Contacts of the helix formed by residues 234 - 243 (chain H) in PDB entry 4IBL
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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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91H PRO* 4.4 3.6 - - + -
101H HIS* 2.7 39.2 + - - -
103H ILE* 3.8 48.5 - - + -
179H TYR* 3.2 21.6 - + + +
229H THR* 3.8 16.2 - - + -
230H ARG 3.3 24.0 - - - -
231H VAL* 2.8 9.6 + - - +
233H GLN* 1.4 82.9 - - + +
235H ILE* 1.3 59.4 + - - +
236H GLU 3.3 2.5 - - - -
237H TRP* 3.2 14.7 + + + +
238H LEU* 2.8 35.7 + - + +
256H PHE* 3.4 33.7 - + - -
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Residues in contact with ILE 235 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H LEU* 3.8 27.1 - - + -
124H PRO* 3.4 33.7 - - + +
125H GLU* 4.3 3.4 - - - -
126H ARG* 3.9 23.6 - - + +
231H VAL* 3.4 23.8 - - + +
232H SER* 3.6 17.0 - - - +
233H GLN 3.6 1.8 - - - -
234H TYR* 1.3 77.5 - - - +
236H GLU* 1.3 66.7 + - + +
238H LEU* 3.3 4.8 + - + +
239H GLN* 2.9 59.0 + - + +
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Residues in contact with GLU 236 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126H ARG* 3.1 50.5 + - - +
233H GLN 4.2 2.1 - - - +
235H ILE* 1.3 88.4 + - + +
237H TRP* 1.3 57.2 + - - +
239H GLN* 3.9 8.1 - - - +
240H LYS* 3.0 33.1 + - - +
243H ARG* 5.2 0.5 + - - -
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Residues in contact with TRP 237 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89H ILE* 3.7 20.4 - - + -
90H ILE 3.7 4.5 - - - -
91H PRO* 3.5 40.4 - - + -
103H ILE* 4.4 16.6 - - + -
105H LEU* 4.4 5.6 - - + -
233H GLN 5.7 0.2 + - - -
234H TYR* 3.2 17.5 + + + +
236H GLU* 1.3 77.8 - - - +
238H LEU* 1.3 97.7 + - + +
240H LYS* 3.9 4.4 - - - +
241H LEU* 3.1 56.8 + - + +
254H ALA* 3.9 5.0 + - + +
255H PRO 2.9 31.5 + - - -
256H PHE* 3.6 32.3 - + + +
257H PRO 3.8 13.6 + - - +
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Residues in contact with LEU 238 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H ILE* 5.6 0.2 - - + -
53H VAL* 4.6 11.9 - - + -
103H ILE* 4.0 20.9 - - + -
105H LEU* 3.9 30.8 - - + +
123H LEU* 3.8 38.8 - - + -
231H VAL* 4.4 6.7 - - + -
234H TYR* 2.8 30.1 + - + +
235H ILE* 3.6 3.8 - - - +
237H TRP* 1.3 100.0 - - + +
239H GLN* 1.3 56.8 + - - +
241H LEU* 3.2 1.2 + - - -
242H MET* 2.9 40.4 + - + +
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Residues in contact with GLN 239 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123H LEU* 4.4 11.0 + - + +
125H GLU* 6.3 0.6 - - - +
235H ILE* 2.9 42.7 + - + +
236H GLU* 3.9 8.0 - - - +
238H LEU* 1.3 73.6 - - - +
240H LYS* 1.3 63.6 + - - +
242H MET* 3.5 19.4 + - + +
243H ARG* 3.4 44.9 + - - +
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Residues in contact with LYS 240 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236H GLU 3.0 18.1 + - - +
237H TRP* 3.9 4.9 - - - +
239H GLN* 1.3 77.9 - - - +
241H LEU* 1.3 67.2 + - + +
243H ARG* 3.1 29.8 + - - +
244H SER* 3.4 9.7 + - - -
257H PRO 6.2 0.2 - - - -
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Residues in contact with LEU 241 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51H TRP* 3.9 6.6 - - - -
89H ILE* 3.7 25.1 - - + +
105H LEU* 3.8 15.9 - - + -
237H TRP* 3.1 65.9 + - + +
240H LYS* 1.3 81.6 - - + +
242H MET* 1.3 57.6 + - - +
244H SER* 2.6 40.8 + - - +
252H LEU* 4.5 7.6 - - + -
254H ALA* 3.7 20.4 - - + -
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Residues in contact with MET 242 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47H ILE* 3.7 24.9 - - + -
48H ASN* 3.6 26.2 - - - +
51H TRP* 3.6 49.9 + - + +
105H LEU* 3.7 10.1 - - + -
107H ARG* 5.1 1.0 + - - -
123H LEU* 4.0 14.4 - - + -
238H LEU* 2.9 29.7 + - + +
239H GLN* 3.9 15.5 - - + +
240H LYS 3.3 0.2 - - - -
241H LEU* 1.3 75.6 - - - +
243H ARG* 1.3 60.7 + - + +
244H SER 3.4 1.6 - - - +
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Residues in contact with ARG 243 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236H GLU 5.2 0.6 + - - -
239H GLN* 3.4 29.3 + - - +
240H LYS* 3.1 33.2 + - - +
241H LEU 3.1 1.0 - - - -
242H MET* 1.3 80.0 - - + +
244H SER* 1.3 61.9 + - - +
245H GLU* 4.8 4.5 - - - +
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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