Contacts of the helix formed by residues 234 - 243 (chain B) in PDB entry 1H1B
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 PHE 234 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ASN* 4.4 19.3 - - + -
101B ASN* 3.2 45.1 - - + -
103B ILE* 4.1 33.0 - - + -
126B GLN* 3.8 0.7 - - - -
229B ALA* 5.2 1.6 - - + -
230B PRO* 3.6 39.3 - - + -
231B VAL 2.9 10.8 + - - +
233B GLN* 1.3 83.1 - - + +
235B VAL* 1.3 54.9 + - - +
236B ASN 3.5 2.2 - - - -
237B TRP* 3.1 28.3 + + + +
238B ILE* 2.7 44.5 + - + +
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Residues in contact with VAL 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B LEU* 5.0 8.3 - - + -
124B PRO* 2.9 29.4 - - + +
125B ALA* 4.6 1.1 - - - -
126B GLN* 2.9 32.3 + - - +
231B VAL* 3.4 17.7 + - + +
232B ALA* 3.7 13.0 - - - +
234B PHE* 1.3 78.6 - - - +
236B ASN* 1.3 63.8 + - - +
238B ILE* 3.7 5.3 - - - +
239B ASP* 2.8 43.3 + - - +
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Residues in contact with ASN 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B GLN* 3.1 41.5 + - - +
234B PHE 3.5 0.2 - - - -
235B VAL* 1.3 75.5 - - - +
237B TRP* 1.3 60.1 + - - +
239B ASP* 3.6 8.1 + - - +
240B SER* 2.8 29.8 + - - -
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Residues in contact with TRP 237 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A GLU 5.2 1.5 + - - -
237A TRP* 6.0 2.2 - - - +
89B PHE* 3.6 34.2 - - + +
90B GLU* 3.8 7.7 + - - -
91B ASN* 3.7 42.3 - - + +
103B ILE* 4.4 24.2 - - + -
105B ILE* 3.8 23.8 - - + -
234B PHE* 3.1 24.0 + + + +
236B ASN* 1.3 76.7 - - - +
238B ILE* 1.3 86.6 + - + +
240B SER* 2.6 29.1 + - - -
241B ILE* 3.5 25.5 + - + +
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Residues in contact with ILE 238 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 4.1 16.4 - - + -
53B MET* 3.8 25.6 - - - -
103B ILE* 3.9 13.2 - - + -
105B ILE* 4.0 11.9 - - + -
123B LEU* 4.0 20.4 - - + -
231B VAL* 4.4 4.3 - - + +
234B PHE* 2.7 29.7 + - + +
235B VAL* 3.7 4.9 - - - +
237B TRP* 1.3 88.9 - - + +
239B ASP* 1.3 69.3 + - - +
241B ILE* 2.8 25.7 + - - +
242B ILE* 3.1 27.8 + - + -
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Residues in contact with ASP 239 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235B VAL* 2.8 34.3 + - - +
236B ASN* 3.8 9.5 + - - +
238B ILE* 1.3 80.0 - - - +
240B SER* 1.3 57.1 + - - +
241B ILE 2.8 5.6 + - - -
242B ILE* 4.0 16.2 - - - +
243B GLN* 3.3 57.4 + - - +
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Residues in contact with SER 240 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236B ASN 2.8 18.6 + - - -
237B TRP* 2.6 28.4 + - - -
239B ASP* 1.3 71.1 - - - +
241B ILE* 1.3 60.8 + - - +
243B GLN 4.8 5.6 - - - +
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Residues in contact with ILE 241 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91A ASN* 5.9 0.7 - - - +
51B PHE* 3.9 30.9 - - + -
89B PHE* 3.7 47.1 - - + -
105B ILE* 4.3 13.5 - - + -
237B TRP* 3.6 43.5 - - + +
238B ILE* 2.8 9.7 + - - +
239B ASP 2.8 0.4 + - - -
240B SER* 1.3 85.3 - - - +
242B ILE* 1.3 65.1 + - + +
243B GLN 3.4 3.6 - - - +
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Residues in contact with ILE 242 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B ILE* 4.0 37.7 - - + +
48B ALA* 4.4 9.8 - - + +
51B PHE* 3.7 43.3 - - + -
105B ILE* 4.5 1.8 - - + -
123B LEU* 6.3 2.0 - - + -
238B ILE* 3.1 28.4 + - + +
239B ASP* 4.0 12.1 - - - +
241B ILE* 1.3 86.2 - - + +
243B GLN* 1.3 72.4 + - + +
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Residues in contact with GLN 243 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B ASP* 3.3 50.7 + - - +
240B SER* 4.8 5.9 - - - +
241B ILE 3.4 1.7 - - - -
242B ILE* 1.3 87.3 + - + +
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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