Contacts of the helix formed by residues 359 - 368 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118D TRP* 3.8 36.7 + + - -
120D PRO* 4.1 9.6 - - + +
133D CYS* 3.7 28.8 - - + +
137D LEU* 4.3 5.6 - - + +
204D VAL* 4.0 23.6 - - + -
208D LEU* 4.2 5.8 - - + -
352D LEU* 4.4 21.8 - - + -
356D PHE* 3.4 21.6 + - + +
357D PRO 2.9 4.6 + - - +
358D THR* 1.3 82.2 + - - +
360D ASP* 1.3 77.2 + - - +
361D ILE* 3.1 16.2 + - + +
362D PHE* 3.1 22.6 + - + -
363D LEU* 3.4 7.6 - - - +
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Residues in contact with ASP 360 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120D PRO* 5.7 0.2 - - - +
132D THR* 4.0 6.8 + - - -
133D CYS* 3.0 42.8 + - + +
134D GLN 4.4 1.6 + - - -
208D LEU* 4.0 19.4 - - + +
213D VAL* 4.0 12.9 - - + +
358D THR 4.5 3.5 - - - +
359D HIS* 1.3 76.0 + - - +
361D ILE* 1.3 63.7 + - - +
363D LEU* 2.9 34.5 + - + +
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Residues in contact with ILE 361 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D VAL* 4.1 18.6 - - + -
207D TYR* 3.7 32.0 - - + -
208D LEU* 4.1 15.0 - - + +
213D VAL* 4.9 3.4 - - - -
325D LEU* 5.8 1.3 - - + -
345D LEU* 4.3 11.4 - - + -
349D LEU* 4.2 24.5 - - + -
352D LEU* 4.6 5.8 - - + -
359D HIS* 3.1 15.2 + - + +
360D ASP* 1.3 79.4 - - - +
362D PHE* 1.3 98.3 + - + +
363D LEU 3.1 1.3 + - - -
364D ASP* 3.5 17.0 + - - +
367D LEU* 4.0 12.2 - - + +
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Residues in contact with PHE 362 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349D LEU* 4.0 15.7 - - + -
352D LEU* 3.9 10.8 - - + -
353D TYR* 3.3 57.0 - + + -
356D PHE 3.2 19.7 - - - -
357D PRO* 2.9 29.4 - - + +
359D HIS* 3.1 11.2 + - + +
360D ASP 3.1 1.4 - - - -
361D ILE* 1.3 99.5 - - + +
363D LEU* 1.3 61.9 + - + +
364D ASP 3.3 1.9 - - - +
367D LEU* 4.4 9.2 - - + +
368D LYS* 3.2 30.9 + - - +
376D LEU* 3.7 20.2 - - + -
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Residues in contact with LEU 363 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213D VAL* 4.7 3.4 - - + -
216D TYR* 3.5 56.8 + - + +
357D PRO 5.0 1.1 - - - +
358D THR* 4.1 11.9 - - - +
359D HIS 3.4 20.4 - - - +
360D ASP* 2.9 23.8 + - + +
362D PHE* 1.3 82.8 - - + +
364D ASP* 1.3 63.3 + - - +
365D PRO* 3.6 3.5 - - - +
368D LYS* 4.2 14.3 - - - +
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Residues in contact with ASP 364 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D TYR* 3.1 10.7 + - + +
211D HIS* 2.3 44.4 + - - -
212D GLY 4.4 2.2 - - - -
213D VAL* 4.5 10.4 - - + +
214D LYS* 2.8 29.3 + - - +
360D ASP 4.1 1.8 + - - -
361D ILE 3.5 12.4 + - - +
362D PHE 3.3 1.2 - - - -
363D LEU* 1.3 78.8 - - - +
365D PRO* 1.3 73.5 - - - +
366D SER* 3.0 10.7 + - - +
367D LEU* 3.2 11.8 + - + +
368D LYS* 2.9 15.0 - - - +
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Residues in contact with PRO 365 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214D LYS* 3.4 37.7 - - + +
215D LYS* 6.1 1.3 - - + -
363D LEU 3.6 5.3 - - - +
364D ASP* 1.3 98.7 - - - +
366D SER* 1.3 56.7 + - - +
368D LYS* 2.2 46.2 + - + +
369D THR* 3.4 5.0 + - - +
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Residues in contact with SER 366 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D TYR* 3.7 11.4 - - - -
211D HIS* 3.4 10.5 - - - -
325D LEU* 6.3 1.1 - - - -
364D ASP* 3.0 20.3 + - - -
365D PRO* 1.3 79.7 - - - +
367D LEU* 1.3 54.2 + - - +
369D THR* 3.0 23.5 + - - +
372D ASN* 2.7 28.6 + - - -
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Residues in contact with LEU 367 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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207D TYR* 3.4 32.8 - - + +
325D LEU* 4.6 16.6 - - + -
349D LEU* 4.5 17.5 - - + -
361D ILE* 4.0 24.7 - - + +
362D PHE* 4.4 13.9 - - + +
364D ASP* 3.2 10.7 + - + +
365D PRO 2.9 1.0 - - - -
366D SER* 1.3 79.5 - - - +
368D LYS* 1.3 56.6 - - - +
369D THR 3.3 2.8 + - - -
372D ASN* 3.7 29.6 - - + +
373D ILE* 3.4 18.5 + - - +
375D PHE* 5.7 1.6 - - + -
376D LEU* 4.1 26.1 - - + +
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Residues in contact with LYS 368 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D PHE* 3.2 29.8 + - - +
363D LEU* 4.2 16.0 - - - +
364D ASP 2.9 16.8 - - - +
365D PRO* 2.2 36.1 + - + +
367D LEU* 1.3 66.9 - - - +
369D THR* 1.3 56.6 + - - +
370D PRO* 3.8 1.6 - - - +
373D ILE* 3.0 25.1 - - + +
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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