Contacts of the helix formed by residues 252 - 261 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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324B SER* 3.5 27.6 + - - +
222H GLY* 5.1 4.5 - - - -
248H ASP* 3.1 38.3 + - - +
249H ARG* 3.4 4.7 - - - +
251H GLN* 1.3 85.6 + - - +
253H GLY* 1.3 65.1 + - - +
254H GLY 3.3 3.1 - - - +
255H THR* 2.7 37.4 + - - +
256H GLU* 3.4 7.9 + - - +
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Residues in contact with GLY 253 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90G HIS* 3.1 25.6 - - - -
196H ARG* 3.7 23.1 - - - +
200H PHE* 4.3 4.5 - - - -
249H ARG 2.9 14.7 + - - -
250H ILE 3.5 3.2 + - - -
251H GLN 3.5 3.0 + - - -
252H ASN* 1.3 77.6 - - - +
254H GLY* 1.3 64.0 + - - +
256H GLU* 3.1 15.3 - - - +
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Residues in contact with GLY 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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196H ARG* 3.2 31.6 - - - +
251H GLN 5.3 0.6 + - - -
252H ASN* 3.3 1.0 - - - +
253H GLY* 1.3 75.3 - - - +
255H THR* 1.3 56.3 + - - +
257H VAL* 2.8 24.0 + - - +
258H VAL* 3.1 15.5 + - - +
266H SER* 6.1 1.1 - - - -
267H ALA* 5.2 1.6 + - - -
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Residues in contact with THR 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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321B GLU* 4.7 11.9 - - - +
323B TYR* 4.2 15.7 - - - -
324B SER* 3.2 18.9 + - - -
251H GLN 5.8 0.2 - - - +
252H ASN* 2.7 34.3 + - + +
254H GLY* 1.3 74.6 - - - +
256H GLU* 1.3 52.7 + - - +
258H VAL* 3.5 11.9 - - + +
259H GLU* 2.7 37.9 + - - +
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Residues in contact with GLU 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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324B SER* 4.9 6.4 + - - +
326B GLY* 3.4 29.1 + - - +
327B PRO* 3.7 5.8 - - + +
86G ALA* 4.4 3.4 - - + +
90G HIS* 3.5 15.1 + - + +
249H ARG* 3.0 60.9 + - - +
252H ASN* 3.4 6.4 + - - +
253H GLY* 3.1 17.2 + - - +
254H GLY 3.0 0.8 - - - -
255H THR* 1.3 82.2 + - - +
257H VAL* 1.3 56.4 + - - +
259H GLU* 3.5 9.1 - - - +
260H ALA* 3.2 24.8 + - - +
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Residues in contact with VAL 257 (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 GLY 4.5 0.7 - - - +
86G ALA* 4.0 18.2 - - - +
87G ASP* 4.1 15.7 - - + +
90G HIS* 3.6 31.4 - - + +
196H ARG* 4.6 0.9 - - - +
253H GLY 4.0 0.2 - - - +
254H GLY 2.8 10.4 + - - +
256H GLU* 1.3 75.6 - - - +
258H VAL* 1.3 66.2 + - - +
259H GLU 3.1 1.3 - - - -
260H ALA* 3.1 10.6 + - - +
261H LYS* 3.1 38.5 + - + +
266H SER 3.9 0.7 - - - -
267H ALA* 3.6 39.3 - - + +
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Residues in contact with VAL 258 (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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321B GLU* 3.9 13.0 - - - +
323B TYR* 3.7 11.9 - - + +
124H ARG* 5.0 11.4 - - - +
254H GLY 3.1 12.6 + - - +
255H THR* 3.0 14.8 + - + +
257H VAL* 1.3 76.0 - - - +
259H GLU* 1.3 59.0 + - - +
261H LYS* 3.1 6.9 + - - +
263H GLY* 2.7 54.2 + - - +
265H GLY 3.6 17.7 - - - +
266H SER* 4.0 17.5 - - - -
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Residues in contact with GLU 259 (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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233B LYS* 5.0 10.9 + - - -
293B ILE* 3.6 18.2 - - - +
311B LYS* 3.7 30.9 + - + +
323B TYR* 3.5 45.3 - - + -
324B SER 5.6 2.0 - - - +
255H THR 2.7 19.8 + - - +
256H GLU* 3.5 11.1 - - - +
258H VAL* 1.3 74.6 - - - +
260H ALA* 1.3 67.4 + - - +
262H ALA 3.2 9.9 + - - -
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Residues in contact with ALA 260 (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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233B LYS* 5.7 6.3 - - - +
80G ASN* 6.1 0.2 - - - -
82G PRO* 3.7 18.6 - - + +
83G GLY* 3.3 17.8 + - - -
86G ALA* 3.4 33.4 - - + -
256H GLU 3.2 9.9 + - - +
257H VAL 3.1 4.1 + - - +
259H GLU* 1.3 84.0 + - - +
261H LYS* 1.3 57.5 + - - +
262H ALA 3.3 1.5 + - - -
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Residues in contact with LYS 261 (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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58G GLN* 5.2 7.3 + - - +
83G GLY* 3.6 35.0 - - - -
84G VAL* 4.5 4.7 - - - +
87G ASP* 3.9 13.7 + - - +
257H VAL* 3.1 27.4 + - + +
258H VAL 3.1 4.2 + - - +
259H GLU 3.1 0.4 - - - -
260H ALA* 1.3 76.8 - - - +
262H ALA* 1.3 71.1 + - - +
263H GLY 3.1 0.9 - - - -
264H ALA* 3.1 21.1 + - - +
265H GLY* 3.5 28.1 - - - +
266H SER 3.2 16.9 + - - +
268H THR* 4.6 7.9 + - - -
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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