Contacts of the helix formed by residues 359 - 368 (chain A) in PDB entry 3T79
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 HIS 359 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118A TRP* 3.7 29.9 + + - -
120A PRO* 4.0 7.6 - - + +
133A CYS* 3.7 30.6 - - + +
137A LEU* 4.1 14.3 - - + +
204A VAL* 4.0 22.4 - - + -
208A LEU* 4.8 3.1 - - + -
352A LEU* 4.4 17.9 - - + -
356A PHE* 3.0 20.0 + - + +
357A PRO 3.2 1.4 - - - -
358A THR* 1.3 80.8 + - - +
360A ASP* 1.3 78.9 + - + +
361A ILE* 3.1 19.0 + - + +
362A PHE* 3.1 30.3 + - + +
363A LEU* 3.8 6.1 - - - +
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Residues in contact with ASP 360 (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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120A PRO* 5.1 1.4 - - - +
132A THR* 4.4 3.3 - - - -
133A CYS* 3.4 40.9 + - + +
208A LEU* 4.1 13.7 - - + +
213A VAL* 4.4 9.3 - - + +
217A TYR* 3.4 34.7 + - + -
358A THR 4.5 4.0 - - - +
359A HIS* 1.3 76.1 + - - +
361A ILE* 1.3 63.8 + - - +
363A LEU* 2.9 34.0 + - - +
364A ASP 4.1 1.7 + - - -
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Residues in contact with ILE 361 (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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204A VAL* 4.0 24.5 - - + -
207A TYR* 3.8 31.0 - - + -
208A LEU* 4.8 8.9 - - + +
213A VAL* 5.3 3.8 - - - -
325A LEU* 5.5 0.4 - - + -
345A LEU* 4.5 8.3 - - + -
349A LEU* 4.1 27.1 - - + -
352A LEU* 4.3 6.1 - - + -
359A HIS* 3.1 19.5 + - + +
360A ASP* 1.3 77.6 - - - +
362A PHE* 1.3 97.7 + - + +
363A LEU 3.1 1.1 + - - -
364A ASP* 3.5 17.5 + - - +
367A LEU* 3.8 12.1 - - + +
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Residues in contact with PHE 362 (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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349A LEU* 4.1 15.3 - - + -
352A LEU* 3.8 13.0 - - + -
353A TYR* 3.2 57.2 - + + -
356A PHE 3.2 21.3 - - - -
357A PRO* 3.5 24.0 - - + +
359A HIS* 3.1 21.4 + - + +
360A ASP 3.1 0.4 + - - -
361A ILE* 1.3 89.2 - - + +
363A LEU* 1.3 63.7 + - + +
364A ASP 3.3 6.2 + - - +
367A LEU* 4.5 12.7 - - + +
368A LYS* 3.3 19.2 + - - +
376A LEU* 3.9 19.3 - - + -
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Residues in contact with LEU 363 (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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213A VAL* 5.2 1.6 - - + -
216A TYR* 3.8 52.7 + - + +
217A TYR* 5.8 2.9 - - + +
357A PRO 5.1 4.5 - - - +
358A THR* 5.1 7.0 - - - +
359A HIS 3.8 13.2 - - - +
360A ASP* 2.9 28.9 + - - +
362A PHE* 1.3 84.9 - - + +
364A ASP* 1.3 64.3 + - - +
365A PRO* 3.5 4.0 - - - +
368A LYS* 3.9 14.6 + - - +
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Residues in contact with ASP 364 (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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207A TYR* 2.8 14.7 + - + +
211A HIS* 2.2 39.3 + - - -
212A GLY 4.1 2.7 - - - -
213A VAL* 3.4 8.7 - - + +
214A LYS* 2.9 33.8 + - - +
360A ASP 4.1 1.4 + - - -
361A ILE 3.5 13.7 + - - +
362A PHE 3.3 4.4 - - - +
363A LEU* 1.3 80.1 - - - +
365A PRO* 1.3 78.4 - - - +
366A SER* 3.1 8.7 + - - +
367A LEU* 3.2 10.5 + - + +
368A LYS* 3.5 9.8 + - - +
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Residues in contact with PRO 365 (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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214A LYS* 3.7 27.6 - - + +
215A LYS* 6.3 0.7 - - + -
363A LEU 3.5 4.6 - - - +
364A ASP* 1.3 95.4 - - - +
366A SER* 1.3 57.3 + - - +
368A LYS* 2.2 47.4 + - + +
369A THR* 3.4 3.5 + - - +
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Residues in contact with SER 366 (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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207A TYR* 3.7 11.0 + - - -
211A HIS* 4.1 10.1 - - - -
214A LYS* 5.7 0.7 - - - -
325A LEU* 5.8 2.6 - - - +
364A ASP* 3.0 19.8 - - - -
365A PRO* 1.3 81.6 - - - +
367A LEU* 1.3 51.4 - - - +
369A THR* 2.7 32.5 - - - +
372A ASN* 2.7 20.6 + - - -
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Residues in contact with LEU 367 (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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207A TYR* 3.6 31.0 - - + +
325A LEU* 4.1 25.8 - - + -
349A LEU* 4.2 11.0 - - + -
361A ILE* 3.8 26.5 - - + +
362A PHE* 4.5 14.4 - - + +
364A ASP* 3.2 11.1 + - + +
365A PRO 3.0 1.0 - - - -
366A SER* 1.3 79.4 - - - +
368A LYS* 1.3 59.7 + - - +
369A THR 3.4 1.3 + - - -
372A ASN* 3.7 27.7 - - + +
373A ILE* 3.9 12.0 + - - +
375A PHE* 4.8 2.7 - - + -
376A LEU* 4.1 29.7 - - + +
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Residues in contact with LYS 368 (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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362A PHE 3.3 21.8 + - - +
363A LEU* 3.9 19.6 + - - +
364A ASP 3.5 11.7 - - - +
365A PRO* 2.2 37.2 + - + +
367A LEU* 1.3 68.1 - - - +
369A THR* 1.3 66.5 + - - +
370A PRO* 3.7 0.7 - - - +
373A ILE* 4.6 10.8 - - + +
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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