Contacts of the helix formed by residues 252 - 261 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222F GLY* 5.4 3.1 - - - -
248F ASP* 2.9 38.1 + - - +
249F ARG* 3.4 3.8 - - - +
251F GLN* 1.3 86.7 + - - +
253F GLY* 1.3 64.1 + - - +
254F GLY 3.2 2.9 - - - -
255F THR* 2.8 43.8 + - + +
256F GLU* 3.8 4.0 + - - +
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Residues in contact with GLY 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90E HIS* 3.3 9.7 - - - -
196F ARG* 3.9 19.3 - - - -
200F PHE* 4.4 2.2 - - - -
249F ARG 2.7 17.4 + - - -
250F ILE 3.5 8.8 + - - -
251F GLN 3.5 0.8 - - - -
252F ASN* 1.3 77.1 - - - +
254F GLY* 1.3 63.1 + - - +
256F GLU* 2.9 31.1 + - - +
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Residues in contact with GLY 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196F ARG* 3.4 29.1 - - - +
251F GLN 5.4 0.4 + - - -
252F ASN 3.2 1.4 + - - -
253F GLY* 1.3 75.8 - - - +
255F THR* 1.3 61.7 + - - +
256F GLU 3.1 0.9 + - - -
257F VAL* 3.2 13.2 + - - +
258F VAL* 3.4 16.0 + - - +
266F SER* 5.6 1.2 - - - -
267F ALA 5.7 0.2 + - - -
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Residues in contact with THR 255 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252F ASN* 2.8 34.7 + - + +
254F GLY* 1.3 76.1 - - - +
256F GLU* 1.3 64.7 + - - +
258F VAL* 3.7 10.1 - - - +
259F GLU* 3.0 26.3 + - - +
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Residues in contact with GLU 256 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86E ALA* 4.2 4.6 - - + +
89E SER* 5.5 0.2 + - - -
90E HIS* 3.0 20.2 + - - +
200F PHE* 4.1 1.4 - - - -
249F ARG* 2.8 62.6 + - - +
252F ASN 4.5 3.5 - - - +
253F GLY 2.9 13.7 + - - +
255F THR* 1.3 80.4 + - - +
257F VAL* 1.3 62.9 + - - +
259F GLU* 3.6 8.7 + - - +
260F ALA* 3.2 21.8 + - - +
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Residues in contact with VAL 257 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83E GLY 4.2 0.9 - - - +
86E ALA* 4.0 9.2 - - - +
87E ASP* 3.9 28.7 - - - +
90E HIS* 3.7 28.3 - - + +
196F ARG* 4.3 3.8 - - - +
254F GLY 3.2 7.4 + - - +
256F GLU* 1.3 73.9 - - - +
258F VAL* 1.3 65.6 + - - +
260F ALA* 3.3 1.9 + - - +
261F LYS* 3.0 53.2 + - - +
266F SER 3.9 0.4 - - - -
267F ALA* 3.8 35.7 - - + +
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Residues in contact with VAL 258 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124F ARG* 3.0 34.1 - - - +
130F ARG* 6.1 2.5 - - - +
254F GLY 3.4 13.4 + - - +
255F THR* 3.3 12.3 + - + +
256F GLU 3.3 0.4 - - - -
257F VAL* 1.3 77.6 - - - +
259F GLU* 1.3 58.0 + - - +
261F LYS* 3.0 8.0 + - - +
263F GLY* 2.6 49.7 + - - +
265F GLY 3.7 7.4 - - - +
266F SER* 4.1 10.1 - - - -
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Residues in contact with GLU 259 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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255F THR 3.0 17.0 + - - +
256F GLU* 3.9 7.5 - - - +
258F VAL* 1.3 78.3 - - - +
260F ALA* 1.3 71.0 + - - +
262F ALA* 2.9 19.8 + - - -
263F GLY* 4.4 2.9 - - - +
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Residues in contact with ALA 260 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E ASN* 5.9 0.9 - - - -
82E PRO* 3.7 21.1 - - + +
83E GLY* 3.1 19.3 + - - -
86E ALA* 3.3 33.7 - - + -
256F GLU 3.2 8.7 + - - +
257F VAL 3.7 2.7 - - - +
258F VAL 3.3 0.2 - - - -
259F GLU* 1.3 89.6 + - - +
261F LYS* 1.3 56.8 + - - +
262F ALA 3.3 1.9 + - - -
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Residues in contact with LYS 261 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58E GLN* 4.6 11.3 + - - +
80E ASN* 6.6 0.2 - - - -
83E GLY* 3.6 33.8 + - - -
84E VAL* 4.8 5.3 - - - +
87E ASP* 4.0 13.3 + - - +
257F VAL* 3.0 24.2 - - - +
258F VAL 3.0 3.7 + - - +
260F ALA* 1.3 76.8 - - - +
262F ALA* 1.3 71.5 + - - +
263F GLY 3.1 0.2 - - - -
264F ALA* 3.1 21.4 + - - +
265F GLY* 3.6 28.0 - - - +
266F SER 3.6 19.9 + - - +
268F THR* 4.1 9.3 + - - +
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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