Contacts of the helix formed by residues 232 - 242 (chain X) in PDB entry 1SGF
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 ILE 232 (chain X).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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124X PRO* 3.8 22.7 - - + +
125X THR 4.5 7.9 - - - +
128X GLU 3.0 35.0 - - - +
129X GLU* 3.5 31.9 - - + +
130X PRO* 4.3 5.2 - - + -
210X GLN* 4.0 6.9 + - - +
230X LYS* 3.6 10.3 - - + +
231X LEU* 1.3 71.5 - - - +
233X LYS* 1.3 57.8 + - - +
234X PHE 2.6 16.3 + - - -
235X SER* 2.8 25.3 + - - +
236X SER 4.8 0.3 + - - -
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Residues in contact with LYS 233 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178X ASP* 2.8 39.0 + - - +
179X ALA* 3.8 16.4 - - + +
230X LYS* 4.3 21.0 + - + +
231X LEU 3.4 0.2 - - - -
232X ILE* 1.3 76.7 - - - +
234X PHE* 1.3 84.1 + - + +
236X SER* 5.5 0.5 + - - -
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Residues in contact with PHE 234 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91X HIS* 3.5 32.5 - + - -
101X ASN* 3.0 43.3 - - - -
103X LEU* 3.7 25.1 - - + -
179X ALA* 4.1 25.1 - - + -
229X THR* 4.3 8.7 - - + -
230X LYS 3.1 22.9 - - - +
231X LEU 3.2 6.4 + - - +
232X ILE 2.6 6.7 + - - -
233X LYS* 1.3 96.1 - - + +
235X SER* 1.3 61.5 + - - -
236X SER 3.3 3.4 - - - -
237X TRP* 3.0 19.1 + - + +
238X ILE* 3.2 14.4 + - + +
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Residues in contact with SER 235 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123X LEU* 5.2 4.9 - - - +
124X PRO* 5.4 7.4 - - - -
231X LEU 3.2 9.1 + - - -
232X ILE* 2.8 26.2 + - - -
233X LYS 3.7 0.2 - - - -
234X PHE* 1.3 71.6 - - - +
236X SER* 1.3 64.8 + - - +
238X ILE* 3.2 9.0 + - - +
239X ARG* 3.0 57.2 + - - +
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Residues in contact with SER 236 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232X ILE 4.8 0.4 + - - -
233X LYS 6.1 0.2 - - - -
234X PHE 3.3 0.8 - - - -
235X SER* 1.3 79.5 + - - +
237X TRP* 1.3 63.5 + - - +
239X ARG* 3.9 4.4 - - - +
240X GLU* 3.1 40.5 + - - +
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Residues in contact with TRP 237 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89X ILE* 3.7 40.2 - - + -
90X PRO 4.0 0.9 - - - -
91X HIS* 3.5 54.2 - + + +
92X PRO* 3.9 11.2 - - + +
103X LEU* 4.2 23.1 - - + -
104X MET* 4.8 1.3 - - - -
105X LEU* 3.8 28.3 - - + -
234X PHE* 3.0 13.0 + - + +
236X SER* 1.3 78.9 - - - +
238X ILE* 1.3 74.1 + - + +
240X GLU* 4.2 5.3 - - - +
241X THR* 2.8 42.5 + - - -
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Residues in contact with ILE 238 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X LEU* 4.1 11.7 - - + -
53X LEU* 4.5 11.4 - - + -
103X LEU* 4.6 6.5 - - + -
105X LEU* 4.3 12.2 - - + +
123X LEU* 4.1 28.3 - - + -
124X PRO* 6.2 0.2 - - + -
231X LEU* 4.4 25.1 - - + +
234X PHE 3.2 15.4 + - - +
235X SER* 3.2 11.4 + - - +
237X TRP* 1.3 92.4 - - + +
239X ARG* 1.3 53.7 + - + +
241X THR* 2.8 26.0 + - - -
242X MET* 2.8 39.6 + - - +
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Residues in contact with ARG 239 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123X LEU* 4.1 30.4 + - + +
124X PRO 3.5 23.2 + - - -
125X THR* 4.8 9.1 - - - +
235X SER* 3.0 32.9 + - - +
236X SER* 4.0 3.8 - - - +
238X ILE* 1.3 78.3 - - - +
240X GLU* 1.3 59.0 + - + +
242X MET* 3.9 12.6 - - + +
243X ALA* 3.3 25.5 + - - +
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Residues in contact with GLU 240 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236X SER* 3.1 30.3 + - - +
237X TRP* 4.2 4.5 - - - +
238X ILE 2.9 1.0 + - - -
239X ARG* 1.3 75.2 - - + +
241X THR* 1.3 57.6 + - - +
242X MET 3.1 4.5 - - - -
243X ALA* 4.4 2.2 - - - +
244X ASN* 2.6 52.6 + - + +
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Residues in contact with THR 241 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51X TRP* 3.5 18.2 - - + -
89X ILE* 4.3 31.2 - - + -
105X LEU* 4.0 20.9 - - + -
237X TRP* 2.8 35.6 + - + -
238X ILE 2.8 3.8 + - - -
240X GLU* 1.3 78.2 - - - +
242X MET* 1.3 59.2 + - - +
244X ASN* 4.5 10.0 - - - -
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Residues in contact with MET 242 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X LEU* 4.0 26.2 - - + +
48X ASP* 4.9 10.5 - - + +
51X TRP* 3.6 46.0 + - + -
105X LEU* 5.0 3.8 - - + +
123X LEU* 3.9 23.8 - - + -
238X ILE* 2.8 29.7 + - + +
239X ARG* 4.0 10.5 - - + +
241X THR* 1.3 81.3 - - - +
243X ALA* 1.3 57.5 + - - +
244X ASN 5.3 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