Contacts of the helix formed by residues 319 - 323 (chain B) in PDB entry 3MYV
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 319 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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313B MSE 3.5 18.9 - - + +
316B ASP* 2.9 32.6 + - - +
317B PRO 4.0 1.2 - - - +
318B GLY* 1.3 75.2 - - - +
320B VAL* 1.3 64.5 + - - +
321B ARG* 2.8 53.1 + - - +
322B GLY* 3.1 13.0 + - - -
323B HIS* 3.4 10.4 + - - -
390B VAL 4.8 0.5 - - - +
393B GLY 3.2 14.9 - - - +
394B ASN* 3.8 6.7 + - + +
397B ASN* 4.5 2.9 + - - -
415B LYS* 4.8 4.2 + - - +
512B EDO 4.5 0.5 + - - -
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Residues in contact with VAL 320 (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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332A GLY* 3.8 8.5 - - - +
257B HIS* 3.5 44.4 - - + +
260B TYR* 3.7 36.7 - - + -
261B VAL* 4.1 10.9 - - + +
319B ASP* 1.3 71.3 + - - +
321B ARG* 1.3 67.2 + - + +
322B GLY 3.2 0.2 - - - -
323B HIS* 3.0 42.2 + - + +
324B LEU* 4.0 2.6 + - - +
392B ARG* 3.9 7.4 - - - +
393B GLY* 3.0 18.7 + - - +
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Residues in contact with ARG 321 (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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260B TYR* 3.5 29.8 - - + +
309B TYR* 4.2 9.4 + - - +
313B MSE 3.8 12.0 - - + +
319B ASP* 2.8 41.1 + - - +
320B VAL* 1.3 79.3 - - + +
322B GLY* 1.3 59.5 + - - +
323B HIS 3.4 0.3 + - - -
324B LEU* 3.6 19.8 + - + +
325B LEU* 4.7 3.3 + - - +
338B LEU* 5.7 0.7 - - - +
389B ILE* 4.0 5.0 + - - +
390B VAL* 4.4 3.6 + - - +
392B ARG* 5.6 0.4 - - - +
393B GLY* 4.0 17.3 - - - -
412B GLU* 2.8 32.5 + - - -
415B LYS* 3.7 32.6 - - - +
416B GLU* 3.1 47.2 + - - +
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Residues in contact with GLY 322 (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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313B MSE 3.6 29.1 - - - +
314B LEU* 4.4 3.4 - - - +
319B ASP 3.1 11.2 + - - -
321B ARG* 1.3 73.2 - - - +
323B HIS* 1.3 55.2 + - - +
324B LEU 3.1 5.8 - - - -
325B LEU* 3.1 32.9 + - - +
512B EDO 3.5 18.5 + - - -
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Residues in contact with HIS 323 (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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329A LYS* 3.4 35.9 + - + +
330A TYR* 5.5 0.8 - - - -
331A ALA 5.5 0.4 + - - -
332A GLY* 4.6 12.5 + - - -
261B VAL* 3.8 18.2 - - + +
317B PRO 2.8 22.5 + - - -
318B GLY 4.2 4.7 - - - -
319B ASP 3.4 10.1 + - - -
320B VAL* 3.0 43.2 + - + +
322B GLY* 1.3 77.1 - - - +
324B LEU* 1.3 57.7 + - - +
325B LEU 3.2 7.5 + - - +
326B GLU* 4.8 4.7 - - - +
342B ARG* 4.5 7.3 + - - -
512B EDO 3.2 26.5 - - - -
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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