Contacts of the helix formed by residues 319 - 328 (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 VAL 319 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103A ILE* 3.9 23.3 - - + +
106A MET* 3.9 22.9 - - + -
107A GLU* 4.7 9.2 - - + +
110A LEU* 4.6 11.2 - - + -
199A PRO* 6.4 0.4 - - + -
217A HIS* 3.2 26.2 + - + +
218A GLN 3.9 21.8 - - - +
219A LEU* 4.1 11.4 - - + +
317A LEU* 4.1 4.7 - - + +
318A GLY* 1.3 71.0 - - - -
320A GLU* 1.3 61.3 + - - +
321A ARG 3.3 0.4 - - - -
322A LEU* 3.2 7.0 + - - +
323A ALA* 2.8 25.8 + - - +
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Residues in contact with GLU 320 (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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103A ILE* 3.8 18.0 - - + +
215A VAL 4.2 2.5 - - - +
216A PHE* 3.1 26.5 - - - +
217A HIS* 2.9 46.6 + - - +
318A GLY* 3.7 0.6 - - - -
319A VAL* 1.3 74.8 - - - +
321A ARG* 1.3 58.1 + - - +
323A ALA* 3.2 2.7 + - - +
324A MET* 2.8 36.7 + - - +
332A ILE* 3.7 25.1 - - + -
335A PHE* 3.6 28.7 - - + +
336A PHE* 4.6 3.8 - - - -
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Residues in contact with ARG 321 (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 THR* 3.9 38.4 + - - +
212A HIS* 5.4 2.8 - - - -
279A GLU 5.5 6.7 - - - +
280A LEU* 5.8 5.2 - - + -
318A GLY* 4.1 13.8 + - - +
319A VAL 3.3 0.2 - - - -
320A GLU* 1.3 80.8 - - - +
322A LEU* 1.3 57.6 + - - +
324A MET* 3.1 35.2 + - - +
325A LEU* 2.9 28.0 + - - +
332A ILE* 5.1 5.2 - - - -
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Residues in contact with LEU 322 (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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106A MET* 3.8 15.7 - - + -
110A LEU* 3.6 41.3 - - + -
244A LEU* 3.9 25.4 - - + -
245A PHE* 4.5 15.7 - - + -
278A LEU* 5.9 2.0 - - + -
280A LEU* 4.4 25.3 - - + +
317A LEU* 5.9 4.3 - - + -
318A GLY 3.9 9.8 + - - +
319A VAL* 3.2 6.9 + - - +
321A ARG* 1.3 76.8 - - - +
323A ALA* 1.3 56.0 + - - +
325A LEU* 3.2 10.6 + - + +
326A ARG* 2.6 42.6 + - + +
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Residues in contact with ALA 323 (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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102A PRO 4.8 1.8 - - - +
103A ILE* 4.7 4.9 - - + -
106A MET* 3.7 32.0 - - + -
319A VAL 2.8 21.0 + - - +
320A GLU* 3.5 7.0 - - - +
322A LEU* 1.3 72.6 - - - +
324A MET* 1.3 58.1 + - - +
327A TYR* 2.8 43.0 + - + +
329A ILE* 3.6 2.1 - - - +
335A PHE* 4.1 16.8 - - + -
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Residues in contact with MET 324 (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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210A ALA 4.9 1.1 - - - +
211A THR* 5.4 3.8 - - + -
320A GLU 2.8 16.4 + - - +
321A ARG* 3.2 57.7 - - - +
323A ALA* 1.3 74.4 - - - +
325A LEU* 1.3 60.5 + - - +
328A GLY* 2.9 12.5 + - - -
329A ILE* 2.8 50.4 + - + +
330A PRO 4.8 4.5 - - - +
331A ASP 4.3 2.5 - - - -
332A ILE* 3.7 42.2 - - + -
335A PHE* 3.5 17.5 - - + -
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Residues in contact with LEU 325 (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 PHE* 4.4 12.8 - - + -
271A TRP* 3.8 48.7 - - + +
276A LYS* 5.9 1.1 - - + -
278A LEU* 3.2 43.1 - - + -
321A ARG 2.9 11.8 + - - +
322A LEU* 3.6 13.0 - - + +
324A MET* 1.3 77.1 - - - +
326A ARG* 1.3 68.9 + - - +
328A GLY* 3.6 5.2 + - - -
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Residues in contact with ARG 326 (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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106A MET* 3.9 18.4 - - - -
109A GLU* 3.3 34.9 + - - -
243A ALA 5.3 0.4 + - - -
244A LEU* 2.6 40.8 + - - +
245A PHE* 3.5 26.5 - - - -
322A LEU* 2.6 25.9 + - + +
323A ALA 3.8 2.2 - - - +
325A LEU* 1.3 79.0 - - - +
327A TYR* 1.3 76.1 + - + +
328A GLY* 3.0 4.4 + - - -
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Residues in contact with TYR 327 (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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102A PRO* 3.4 39.7 - - + -
105A LEU* 3.3 18.2 + - + +
106A MET* 3.2 33.8 + - + -
109A GLU* 3.5 12.5 + - - +
323A ALA* 2.8 17.8 + - + -
326A ARG* 1.3 93.1 - - + +
328A GLY* 1.3 62.2 + - - +
329A ILE* 3.5 19.0 + - + +
346A PHE* 3.5 22.8 - + + -
349A VAL* 4.4 20.9 - - + +
350A LEU* 5.2 2.6 - - + +
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Residues in contact with GLY 328 (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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324A MET 2.9 13.1 + - - -
325A LEU 4.1 4.5 - - - -
326A ARG 3.0 7.7 + - - -
327A TYR* 1.3 79.7 - - - +
329A ILE* 1.3 58.5 + - - +
330A PRO* 4.1 3.8 - - - +
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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