Contacts of the helix formed by residues 239 - 245 (chain B) in PDB entry 1HTI
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 GLU 239 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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213B THR* 4.0 7.4 - - - +
214B GLY* 3.5 27.7 + - - +
234B ALA* 3.8 27.2 - - + +
237B LYS* 3.3 33.3 + - + +
238B PRO* 1.3 74.9 - - - +
240B PHE* 1.3 65.7 + - - +
241B VAL 3.0 2.2 - - - -
242B ASP* 3.0 32.5 + - - +
243B ILE* 3.2 13.4 + - + +
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Residues in contact with PHE 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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8B VAL* 3.5 34.1 - - + -
10B GLY* 4.0 18.8 - - - -
12B TRP* 5.7 0.9 - - - -
24B LEU* 5.9 0.7 - - + -
28B LEU* 3.6 40.6 - - + -
39B VAL* 5.2 2.7 - - + -
40B VAL 5.0 0.7 - - - -
41B CYS* 4.5 9.4 - - - -
231B VAL* 3.8 17.7 - - + -
234B ALA 3.7 6.3 - - - +
235B SER* 3.5 35.4 - - - +
237B LYS 3.1 16.9 + - - +
238B PRO* 4.5 1.3 - - + -
239B GLU* 1.3 79.1 - - - +
241B VAL* 1.3 62.7 + - + +
243B ILE* 3.0 18.9 + - + +
244B ILE* 3.0 26.9 + - + +
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Residues in contact with VAL 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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27B THR* 4.5 17.9 - - + -
28B LEU* 4.7 11.2 - - + -
31B ALA* 3.7 33.2 - - + -
32B LYS 5.3 1.1 - - - +
238B PRO* 3.1 20.0 - - + +
240B PHE* 1.3 76.4 - - + +
242B ASP* 1.3 62.8 + - - +
244B ILE* 3.0 22.5 + - + +
245B ASN* 2.9 31.4 + - - +
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Residues in contact with ASP 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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214B GLY* 4.8 16.2 - - - +
217B CYS* 4.1 7.1 - - - -
238B PRO 5.3 0.2 - - - -
239B GLU* 3.0 24.1 + - - +
241B VAL* 1.3 85.9 - - - +
243B ILE* 1.3 53.2 + - - +
245B ASN* 2.7 43.1 + - - +
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Residues in contact with ILE 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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6B PHE* 4.1 7.8 - - - -
8B VAL* 4.2 7.2 - - + +
212B VAL* 3.6 32.1 - - + +
213B THR* 4.0 17.9 - - - +
214B GLY* 4.4 1.6 - - - +
217B CYS* 3.8 20.6 - - + -
229B PHE* 3.5 28.4 - - + -
231B VAL* 3.9 28.5 - - + -
234B ALA* 4.5 4.7 - - + -
239B GLU 3.2 9.8 + - - +
240B PHE* 3.0 14.6 + - + +
242B ASP* 1.3 74.5 - - - +
244B ILE* 1.3 59.1 + - - +
245B ASN 3.3 0.2 - - - -
246B ALA* 3.6 10.7 - - - +
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Residues in contact with ILE 244 (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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6B PHE* 4.2 3.6 - - - -
8B VAL* 4.0 11.9 - - + -
28B LEU* 5.0 9.9 - - + -
31B ALA* 5.6 4.3 - - + -
32B LYS 5.1 0.7 - - - +
33B VAL* 3.7 28.7 - - + -
34B PRO* 3.8 13.9 - - + +
36B ASP* 4.9 0.9 - - - +
37B THR* 3.4 28.4 + - + +
39B VAL* 3.6 36.8 - - + -
59B ILE* 6.1 0.4 - - + -
240B PHE* 3.0 31.6 + - + +
241B VAL* 3.0 14.3 + - - +
243B ILE* 1.3 77.9 - - - +
245B ASN* 1.4 61.4 + - - +
246B ALA 3.4 4.2 + - - -
248B GLN 4.9 0.2 - - - +
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Residues in contact with ASN 245 (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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32B LYS* 3.3 34.3 + - - +
34B PRO* 3.3 21.8 - - - +
217B CYS* 4.9 1.7 - - - -
218B LYS* 5.0 5.5 - - - +
241B VAL* 2.9 30.3 + - - +
242B ASP* 2.7 17.6 + - - +
244B ILE* 1.4 78.3 - - - +
246B ALA* 1.3 59.7 + - - +
248B GLN 3.4 14.6 - - - +
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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