Contacts of the helix formed by residues 363 - 369 (chain B) in PDB entry 3HI7
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 THR 363 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B GLU* 2.6 32.1 + - - +
237B TRP* 3.3 28.5 - - + -
361B GLY* 3.5 0.6 - - - -
362B HIS* 1.3 106.3 + - + +
364B PRO* 1.3 72.6 - - - +
366B GLY* 3.2 12.1 + - - -
367B MET* 3.0 23.1 + - - +
488B THR* 3.8 12.9 - - - +
489B PHE 4.2 3.8 - - - +
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Residues in contact with PRO 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
542A PRO* 6.3 0.2 - - + -
543A TRP* 3.9 11.7 + - + -
200B TRP* 3.5 32.7 + - + +
218B GLU* 3.3 13.9 - - - +
237B TRP* 3.5 30.1 - - + +
242B PHE* 3.7 26.2 - - + -
362B HIS 4.5 0.7 - - - +
363B THR* 1.3 86.1 - - - +
365B ALA* 1.3 59.1 + - - +
367B MET* 3.5 15.1 + - + +
368B GLN* 3.1 25.3 + - - +
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Residues in contact with ALA 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B VAL* 3.5 7.8 - - + +
200B TRP* 3.9 25.4 - - + -
202B ILE* 3.5 26.2 - - + -
218B GLU* 2.8 33.1 + - + +
364B PRO* 1.3 72.9 - - - +
366B GLY* 1.3 57.4 + - - +
368B GLN* 3.3 10.0 + - - +
369B THR* 2.7 26.8 + - - -
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Residues in contact with GLY 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B TYR* 3.8 17.3 - - - +
360B GLY 3.9 1.9 - - - -
361B GLY* 3.9 7.6 - - - -
363B THR* 3.2 14.8 + - - -
365B ALA* 1.3 78.9 - - - +
367B MET* 1.3 60.9 + - - +
368B GLN 3.2 0.7 + - - -
369B THR* 3.2 15.7 + - - -
486B HIS* 5.2 2.0 - - - -
488B THR* 4.4 6.8 - - - +
508B ASN* 3.8 21.8 - - - -
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Residues in contact with MET 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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539A ILE* 4.5 6.5 - - + -
542A PRO* 3.8 37.9 - - + -
543A TRP* 5.1 5.2 - - - +
549A VAL* 4.0 31.0 - - + +
551A GLN* 3.1 38.1 - - - +
359B TYR 4.6 4.3 - - - +
360B GLY* 4.5 0.7 - - - -
361B GLY 3.5 16.8 - - - +
362B HIS* 3.6 20.2 - - - +
363B THR 3.0 13.5 + - - +
364B PRO* 3.5 15.9 - - + +
366B GLY* 1.3 74.8 - - - +
368B GLN* 1.3 62.8 + - - +
369B THR 3.4 0.4 + - - -
370B LYS* 4.2 12.1 + - - -
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Residues in contact with GLN 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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541A ASN* 5.2 1.4 + - - -
543A TRP* 3.4 28.9 + - - -
549A VAL* 5.8 2.8 - - - +
187B VAL* 3.9 14.6 - - + -
188B ALA 3.6 4.5 - - - +
189B PRO* 2.9 43.8 + - - +
191B GLY 3.0 28.2 + - - +
192B VAL* 5.6 0.3 - - - +
198B ARG 6.0 0.4 - - - +
200B TRP* 4.2 10.8 - - + +
364B PRO 3.1 17.6 + - - +
365B ALA* 3.4 6.7 - - - +
366B GLY 3.1 0.4 - - - -
367B MET* 1.3 80.3 - - - +
369B THR* 1.3 61.0 + - - +
370B LYS* 3.2 11.5 + - - +
611B GLU* 5.9 0.8 + - - -
644B TRP* 5.3 0.2 - - - -
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Residues in contact with THR 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187B VAL* 3.3 8.9 - - + +
188B ALA 3.6 4.5 - - - +
359B TYR* 3.0 46.8 + - + +
365B ALA 2.7 21.0 + - - -
366B GLY 3.2 10.3 + - - -
367B MET 3.4 0.2 - - - -
368B GLN* 1.3 74.5 - - - +
370B LYS* 1.3 64.8 + - - +
371B TYR* 3.3 47.3 - - + -
486B HIS* 3.1 18.6 + - - +
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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