Contacts of the helix formed by residues 246 - 253 (chain A) in PDB entry 2HDH
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 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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214A TYR* 3.4 28.5 - - + +
215A LEU* 3.7 16.9 - - + +
218A ALA* 3.5 25.1 - - + -
232A ILE* 3.5 24.9 - - + -
233A ASP* 3.4 13.7 - - - +
236A MSE 3.8 15.5 - - + -
244A MSE 3.8 0.6 - - - +
245A GLY* 1.3 81.5 - - - +
247A PHE* 1.3 57.5 + - + +
249A LEU* 4.6 1.8 - - + -
250A LEU* 2.9 34.7 + - - +
210B LEU* 5.1 0.4 - - + -
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Residues in contact with PHE 247 (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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218A ALA* 3.6 15.5 - - + -
219A ILE* 4.0 16.2 - - + -
222A TYR* 3.5 31.9 - + + -
229A LYS* 3.8 22.2 - - + -
232A ILE* 3.8 28.7 - - + -
233A ASP* 2.9 20.3 + - - +
246A PRO* 1.3 75.5 - - + +
248A GLU* 1.3 65.5 + - - +
250A LEU* 3.8 8.8 - - + +
251A ASP* 3.2 28.4 + - - +
298A PHE* 3.7 40.4 - + + -
299A TYR* 3.5 22.2 - - + -
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Residues in contact with GLU 248 (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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233A ASP* 3.1 22.2 - - - +
237A LYS* 3.3 28.9 + - - +
243A PRO 4.7 0.2 - - - +
244A MSE 3.5 20.1 - - + +
245A GLY 2.7 28.6 + - - +
247A PHE* 1.3 76.3 - - - +
249A LEU* 1.3 60.1 + - - +
251A ASP* 3.4 4.0 + - - +
252A TYR* 2.9 28.6 + - - +
292A LYS* 5.4 1.4 - - - +
299A TYR* 4.3 7.9 - - + -
301A TYR* 4.5 10.3 + - + +
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Residues in contact with LEU 249 (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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211A LEU* 3.8 35.2 - - + -
214A TYR* 5.5 2.5 - - + -
215A LEU* 4.2 13.0 - - + -
244A MSE 3.2 41.0 - - + +
245A GLY 3.0 14.9 + - - +
246A PRO* 3.9 5.2 - - + +
248A GLU* 1.3 75.5 - - - +
250A LEU* 1.3 65.3 + - - +
252A TYR* 3.1 7.4 + - + +
253A VAL* 2.9 46.0 + - + +
240B ALA* 6.0 3.6 - - + +
242B TYR* 5.9 3.4 - - + +
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Residues in contact with LEU 250 (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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215A LEU* 3.8 35.6 - - + +
218A ALA* 5.6 0.2 - - + -
219A ILE* 3.5 30.3 - - + -
246A PRO* 2.9 26.1 + - + +
247A PHE* 3.8 11.4 - - + +
248A GLU 3.3 0.2 - - - -
249A LEU* 1.3 76.1 - - - +
251A ASP* 1.3 57.6 + - - +
253A VAL* 3.5 5.6 - - - +
254A GLY 3.0 33.3 + - - -
255A LEU* 3.7 16.1 - - + +
258A THR* 4.0 27.4 - - + +
281A LEU* 5.6 0.4 - - + -
298A PHE* 3.4 23.3 - - + -
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Residues in contact with ASP 251 (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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247A PHE 3.2 12.0 + - - +
248A GLU 3.7 2.7 - - - +
250A LEU* 1.3 79.4 - - - +
252A TYR* 1.3 61.0 + - - +
254A GLY* 3.8 4.7 + - - -
255A LEU* 3.6 4.1 - - - +
290A PHE 4.1 0.5 - - - +
291A GLY* 3.6 10.5 - - - -
292A LYS* 3.1 24.1 + - + +
293A LYS* 4.8 1.9 + - - +
297A GLY* 3.2 12.3 - - - -
298A PHE* 2.8 41.6 + - - -
299A TYR* 3.1 15.6 + - - -
301A TYR* 2.4 36.8 + - + +
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Residues in contact with TYR 252 (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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161A ASN* 4.3 22.7 + - - -
162A PRO* 3.9 22.3 - - - +
244A MSE 3.7 32.1 - - + -
248A GLU 2.9 18.0 + - - +
249A LEU* 3.1 15.7 + - + +
251A ASP* 1.3 79.0 - - - +
253A VAL* 1.3 67.0 + - + +
292A LYS* 4.1 28.5 - - + +
293A LYS* 5.8 3.5 - - - +
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Residues in contact with VAL 253 (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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211A LEU* 5.9 5.6 - - + -
215A LEU* 5.0 8.7 - - + -
249A LEU* 2.9 43.7 + - + +
250A LEU* 3.5 9.6 - - - +
252A TYR* 1.3 82.5 - - + +
254A GLY* 1.3 60.1 + - - +
257A THR* 3.5 23.8 + - + +
258A THR* 3.6 18.6 - - - +
293A LYS* 5.3 3.5 + - - +
350A NAD 4.9 8.0 + - - +
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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