Contacts of the helix formed by residues 236 - 242 (chain A) in PDB entry 2HVY
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 236 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A ILE* 3.8 26.6 + - + +
230A TRP* 3.7 26.0 + - + +
234A GLY 3.4 5.0 + - - +
235A ILE* 1.3 72.5 - - - +
237A GLU* 1.3 68.4 + - - +
238A TYR 3.3 1.7 + - - -
239A PHE* 3.3 3.7 + - - +
240A ARG* 2.9 61.9 + - - +
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Residues in contact with GLU 237 (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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235A ILE* 3.6 27.1 - - + +
236A GLU* 1.3 87.0 + - - +
238A TYR* 1.3 72.2 + - + +
240A ARG* 3.6 8.4 + - - +
241A LYS* 3.2 38.9 + - - +
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Residues in contact with TYR 238 (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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226A TYR* 3.4 54.0 - + + +
229A PHE* 4.4 7.6 - + + -
235A ILE* 3.7 25.5 + - + +
236A GLU 3.3 0.4 - - - -
237A GLU* 1.3 84.4 - - + +
239A PHE* 1.3 59.4 + - - +
241A LYS* 3.4 12.9 + - + +
242A ALA 3.2 19.9 + - - -
53C LEU* 3.9 41.2 + - + +
55C ILE* 3.8 24.3 - - + +
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Residues in contact with PHE 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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43A ILE* 4.4 5.8 - - + -
47A ILE* 3.6 23.6 - - + -
73A LEU* 3.9 17.5 - - + -
223A LEU* 3.9 25.8 - - + -
226A TYR* 3.5 18.0 + - + +
227A TYR* 3.6 42.8 - + + -
230A TRP* 3.6 32.8 - + + -
235A ILE 5.0 0.4 + - - -
236A GLU 3.3 6.0 + - - +
238A TYR* 1.3 76.0 - - - +
240A ARG* 1.3 66.0 + - - +
242A ALA* 3.3 18.8 + - + +
243A ILE* 3.6 34.8 + - + +
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Residues in contact with ARG 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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38A PRO 4.3 9.5 + - - -
39A GLU* 4.5 7.9 + - - +
41A ARG 2.5 30.1 + - - -
42A PRO* 3.3 2.2 - - - +
43A ILE* 3.1 39.0 - - + +
46A HIS* 3.1 35.0 + - + +
236A GLU* 2.9 38.5 + - - +
237A GLU* 3.7 8.7 - - - +
238A TYR 3.3 0.2 - - - -
239A PHE* 1.3 76.6 - - - +
241A LYS* 1.3 61.4 + - + +
243A ILE 2.9 24.3 + - - +
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Residues in contact with LYS 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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216A THR* 4.8 7.4 - - - +
226A TYR* 6.1 1.3 - - + -
237A GLU* 3.2 26.0 + - + +
238A TYR* 3.7 11.7 - - + +
239A PHE 3.3 0.2 - - - -
240A ARG* 1.3 77.3 - - + +
242A ALA* 1.3 58.8 + - - +
243A ILE 3.2 3.1 - - - -
244A GLN* 3.2 21.5 + - - +
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Residues in contact with ALA 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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52A ILE* 3.7 25.5 - - - +
53A ASN 4.4 1.2 + - - -
216A THR 4.9 1.2 - - - +
218A ILE* 3.6 36.0 - - + +
223A LEU* 4.1 17.0 - - + -
226A TYR* 4.4 2.7 - - + -
238A TYR 3.2 11.5 + - - +
239A PHE* 3.4 20.4 - - + +
240A ARG 3.2 0.6 - - - -
241A LYS* 1.3 77.1 - - - +
243A ILE* 1.3 59.0 + - + +
244A GLN* 4.2 3.9 + - - -
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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