Contacts of the helix formed by residues 361 - 369 (chain B) in PDB entry 4YC3
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 361 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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359B GLU* 3.0 23.9 + - - +
360B TRP* 1.3 74.4 - - - +
362B PRO* 1.3 69.9 - - + +
363B THR* 3.7 10.1 + - - -
364B LEU* 3.2 32.6 + - + +
365B GLN* 3.0 29.3 + - - +
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Residues in contact with PRO 362 (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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360B TRP 4.6 1.8 - - - +
361B THR* 1.3 89.5 - - + +
363B THR* 1.3 57.9 + - - +
365B GLN* 3.4 10.5 + - + +
366B HIS* 2.8 31.1 + - - +
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Residues in contact with THR 363 (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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311B ILE* 3.9 18.2 - - + -
361B THR* 3.2 10.4 + - - -
362B PRO* 1.3 79.5 - - - +
364B LEU* 1.3 62.9 + - - +
366B HIS* 3.3 4.4 + - - +
367B TYR* 3.0 47.7 + - + -
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Residues in contact with LEU 364 (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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308B ALA 4.3 6.7 - - - +
311B ILE* 4.3 22.2 - - + -
312B GLY* 5.4 2.5 - - - +
348B PHE* 3.9 20.6 - - + -
352B LEU* 4.0 17.9 - - + -
359B GLU 4.2 2.7 - - - +
360B TRP* 3.9 30.5 - - + +
361B THR* 3.2 31.8 + - + +
363B THR* 1.3 81.4 - - - +
365B GLN* 1.3 57.8 + - - +
367B TYR* 5.1 0.9 - - - -
368B LEU* 2.8 52.6 + - + +
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Residues in contact with GLN 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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360B TRP* 3.2 24.1 - - + +
361B THR 3.0 15.3 + - - +
362B PRO* 3.8 8.7 - - - +
364B LEU* 1.3 76.4 - - - +
366B HIS* 1.3 57.3 - - - +
369B SER* 2.8 29.2 + - - -
370B TYR 3.6 10.8 - - - +
371B THR* 3.8 29.9 - - + +
372B GLU 4.5 1.0 + - - -
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Residues in contact with HIS 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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362B PRO 2.8 19.3 + - - +
363B THR* 3.5 7.0 - - - +
365B GLN* 1.3 80.7 - - - +
367B TYR* 1.3 97.5 + + - +
369B SER* 3.6 11.8 + - - -
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Residues in contact with TYR 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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174B TYR* 3.9 8.0 + - - -
307B ARG* 3.2 41.0 + - - +
311B ILE* 3.5 33.4 - - + -
363B THR* 3.0 43.2 + - + +
366B HIS* 1.3 101.2 + + - +
368B LEU* 1.3 61.7 + - - +
369B SER* 4.9 0.7 + - - -
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Residues in contact with LEU 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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174B TYR* 3.9 8.3 + - - -
178B ARG* 4.6 0.7 + - - -
304B PHE* 4.6 7.2 - - + +
307B ARG* 3.8 19.5 - - - +
308B ALA* 4.1 35.4 - - + +
311B ILE* 4.1 8.3 - - + -
345B ALA* 4.6 19.7 - - + -
348B PHE* 5.1 2.5 - - + -
360B TRP* 3.8 29.2 - - + +
364B LEU* 2.8 36.3 + - + +
367B TYR* 1.3 74.6 - - - +
369B SER* 1.3 71.1 + - - +
370B TYR* 3.3 15.2 - - - -
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Residues in contact with SER 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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174B TYR* 4.5 8.5 + - - -
178B ARG* 4.3 18.3 + - - -
365B GLN 2.8 17.4 + - - -
366B HIS 3.6 8.5 + - - -
367B TYR 3.5 1.1 + - - -
368B LEU* 1.3 79.2 - - - +
370B TYR* 1.3 68.9 + - - +
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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