Contacts of the helix formed by residues 410 - 419 (chain D) in PDB entry 3M0V
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 GLY 410 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406D TYR 3.5 1.0 + - - -
407D ARG* 3.1 15.3 + - - -
408D ALA 3.3 1.0 - - - -
409D SER* 1.3 80.3 + - - +
411D TYR* 1.3 64.9 + - - +
412D ARG 3.3 2.7 - - - -
413D ALA* 3.3 12.3 + - - +
414D ARG* 3.1 21.1 + - - +
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Residues in contact with TYR 411 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ARG* 2.8 40.6 + - + -
6D ILE* 3.9 17.3 - - + -
83D ASP 3.7 3.6 + - - -
84D ASP* 2.6 29.6 + - - -
87D VAL* 3.5 17.3 - - + -
336D ILE* 3.7 13.7 - - + -
406D TYR* 3.6 33.4 + + + -
409D SER* 3.1 19.0 + - - +
410D GLY* 1.3 76.3 - - - +
412D ARG* 1.3 65.6 + - - +
414D ARG* 3.0 37.4 + - - +
415D VAL* 3.0 33.4 + - + +
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Residues in contact with ARG 412 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59D VAL 5.0 2.2 + - - -
72D THR* 3.2 34.4 + - - +
73D GLY 3.0 26.1 + - - -
74D GLU* 4.8 3.6 + - - +
75D PRO* 5.1 2.6 - - - +
84D ASP* 4.7 3.8 + - - -
334D ASP* 2.8 42.4 + - - +
335D PRO* 4.3 12.2 - - - +
336D ILE* 3.5 20.3 - - - +
406D TYR* 3.3 22.9 + - + +
410D GLY 3.3 1.2 - - - -
411D TYR* 1.3 78.9 - - - +
413D ALA* 1.3 58.8 + - - +
415D VAL* 3.1 17.1 - - - +
416D ALA* 2.9 28.8 + - - +
419D ARG* 4.5 3.6 - - - +
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Residues in contact with ALA 413 (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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72D THR* 5.5 0.4 - - - -
410D GLY* 3.3 13.0 + - - +
411D TYR 3.3 0.6 - - - -
412D ARG* 1.3 81.4 - - - +
414D ARG* 1.3 62.0 + - - +
416D ALA* 3.4 8.7 + - - +
417D ALA* 3.2 21.7 + - - +
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Residues in contact with ARG 414 (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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4D PHE 5.2 0.4 + - - -
5D ARG* 2.9 64.2 + - - +
410D GLY 3.1 12.5 + - - +
411D TYR* 3.0 29.1 + - - +
413D ALA* 1.3 78.1 - - - +
415D VAL* 1.3 62.5 + - - +
417D ALA* 3.2 13.6 + - - +
418D GLU* 3.1 44.2 + - - +
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Residues in contact with VAL 415 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ARG* 4.1 2.9 - - - +
73D GLY* 3.9 4.7 - - - +
411D TYR* 3.0 50.1 + - + +
412D ARG* 3.1 41.5 - - - +
414D ARG* 1.3 75.4 - - + +
416D ALA* 1.3 59.9 + - - +
418D GLU* 3.6 17.9 - - - +
419D ARG* 2.8 60.5 + - - +
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Residues in contact with ALA 416 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D THR* 3.6 28.7 - - - +
73D GLY* 3.4 12.9 + - - +
412D ARG 2.9 19.3 + - - +
413D ALA* 3.5 10.8 - - - +
414D ARG 3.2 0.4 - - - -
415D VAL* 1.3 77.3 - - - +
417D ALA* 1.3 57.6 + - - +
419D ARG 2.9 20.3 - - - +
421D ALA* 6.0 0.2 - - - -
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Residues in contact with ALA 417 (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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413D ALA 3.2 11.2 + - - +
414D ARG* 3.2 10.7 + - - +
415D VAL 3.1 0.6 - - - -
416D ALA* 1.3 77.9 - - - +
418D GLU* 1.3 61.5 + - + +
419D ARG 3.4 1.1 - - - +
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Residues in contact with GLU 418 (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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5D ARG* 4.5 6.2 + - - -
76D ARG* 4.0 16.1 + - - +
414D ARG* 3.1 46.6 + - + +
415D VAL* 3.2 20.5 + - - +
417D ALA* 1.3 78.4 - - + +
419D ARG* 1.3 68.0 + - + +
420D PRO* 4.4 1.0 - - - +
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Residues in contact with ARG 419 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5D ARG* 4.3 5.7 - - - +
73D GLY* 2.9 32.2 + - - -
74D GLU 3.5 16.2 - - - +
75D PRO* 3.7 9.1 - - - +
76D ARG* 4.1 8.5 - - - +
80D ASP* 3.5 41.6 + - - +
83D ASP* 4.4 2.0 + - - +
84D ASP* 2.8 43.0 + - - -
411D TYR* 3.9 2.8 + - - -
415D VAL* 2.8 40.2 + - - +
416D ALA* 2.9 18.5 - - - +
417D ALA 4.4 1.8 - - - +
418D GLU* 1.3 89.6 + - + +
420D PRO* 1.3 75.6 - - + +
421D ALA 3.7 0.3 + - - -
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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