Contacts of the helix formed by residues 246 - 259 (chain A) in PDB entry 3PWH
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 TRP 246 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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84A VAL* 4.4 18.2 - - + -
85A LEU* 6.1 1.1 - - + -
88A ALA* 3.6 29.2 - - + -
186A VAL* 5.8 2.7 - - + -
242A PHE* 2.9 56.6 + + + +
243A ALA* 4.3 2.0 - - - +
244A LEU 3.5 0.6 - - - -
245A CYS* 1.3 86.5 + - + +
247A LEU* 1.3 67.2 + - - +
248A PRO* 3.2 3.6 - - - +
249A LEU* 3.1 11.4 + - + +
250A HIS* 2.9 49.1 + + + +
277A ALA* 3.7 36.8 - - + -
278A HIS* 6.6 0.4 - + - -
280A ASN* 3.5 23.6 + - + +
401A ZMA 4.1 22.9 - + - -
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Residues in contact with LEU 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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182A PHE* 4.0 27.1 - - + -
186A VAL* 5.8 0.7 - - + -
187A LEU* 5.0 7.0 - - + -
190A LEU* 4.5 16.6 - - + -
243A ALA* 2.9 36.9 + - + +
244A LEU* 5.3 1.8 - - - -
246A TRP* 1.3 76.9 - - + +
248A PRO* 1.3 58.3 - - + +
250A HIS* 3.0 4.9 + - + +
251A ILE* 2.7 53.2 + - + +
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Residues in contact with PRO 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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244A LEU* 3.8 10.5 - - + +
245A CYS 4.4 0.2 - - - -
246A TRP 3.3 11.9 - - - +
247A LEU* 1.3 94.8 - - + +
249A LEU* 1.3 61.7 + - - +
251A ILE* 3.4 9.7 + - + +
252A ILE* 3.1 31.3 + - + +
273A ALA* 4.8 10.3 - - + +
276A LEU* 3.8 25.6 - - + -
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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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246A TRP* 3.1 12.8 + - + +
248A PRO* 1.3 79.4 - - - +
250A HIS* 1.3 63.5 + - + +
252A ILE* 3.5 3.9 - - + +
253A ASN* 3.3 22.9 + - - +
270A MET* 4.0 20.0 - - - -
273A ALA* 4.0 22.6 + - + +
274A ILE* 3.7 40.2 - - + -
277A ALA* 4.7 11.4 - - + -
401A ZMA 3.3 52.5 - - + +
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Residues in contact with HIS 250 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A LEU* 6.3 0.4 - - + -
177A MET* 4.7 2.7 + - + -
181A ASN* 3.6 23.1 - - - -
182A PHE* 3.1 51.7 - + + +
186A VAL* 4.4 15.7 - - + +
246A TRP* 2.9 52.9 + + + +
247A LEU* 3.0 7.7 + - + +
249A LEU* 1.3 75.5 - - + +
251A ILE* 1.3 64.8 + - - +
253A ASN* 3.0 12.6 + - - +
254A CYS* 3.0 27.4 + - - -
401A ZMA 4.1 18.7 - + - -
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Residues in contact with ILE 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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182A PHE* 5.6 4.7 - - + -
247A LEU* 2.7 42.9 + - + +
248A PRO* 3.7 7.6 - - + +
250A HIS* 1.3 72.9 - - + +
252A ILE* 1.3 59.6 + - + +
254A CYS* 3.0 13.7 + - + +
255A PHE* 2.9 48.2 + - + -
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Residues in contact with ILE 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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248A PRO* 3.1 13.9 + - + +
249A LEU* 3.5 9.2 - - - +
250A HIS 3.2 0.2 - - - -
251A ILE* 1.3 77.0 - - + +
253A ASN* 1.3 60.0 + - - +
255A PHE* 2.9 11.6 + - + +
256A THR* 2.9 29.7 + - - +
265A ALA* 3.5 21.1 - - + -
269A LEU* 4.5 17.5 - - + +
270A MET* 3.4 36.1 - - + -
273A ALA* 3.6 30.7 - - + -
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Residues in contact with ASN 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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174A MET* 3.3 22.0 - - + +
177A MET* 3.8 21.1 + - - +
178A VAL* 4.0 10.9 - - + +
182A PHE* 6.5 0.9 - - + -
249A LEU* 3.3 13.6 + - - +
250A HIS* 3.0 15.3 + - - +
252A ILE* 1.3 80.0 - - - +
254A CYS* 1.3 58.5 + - - +
256A THR* 4.6 2.7 - - - +
257A PHE* 3.0 30.7 + - - +
401A ZMA 3.1 53.9 + - - -
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Residues in contact with CYS 254 (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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178A VAL* 4.7 4.7 - - - -
182A PHE* 3.9 30.5 - - - -
183A PHE* 4.4 6.3 - - - -
250A HIS 3.0 19.2 + - - -
251A ILE* 3.0 13.6 + - + +
253A ASN* 1.3 75.4 - - - +
255A PHE* 1.3 63.9 + - + +
258A PHE* 3.0 59.6 + - + +
259A CYS* 4.0 0.3 + - - +
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Residues in contact with PHE 255 (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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251A ILE* 2.9 33.0 + - + +
252A ILE* 2.9 15.0 + - + +
254A CYS* 1.3 79.5 - - + +
256A THR* 1.3 63.2 + - - +
259A CYS* 2.9 37.9 + - + +
262A CYS* 4.3 17.8 - - + +
263A SER 5.7 7.2 - - - +
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Residues in contact with THR 256 (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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174A MET* 4.7 13.5 - - + -
252A ILE* 2.9 20.3 + - - +
253A ASN* 4.2 6.3 - - - -
255A PHE* 1.3 78.0 - - - +
257A PHE* 1.3 63.3 + - - +
259A CYS 3.8 9.0 - - - +
260A PRO* 4.1 2.6 - - - +
262A CYS 5.6 0.7 - - - -
264A HIS* 3.3 40.0 + - + +
265A ALA* 4.2 15.2 + - - +
270A MET* 5.0 3.5 - - - +
401A ZMA 5.7 4.7 + - - +
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Residues in contact with PHE 257 (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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174A MET* 3.5 32.5 - - + +
175A ASN* 3.5 30.3 - - + -
178A VAL* 4.1 6.7 - - + -
179A TYR* 3.3 41.3 - + - -
253A ASN 3.0 20.9 + - - +
255A PHE 3.2 0.2 - - - -
256A THR* 1.3 79.0 - - - +
258A PHE* 1.3 91.4 + + + +
259A CYS 3.1 1.8 + - - -
260A PRO* 3.8 12.8 - - - +
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Residues in contact with PHE 258 (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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178A VAL* 3.3 28.0 - - + -
179A TYR* 4.0 22.2 - + - -
183A PHE* 3.4 30.5 - + - -
254A CYS* 3.0 41.8 + - + +
257A PHE* 1.3 90.4 - + - +
259A CYS* 1.3 58.2 + - + +
260A PRO* 3.3 8.4 - - - +
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Residues in contact with CYS 259 (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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254A CYS 4.0 0.4 + - - +
255A PHE* 2.9 27.0 + - + +
256A THR* 3.8 4.1 - - - +
258A PHE* 1.3 80.4 - - + +
260A PRO* 1.3 65.9 - - - +
261A ASP* 3.1 21.5 - - - -
262A CYS* 2.0 62.5 + - - +
264A HIS* 5.0 0.2 - - - -
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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