Contacts of the helix formed by residues 234 - 244 (chain T) in PDB entry 1V2J
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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91T HIS* 4.0 27.6 - + - -
101T ASN* 2.6 47.4 + - - -
103T ILE* 4.0 26.5 - - + -
179T ASN* 3.2 30.3 + - + +
229T THR* 3.6 24.0 - - + +
230T LYS 3.2 29.6 - - - -
231T VAL* 2.9 9.0 + - + +
233T ASN* 1.3 84.4 - - + +
235T VAL* 1.3 65.8 + - - +
236T SER 3.3 3.1 - - - -
237T TRP* 3.1 12.7 + + + +
238T ILE* 2.9 28.9 + - + +
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Residues in contact with VAL 235 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
123T LEU* 4.5 12.1 - - + -
124T PRO* 3.4 40.6 - - + +
231T VAL* 3.4 15.2 + - + +
232T CYS* 3.8 12.7 + - - +
233T ASN 3.7 1.2 - - - -
234T TYR* 1.3 76.9 - - - +
236T SER* 1.3 64.8 + - - +
238T ILE* 3.2 10.1 + - - +
239T LYS* 3.1 49.5 + - + +
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Residues in contact with SER 236 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233T ASN 5.6 0.2 - - - -
234T TYR 3.3 0.6 - - - -
235T VAL* 1.3 80.7 - - - +
237T TRP* 1.3 63.4 + - - +
239T LYS* 3.9 5.0 - - - +
240T GLN* 3.0 37.9 + - - +
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Residues in contact with TRP 237 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89T ILE* 3.9 30.7 - - + -
91T HIS* 3.6 51.5 - + + +
92T PRO* 3.9 18.8 - - + +
103T ILE* 4.3 12.8 - - + -
105T LEU* 3.5 33.2 - - + -
234T TYR* 3.1 16.2 + - + +
236T SER* 1.3 76.4 - - - +
238T ILE* 1.3 77.2 + - + +
240T GLN* 3.2 10.6 + - + +
241T THR* 2.8 56.1 + - - -
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Residues in contact with ILE 238 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47T ILE* 4.0 8.3 - - + -
53T VAL* 4.8 6.1 - - + -
103T ILE* 3.5 31.0 - - + -
105T LEU* 3.6 23.5 - - + +
123T LEU* 3.9 31.0 - - + -
231T VAL* 5.6 4.0 - - + -
234T TYR* 2.9 29.5 + - + +
235T VAL* 3.4 9.6 - - - +
237T TRP* 1.3 83.9 - - + +
239T LYS* 1.3 58.7 + - - +
241T THR* 3.8 1.2 - - - -
242T ILE* 2.9 55.8 + - + +
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Residues in contact with LYS 239 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123T LEU* 4.9 15.3 - - + -
235T VAL* 3.1 36.3 + - + +
236T SER* 3.9 6.1 - - - +
238T ILE* 1.3 82.9 - - + +
240T GLN* 1.3 59.2 + - + +
242T ILE* 3.9 5.1 - - - +
243T ALA* 2.9 32.0 + - - +
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Residues in contact with GLN 240 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236T SER* 3.0 30.6 + - - +
237T TRP* 3.8 8.2 - - + +
239T LYS* 1.3 76.5 - - + +
241T THR* 1.3 61.1 + - - +
243T ALA* 3.8 6.5 - - - +
244T SER* 2.9 26.9 + - - -
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Residues in contact with THR 241 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51T TRP* 5.3 0.2 - - + -
89T ILE* 3.8 25.8 - - + -
105T LEU* 3.8 21.5 - - + -
237T TRP* 2.8 47.5 + - + -
238T ILE 3.8 2.2 - - - -
240T GLN* 1.3 74.1 - - - +
242T ILE* 1.3 61.7 + - - +
244T SER* 3.3 10.0 + - - -
245T ASN* 2.9 40.1 + - - +
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Residues in contact with ILE 242 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47T ILE* 3.5 32.1 - - + -
48T ASN* 4.0 12.6 - - - +
51T TRP* 3.4 46.1 + - + +
105T LEU* 4.1 11.2 - - + -
123T LEU* 5.9 0.4 - - + -
238T ILE* 2.9 30.2 + - + +
239T LYS* 4.0 4.9 - - - +
241T THR* 1.3 75.2 - - - +
243T ALA* 1.3 64.1 + - - +
245T ASN* 3.2 19.1 + - - +
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Residues in contact with ALA 243 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239T LYS 2.9 20.0 + - - +
240T GLN* 3.8 7.2 - - - +
241T THR 3.3 0.2 - - - -
242T ILE* 1.3 80.4 - - - +
244T SER* 1.3 57.2 + - - +
245T ASN* 3.7 3.1 + - - +
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Residues in contact with SER 244 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240T GLN 2.9 18.2 + - - -
241T THR* 3.3 8.5 + - - -
242T ILE 3.2 0.2 - - - -
243T ALA* 1.3 77.0 - - - +
245T ASN* 1.3 70.0 + - - +
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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