Contacts of the helix formed by residues 234 - 242 (chain S) in PDB entry 5JBA
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 TYR 234 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91S HIS* 3.5 41.3 - + - -
101S HIS* 2.6 39.5 + + + -
103S ILE* 3.9 27.4 - - + -
179S ASN* 3.1 27.5 - - + +
229S THR* 3.7 24.7 - - + -
230S LYS 3.3 23.1 - - - -
231S VAL* 2.8 7.6 + - - +
233S ARG* 1.4 89.3 - - + +
235S VAL* 1.3 61.8 + - - +
236S ASN 3.2 3.6 - - - -
237S TRP* 3.1 13.4 + - + +
238S ILE* 2.9 29.7 + - + +
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Residues in contact with VAL 235 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123S ILE* 3.5 19.9 - - + +
124S ALA 3.5 18.6 - - - +
125S ASP* 3.7 5.2 - - - -
126S LYS* 3.4 29.8 - - + +
129S THR* 3.6 11.9 - - - +
231S VAL* 3.1 28.2 + - + +
232S SER* 3.6 11.2 - - - +
233S ARG 3.7 0.2 - - - -
234S TYR* 1.3 77.0 - - - +
236S ASN* 1.3 74.1 + - - +
238S ILE* 3.2 7.6 + - + +
239S LYS* 2.9 32.2 + - + +
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Residues in contact with ASN 236 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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125S ASP* 5.5 2.3 - - - +
126S LYS* 4.7 14.6 + - - +
233S ARG 5.4 2.2 + - - +
234S TYR 3.2 0.8 - - - -
235S VAL* 1.3 87.6 - - - +
237S TRP* 1.3 57.2 + - - +
239S LYS* 3.4 5.8 + - - +
240S GLU* 2.9 30.5 + - - +
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Residues in contact with TRP 237 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89S ILE* 3.5 28.2 - - + +
90S PRO 4.0 1.1 - - - -
91S HIS* 3.6 39.4 - + + +
92S HIS* 4.0 29.0 + + + +
103S ILE* 3.9 26.0 - - + -
104S ALA* 4.0 7.2 - - - -
105S LEU* 3.6 34.5 - - + -
233S ARG 5.7 0.2 - - - +
234S TYR* 3.1 18.4 + - + +
236S ASN* 1.3 77.1 - - - +
238S ILE* 1.3 87.8 + - + +
240S GLU* 3.3 8.8 + - - +
241S LYS* 3.1 58.1 + - + +
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Residues in contact with ILE 238 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47S VAL* 4.1 22.4 - - + -
53S VAL* 4.4 9.0 - - + -
103S ILE* 4.1 19.5 - - + -
105S LEU* 4.3 9.4 - - + -
123S ILE* 4.0 30.3 - - + -
209S LEU* 4.9 1.8 - - + -
231S VAL* 4.4 15.3 - - + -
234S TYR 2.9 23.3 + - - +
235S VAL* 3.6 11.0 - - - +
237S TRP* 1.3 94.4 - - + +
239S LYS* 1.3 62.1 + - + +
242S THR* 2.7 39.2 + - + +
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Residues in contact with LYS 239 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112E THR* 5.0 4.4 + - - -
113E GLU* 5.7 6.3 - - - +
47S VAL* 6.4 1.6 - - + -
123S ILE* 2.9 48.7 + - + +
124S ALA 4.7 4.5 - - - -
125S ASP* 6.1 0.2 - - - +
235S VAL* 2.9 22.4 + - + +
236S ASN* 3.8 5.6 - - - +
238S ILE* 1.3 83.7 - - + +
240S GLU* 1.3 61.8 + - - +
241S LYS 3.4 0.2 + - - -
242S THR* 3.7 8.8 + - - +
243S LYS* 3.4 23.8 + - - +
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Residues in contact with GLU 240 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236S ASN 2.9 17.9 + - - +
237S TRP* 3.3 9.8 + - - +
239S LYS* 1.3 79.3 - - - +
241S LYS* 1.3 85.5 + - + +
243S LYS* 4.0 29.7 + - - +
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Residues in contact with LYS 241 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51S TRP* 3.4 19.8 - - - -
87S ARG* 5.1 1.6 + - - -
89S ILE* 4.3 27.7 - - + +
92S HIS* 5.8 1.1 - - - -
105S LEU* 3.6 23.8 - - + -
237S TRP* 3.1 43.6 + - + +
240S GLU* 1.3 100.5 + - + +
242S THR* 1.3 61.3 + - - +
243S LYS 3.4 2.3 + - - +
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Residues in contact with THR 242 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47S VAL* 3.7 18.3 - - + +
48S ASN* 2.9 24.5 + - - -
51S TRP* 3.5 47.4 - - + +
105S LEU* 3.9 24.0 - - + -
238S ILE* 2.7 24.2 + - + +
239S LYS* 4.0 6.5 + - - +
240S GLU 3.5 0.4 - - - -
241S LYS* 1.3 80.0 - - - +
243S LYS* 1.3 65.3 + - - +
244S LEU 3.3 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