Contacts of the helix formed by residues 306 - 315 (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 THR 306 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72B ASP 2.7 29.3 + - - +
73B ASP* 3.0 10.1 + - - -
74B MSE 3.7 26.9 - - - +
75B GLN* 3.9 13.0 - - - +
305B VAL* 1.3 79.6 - - - +
307B GLN* 1.3 64.8 + - - +
308B LYS* 3.5 5.4 + - - -
309B TYR 3.1 16.1 + - - -
310B ALA* 3.0 18.5 + - - +
440B TYR* 3.5 2.0 - - - -
441B HIS* 3.8 29.2 - - + +
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Residues in contact with GLN 307 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B GLN* 4.9 0.6 + - - -
306B THR* 1.3 75.3 - - - +
308B LYS* 1.3 56.4 + - - +
310B ALA* 3.3 4.6 + - - +
311B GLU* 2.8 60.2 + - + +
334B THR 5.0 1.7 - - - +
336B TRP* 4.4 11.7 - - + -
439B GLY* 3.3 32.8 - - - +
440B TYR* 3.5 33.2 + - + +
441B HIS* 6.1 0.6 - - - -
518B EDO 2.9 30.7 + - - -
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Residues in contact with LYS 308 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B ASP* 2.9 37.2 + - + +
73B ASP* 2.8 30.0 + - - +
306B THR* 3.1 8.4 - - - +
307B GLN* 1.3 78.3 - - - +
309B TYR* 1.3 56.0 + - - +
311B GLU* 3.6 6.7 + - - +
312B GLN* 3.0 40.8 + - - +
411B ASP* 5.5 1.8 + - - -
414B SER* 3.7 7.5 + - - -
423B ARG* 3.3 15.6 - - - +
435B VAL 5.8 1.8 - - - +
441B HIS* 6.1 1.3 - - - +
514B EDO 4.5 9.6 - - - +
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Residues in contact with TYR 309 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73B ASP* 3.4 45.5 - - + +
305B VAL* 3.8 17.5 - - + -
306B THR* 3.1 8.6 + - - +
308B LYS* 1.3 78.0 - - - +
310B ALA* 1.3 65.8 + - - +
312B GLN* 3.2 26.6 + - - +
313B MSE 3.1 45.1 + - + +
321B ARG* 4.2 10.5 + - - +
325B LEU* 3.9 19.1 - - + -
338B LEU* 5.3 0.2 - - + -
414B SER 3.3 21.1 - - - -
415B LYS* 2.8 23.0 + - - -
418B VAL* 3.4 23.0 - - + +
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Residues in contact with ALA 310 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
305B VAL* 4.3 0.9 - - + +
306B THR 3.0 13.4 + - - +
307B GLN 3.8 2.9 - - - +
309B TYR* 1.3 76.3 - - - +
311B GLU* 1.3 52.9 + - + +
313B MSE 3.2 1.2 + - - -
314B LEU* 2.7 47.3 + - + +
325B LEU* 3.9 14.6 - - + -
336B TRP* 3.5 48.7 - - + -
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Residues in contact with GLU 311 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
307B GLN* 2.8 46.6 + - + +
308B LYS* 4.0 5.2 - - - +
310B ALA* 1.3 69.5 - - + +
312B GLN* 1.3 65.8 + - - +
314B LEU* 4.5 2.5 - - - +
315B ALA* 3.2 27.8 + - - +
336B TRP* 6.1 3.1 - - + -
518B EDO 2.7 30.4 + - - -
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Residues in contact with GLN 312 (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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73B ASP* 4.3 3.0 + - - -
308B LYS* 3.0 24.8 + - - +
309B TYR* 3.2 30.3 + - - +
311B GLU* 1.3 77.5 - - - +
313B MSE 1.3 68.9 + - - +
315B ALA* 4.1 9.0 - - - +
316B ASP* 4.5 5.2 + - - +
411B ASP* 3.9 18.9 - - - +
414B SER* 2.9 28.6 + - - -
415B LYS* 3.8 30.7 + - - +
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Residues in contact with MSE 313 (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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309B TYR* 3.1 52.1 + - + +
310B ALA 4.1 1.8 - - - +
312B GLN* 1.3 80.6 - - - +
314B LEU* 1.3 61.6 + - + +
315B ALA 3.2 4.3 - - - -
316B ASP* 2.9 32.9 + - + +
317B PRO* 4.5 0.7 - - - +
319B ASP* 3.5 41.5 - - + +
321B ARG* 3.8 11.4 - - + +
322B GLY* 3.6 25.6 - - - +
325B LEU* 4.3 4.9 - - + -
415B LYS* 3.6 34.8 - - + +
512B EDO 5.0 1.2 + - - -
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Residues in contact with LEU 314 (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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310B ALA* 2.7 31.2 + - + +
311B GLU* 4.8 2.0 - - - +
313B MSE 1.3 69.7 - - + +
315B ALA* 1.3 63.0 + - - +
316B ASP 3.1 1.3 + - - -
317B PRO* 3.8 12.7 - - - +
322B GLY 4.4 9.6 - - - +
325B LEU* 4.4 9.2 - - + -
336B TRP* 3.4 44.9 - - + +
512B EDO 3.5 37.7 - - - +
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Residues in contact with ALA 315 (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 GLU* 3.2 20.3 + - - +
312B GLN* 4.1 7.0 - - - +
314B LEU* 1.3 77.3 - - - +
316B ASP* 1.3 57.9 + - + +
317B PRO* 3.5 7.5 - - - +
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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