Contacts of the helix formed by residues 234 - 243 (chain C) in PDB entry 1SR5
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 LEU 234 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91C HIS* 4.2 16.6 - - + +
101C ARG* 4.1 23.6 - - + +
102C ASP 4.9 0.4 - - - +
103C ILE* 3.4 43.1 - - + -
179C ASN* 3.4 30.5 - - + +
229C THR* 5.0 7.9 - - + -
230C HIS 3.9 7.0 - - - +
231C VAL 3.0 11.0 + - - +
232C PHE 2.8 1.0 - - - -
233C ARG* 1.3 93.0 - - + +
235C LYS* 1.3 62.4 + - - +
236C LYS* 3.3 3.4 - - - +
237C TRP* 3.4 7.1 + - - +
238C ILE* 3.0 21.8 + - - +
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Residues in contact with LYS 235 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123C LEU* 4.4 24.3 + - + -
124C PRO* 2.9 29.7 + - + +
125C ASP* 3.6 18.2 - - - +
231C VAL* 3.3 5.4 + - + +
232C PHE* 2.8 33.9 + - + +
233C ARG 3.6 0.6 - - - -
234C LEU* 1.3 75.4 - - - +
236C LYS* 1.3 58.8 + - - +
238C ILE* 2.7 13.3 + - + +
239C GLN* 2.5 66.8 + - + +
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Residues in contact with LYS 236 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C PHE 4.7 0.2 + - - -
233C ARG 5.4 2.0 + - - +
234C LEU* 5.1 1.3 - - - -
235C LYS* 1.3 77.1 - - - +
237C TRP* 1.3 61.9 + - - +
239C GLN* 3.5 8.3 + - - +
240C LYS* 3.0 25.2 + - - +
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Residues in contact with TRP 237 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89C TYR* 2.9 33.2 - - + -
90C ILE 3.7 11.4 + - - -
91C HIS* 3.7 23.8 - + - +
92C PRO* 3.2 31.7 - - + +
103C ILE* 3.6 31.4 - - + -
104C ALA* 4.1 5.8 - - - -
105C LEU* 3.2 32.3 - - + -
234C LEU* 3.4 8.8 + - - +
235C LYS 3.1 0.4 - - - -
236C LYS* 1.3 76.2 - - - +
238C ILE* 1.3 86.0 + - + +
240C LYS* 2.9 12.2 + - + +
241C VAL* 2.8 37.8 - - + +
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Residues in contact with ILE 238 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C ILE* 4.9 1.6 - - + -
53C LEU* 3.9 16.4 - - + -
103C ILE* 3.2 32.3 - - + -
105C LEU* 4.0 13.0 - - + -
123C LEU* 3.8 27.1 - - + -
231C VAL* 4.1 24.5 - - + +
234C LEU 3.0 18.8 + - - +
235C LYS* 2.7 17.8 + - + +
237C TRP* 1.3 85.3 - - + +
239C GLN* 1.3 63.6 + - + +
241C VAL* 3.4 6.6 - - - +
242C ILE* 3.1 28.7 - - + +
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Residues in contact with GLN 239 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B GLU* 5.2 5.5 - - - -
123C LEU* 6.0 1.7 - - + +
235C LYS* 2.5 57.2 + - + +
236C LYS* 3.5 8.1 - - - +
238C ILE* 1.3 74.9 - - + +
240C LYS* 1.4 57.1 + - - +
241C VAL 2.9 7.0 + - - -
242C ILE* 3.1 10.2 + - - +
243C ASP* 3.0 43.2 + - - +
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Residues in contact with LYS 240 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236C LYS 3.0 16.5 + - - +
237C TRP* 2.9 14.3 + - + +
239C GLN* 1.4 70.3 - - - +
241C VAL* 1.4 61.2 + - + +
243C ASP* 4.3 9.0 - - - +
244C GLN* 3.6 20.2 - - - +
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Residues in contact with VAL 241 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51C TRP* 4.0 17.4 - - + -
89C TYR* 4.7 17.2 - - + -
105C LEU* 3.7 24.5 - - + -
237C TRP* 2.8 52.5 - - + +
238C ILE 3.4 9.9 - - - +
239C GLN 3.0 0.2 - - - -
240C LYS* 1.4 78.6 - - - +
242C ILE* 1.3 76.8 + - + +
243C ASP 3.4 0.9 - - - -
244C GLN* 3.6 27.5 + - - +
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Residues in contact with ILE 242 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B PHE* 3.2 70.4 + - + +
47C ILE* 4.4 6.3 - - + -
51C TRP* 3.4 27.3 + - + +
105C LEU* 4.2 8.1 - - + -
123C LEU* 5.3 1.3 - - + -
238C ILE* 3.1 34.1 - - + +
239C GLN* 3.1 9.3 + - - +
241C VAL* 1.3 85.1 - - + +
243C ASP* 1.3 65.1 + - - +
244C GLN 3.0 9.8 + - - -
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Residues in contact with ASP 243 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B PHE* 5.6 1.9 + - - +
239C GLN* 3.0 37.3 + - - +
240C LYS* 4.2 6.6 + - - -
241C VAL 3.4 0.4 - - - +
242C ILE* 1.3 79.2 - - - +
244C GLN* 1.3 57.2 + - + +
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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