Contacts of the helix formed by residues 331 - 337 (chain A) in PDB entry 1B70
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 ASP 331 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A ALA* 2.9 19.0 - - + -
324A MET* 4.3 3.1 - - - -
329A ILE* 3.8 4.6 - - - +
330A PRO* 1.3 83.8 - - + +
332A ILE* 1.3 55.6 + - - +
333A ARG* 2.8 53.4 + - - +
334A TYR* 2.8 58.0 + - + +
335A PHE* 4.4 0.3 + - - -
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Residues in contact with ILE 332 (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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209A ASP 3.3 22.9 - - - +
210A ALA 3.1 15.5 + - - +
211A THR* 3.6 14.1 - - - +
212A HIS 3.5 13.7 - - - +
213A GLU* 4.1 29.1 - - + +
216A PHE* 5.4 2.7 - - + -
320A GLU* 3.7 36.8 - - + -
321A ARG* 5.1 4.7 - - - -
324A MET* 3.7 26.1 - - + -
331A ASP* 1.3 68.5 - - - +
333A ARG* 1.3 67.3 + - - +
334A TYR 3.0 0.6 + - - -
335A PHE* 3.4 20.4 + - + +
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Residues in contact with ARG 333 (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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208A THR* 3.8 25.4 + - + -
209A ASP* 2.9 34.1 - - - +
210A ALA* 3.4 23.8 - - - +
213A GLU* 4.0 10.0 - - - +
331A ASP* 2.8 35.7 + - - +
332A ILE* 1.3 77.7 - - + +
334A TYR* 1.3 62.9 + - - +
335A PHE 3.0 1.4 + - - -
336A PHE* 3.2 12.8 + - - +
337A GLY* 3.3 9.0 + - - -
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Residues in contact with TYR 334 (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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329A ILE* 4.1 2.9 - - + -
330A PRO* 4.0 21.0 - - + +
331A ASP* 2.8 53.1 + - + +
333A ARG* 1.3 78.5 - - - +
335A PHE* 1.3 60.0 + - - +
337A GLY* 3.3 22.0 + - - +
339A ARG* 6.0 8.5 - - + -
342A PHE* 3.4 47.7 - + + -
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Residues in contact with PHE 335 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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101A HIS* 3.1 44.5 - - - +
102A PRO* 4.0 26.2 - - + -
103A ILE* 4.1 13.9 - - + -
320A GLU* 3.6 29.6 - - + +
323A ALA* 4.1 13.7 - - + -
324A MET* 3.5 36.8 - - + -
329A ILE* 4.0 22.2 - - + -
331A ASP 4.8 0.2 - - - -
332A ILE* 3.4 22.4 + - - +
333A ARG 3.0 0.8 + - - -
334A TYR* 1.3 78.0 - - - +
336A PHE* 1.3 66.4 + - + +
337A GLY 3.2 2.5 + - - -
338A GLY* 4.9 0.7 + - - -
342A PHE* 4.2 8.4 - + - -
343A LEU* 5.3 1.2 - - - +
511B TYR* 4.0 6.6 - - + +
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Residues in contact with PHE 336 (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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201A ARG* 3.3 35.0 - - - -
213A GLU* 3.6 22.0 - - - +
215A VAL* 3.2 46.9 - - + -
216A PHE* 4.3 1.6 - - - -
217A HIS* 4.0 13.5 - + - -
320A GLU* 4.6 3.1 - - - -
332A ILE 4.6 0.4 + - - -
333A ARG 3.2 5.8 + - - +
335A PHE* 1.3 83.1 - - + +
337A GLY* 1.3 58.5 + - - +
338A GLY 3.4 5.6 + - - -
511B TYR* 3.8 27.1 - + + +
512B THR* 3.6 22.7 - - - -
513B TYR* 3.1 37.1 - + + -
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Residues in contact with GLY 337 (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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333A ARG 3.3 8.1 + - - -
334A TYR* 3.3 18.7 + - - +
335A PHE 3.2 4.6 - - - -
336A PHE* 1.3 75.5 - - - +
338A GLY* 1.3 51.2 + - - -
339A ARG* 2.3 31.2 + - - +
342A PHE* 4.6 3.3 - - - +
343A LEU* 5.5 0.5 - - - +
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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