3.0 23.1 + - - +
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Residues in contact with ALA 260 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PRO* 4.3 10.3 - - + +
83C GLY* 3.7 16.9 + - - -
86C ALA* 3.4 31.6 - - + -
256D GLU 3.1 11.1 + - - +
257D VAL 2.9 8.1 + - - +
259D GLU* 1.3 73.4 - - - +
261D LYS* 1.3 60.9 + - - +
262D ALA* 3.0 9.4 + - - +
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Residues in contact with LYS 261 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58C GLN* 4.7 9.1 + - - -
80C ASN* 4.7 4.7 - - - +
83C GLY* 3.8 28.5 - - - -
84C VAL* 4.6 5.1 - - - +
87C ASP* 3.3 22.7 + - - +
257D VAL* 2.8 24.7 + - + +
258D VAL 4.1 0.4 - - - +
260D ALA* 1.3 75.0 - - - +
262D ALA* 1.3 70.0 + - - +
263D GLY 3.3 0.4 - - - -
264D ALA* 2.9 45.5 + - + +
265D GLY 3.6 25.1 - - - +
266D SER 3.1 22.0 + - - +
268D THR* 3.6 12.7 + - - +
269D LEU* 5.7 0.2 - - - +
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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