Contacts of the helix formed by residues 245 - 253 (chain A) in PDB entry 3IH9
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 ALA 245 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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242A MET* 2.9 17.4 + - + +
244A ASP* 1.3 77.0 - - - +
246A ALA* 1.3 57.3 + - - +
247A GLY 3.2 3.7 + - - -
248A GLN* 3.2 13.2 + - + +
249A TRP* 2.9 29.1 + - + +
285A VAL* 6.4 2.0 - - + -
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Residues in contact with ALA 246 (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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91A PRO* 5.4 0.9 - - + -
238A THR 3.9 10.6 - - - +
239A SER* 3.3 29.8 - - - +
242A MET* 3.4 18.6 + - - +
243A TYR 3.2 19.0 + - - +
244A ASP 3.3 1.0 - - - -
245A ALA* 1.3 77.3 - - - +
247A GLY* 1.3 57.6 + - - +
249A TRP* 3.7 3.1 - - - +
250A LEU* 2.8 30.5 + - - +
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Residues in contact with GLY 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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244A ASP 4.8 2.6 + - - -
245A ALA 3.2 0.8 - - - -
246A ALA* 1.3 75.1 - - - +
248A GLN* 1.3 66.8 + - - +
250A LEU* 3.0 16.5 + - - +
251A ALA* 3.0 14.7 + - - +
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Residues in contact with GLN 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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245A ALA* 3.2 15.3 + - + +
247A GLY* 1.3 74.5 - - - +
249A TRP* 1.3 58.5 + - - +
251A ALA* 3.2 6.3 + - - +
252A ASP* 2.9 50.0 + - - +
296A ARG* 5.7 3.6 - - - +
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Residues in contact with TRP 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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238A THR* 5.4 8.1 - - + -
242A MET* 3.6 37.3 - - + +
245A ALA* 2.9 18.2 + - + +
246A ALA* 3.8 5.8 - - - +
248A GLN* 1.3 77.0 - - - +
250A LEU* 1.3 69.9 + - + +
252A ASP* 4.7 1.3 - - - +
253A VAL* 3.1 51.4 + - + +
254A GLY 3.1 7.4 + - - -
255A ILE* 2.9 32.0 + - + +
256A PRO* 5.8 0.7 - - + -
257A ALA* 3.8 19.1 - - + +
265A VAL* 5.7 0.7 - - + -
292A VAL* 3.6 39.7 - - + -
295A CYS* 3.8 25.8 - - + -
296A ARG* 4.8 9.9 - - - +
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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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238A THR* 4.0 29.4 - - + +
246A ALA 2.8 21.7 + - - +
247A GLY* 3.0 8.5 + - - +
249A TRP* 1.3 77.8 - - + +
251A ALA* 1.3 59.3 + - + +
254A GLY* 3.1 23.7 + - - +
255A ILE 6.3 0.2 - - - -
305A HIS* 3.0 27.2 + - + -
306A LEU* 4.3 13.9 - - + -
307A MET* 3.9 27.1 - - + -
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Residues in contact with ALA 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 GLY 3.0 11.0 + - - +
248A GLN* 3.8 7.9 - - - +
249A TRP 3.2 0.2 - - - -
250A LEU* 1.3 79.4 - - + +
252A ASP* 1.3 62.6 + - - +
305A HIS* 3.2 19.7 + - - -
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Residues in contact with ASP 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 GLN* 2.9 46.6 + - - +
249A TRP* 5.3 0.4 - - - -
251A ALA* 1.3 75.4 - - - +
253A VAL* 1.4 60.5 + - + +
296A ARG* 4.2 36.4 + - - +
299A SER* 4.4 4.9 + - - -
300A GLU* 4.5 10.9 - - - +
305A HIS* 4.8 1.6 - - - -
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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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249A TRP* 3.1 51.2 + - + +
252A ASP* 1.4 78.0 - - + +
254A GLY* 1.3 61.8 + - - +
255A ILE* 3.6 25.5 - - + +
295A CYS* 3.6 23.3 - - + +
296A ARG* 3.8 31.6 - - + +
299A SER* 2.6 26.0 + - - -
304A LEU 3.7 1.2 - - - +
305A HIS* 3.3 7.7 - - - -
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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