Contacts of the helix formed by residues 238 - 245 (chain A) 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 PRO 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24A LEU* 5.3 0.9 - - + -
27A THR* 4.0 32.5 - - + +
237A LYS* 1.4 84.3 - - + +
239A GLU* 1.3 57.9 + - + +
240A PHE 3.2 1.6 - - - -
241A VAL* 2.9 30.2 + - + +
242A ASP* 3.8 7.4 + - - +
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Residues in contact with GLU 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A THR* 4.0 10.0 - - - -
214A GLY* 2.8 37.8 + - - +
215A ALA 4.6 0.3 + - - -
234A ALA* 3.9 15.2 - - + +
237A LYS* 3.1 35.5 + - + +
238A PRO* 1.3 72.1 - - + +
240A PHE* 1.3 65.8 + - - +
241A VAL 3.0 1.8 - - - -
242A ASP* 2.8 26.9 + - - +
243A ILE* 3.0 20.5 + - + +
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Residues in contact with PHE 240 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A VAL* 3.8 20.2 - - + -
9A GLY 3.8 2.9 - - - -
10A GLY* 3.4 37.0 - - - -
12A TRP* 5.8 0.7 - - - -
24A LEU* 5.7 0.7 - - + -
28A LEU* 3.5 28.3 - - + -
39A VAL* 3.7 23.6 - - + -
40A VAL 4.2 0.7 - - - -
41A CYS* 4.1 10.3 - - - -
231A VAL* 3.8 22.7 - - + -
234A ALA 3.6 3.9 + - - -
235A SER* 4.0 24.7 - - - +
237A LYS 3.2 17.0 + - - +
239A GLU* 1.3 73.5 - - - +
241A VAL* 1.3 60.4 + - + +
243A ILE* 2.9 12.6 + - + +
244A ILE* 2.9 38.9 + - + +
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Residues in contact with VAL 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27A THR* 4.4 16.8 - - + -
28A LEU* 4.8 13.0 - - + -
31A ALA* 3.7 35.7 - - + -
32A LYS 5.2 2.5 - - - +
238A PRO* 2.9 20.5 + - + +
240A PHE* 1.3 75.5 - - + +
242A ASP* 1.3 61.6 + - - +
244A ILE* 3.5 11.2 - - + +
245A ASN* 3.1 44.9 + - - +
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Residues in contact with ASP 242 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214A GLY* 4.7 15.0 - - - +
217A CYS* 3.6 10.6 - - - -
218A LYS* 4.6 5.2 + - - +
238A PRO 3.8 5.7 - - - +
239A GLU* 2.8 23.9 + - - +
241A VAL* 1.3 85.3 - - - +
243A ILE* 1.3 58.4 + - - +
245A ASN* 3.4 9.6 + - - +
246A ALA* 3.3 14.9 + - - -
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Residues in contact with ILE 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 4.0 7.3 - - - -
8A VAL* 3.7 23.3 - - + +
212A VAL* 3.4 27.1 - - + +
213A THR 4.0 8.5 - - - +
214A GLY 4.4 0.7 - - - +
217A CYS* 3.8 21.8 - - + -
229A PHE* 4.1 13.5 - - + -
231A VAL* 3.9 18.6 - - + -
234A ALA* 3.9 18.4 - - + -
239A GLU* 3.5 19.3 - - + +
240A PHE* 2.9 14.3 + - + +
242A ASP* 1.3 75.9 - - - +
244A ILE* 1.3 65.3 + - - +
246A ALA* 2.9 20.1 + - - +
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Residues in contact with ILE 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 3.7 17.0 - - - -
8A VAL* 4.0 14.4 - - + -
28A LEU* 4.4 8.3 - - + -
31A ALA* 5.8 2.9 - - + -
32A LYS 4.6 2.2 - - - +
33A VAL* 4.2 10.3 - - + -
34A PRO* 3.9 20.2 - - + +
37A THR* 4.4 3.7 - - - +
39A VAL* 3.7 36.6 - - + -
59A ILE* 5.6 1.6 - - + -
240A PHE* 2.9 44.2 + - + +
241A VAL* 3.5 19.3 - - + +
243A ILE* 1.3 73.6 - - - +
245A ASN* 1.3 72.2 + - - +
246A ALA 3.1 4.3 + - - -
247A LYS* 4.4 0.7 + - - +
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Residues in contact with ASN 245 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A LYS* 3.6 13.1 + - - +
34A PRO* 3.1 33.2 - - - +
218A LYS* 5.0 1.6 - - - +
241A VAL* 3.1 30.6 + - - +
242A ASP* 3.4 10.5 + - - +
243A ILE 3.2 0.6 - - - -
244A ILE* 1.3 77.0 - - - +
246A ALA* 1.3 63.3 + - - +
247A LYS 2.9 5.0 + - - -
248A GLN* 3.1 30.8 + - + +
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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