Contacts of the helix formed by residues 410 - 419 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A TYR 3.5 1.2 + - - -
407A ARG* 3.3 14.5 + - - -
408A ALA 3.3 0.8 - - - -
409A SER* 1.3 79.9 + - - +
411A TYR* 1.3 64.2 + - - +
412A ARG* 3.4 2.7 - - - -
413A ALA* 3.4 13.3 + - - +
414A ARG* 3.2 21.1 + - - +
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Residues in contact with TYR 411 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ARG* 2.7 47.3 + - + -
6A ILE* 3.9 18.4 - - + -
83A ASP 3.7 4.7 + - - -
84A ASP* 2.7 29.2 + - - -
87A VAL* 3.5 13.2 - - + -
336A ILE* 3.6 14.8 - - + -
406A TYR* 3.7 30.5 + + + -
409A SER* 3.2 16.7 + - - +
410A GLY* 1.3 75.7 - - - +
412A ARG* 1.3 67.7 + - - +
414A ARG* 3.1 28.7 + - - +
415A VAL* 3.0 39.4 + - + +
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Residues in contact with ARG 412 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A VAL 5.1 2.2 + - - -
72A THR* 3.1 34.4 + - - +
73A GLY 3.0 26.7 + - - -
74A GLU* 4.8 3.0 + - - +
75A PRO* 5.2 1.8 - - - +
84A ASP* 4.9 3.4 + - - -
334A ASP* 2.8 40.4 + - - +
335A PRO* 4.2 11.4 - - - +
336A ILE* 3.5 19.7 - - - +
406A TYR* 3.4 21.9 + - + +
410A GLY 3.4 0.8 - - - -
411A TYR* 1.3 79.1 - - - +
413A ALA* 1.3 58.8 + - - +
415A VAL* 3.1 15.1 - - - +
416A ALA* 2.9 29.8 + - - +
419A ARG* 4.6 2.6 - - - +
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Residues in contact with ALA 413 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 5.5 0.2 - - - -
410A GLY* 3.4 13.0 + - - +
411A TYR 3.3 0.4 - - - -
412A ARG* 1.3 80.1 - - - +
414A ARG* 1.3 63.2 + - - +
416A ALA* 3.3 8.5 + - - +
417A ALA* 3.2 21.1 + - - +
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Residues in contact with ARG 414 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4A PHE 5.2 0.6 + - - -
5A ARG* 2.9 66.5 + - - +
410A GLY 3.2 13.5 + - - +
411A TYR* 3.1 26.1 + - - +
413A ALA* 1.3 75.4 - - - +
415A VAL* 1.3 64.7 + - - +
417A ALA* 3.1 16.9 + - - +
418A GLU* 3.1 41.6 + - + +
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Residues in contact with VAL 415 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 4.1 2.7 - - - +
73A GLY* 4.0 5.4 - - - +
411A TYR* 3.0 52.9 + - + +
412A ARG* 3.1 40.6 - - - +
414A ARG* 1.3 77.1 - - + +
416A ALA* 1.3 57.4 + - - +
418A GLU* 3.6 18.4 - - - +
419A ARG* 2.9 60.1 + - - +
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Residues in contact with ALA 416 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A THR* 3.6 28.7 - - + +
73A GLY* 3.5 13.3 + - - +
412A ARG 2.9 18.2 + - - +
413A ALA* 3.4 11.4 - - - +
414A ARG 3.1 0.2 - - - -
415A VAL* 1.3 77.2 - - - +
417A ALA* 1.3 58.7 + - - +
419A ARG 3.3 18.7 - - - +
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Residues in contact with ALA 417 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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413A ALA 3.2 8.4 + - - +
414A ARG* 3.1 10.8 + - - +
416A ALA* 1.3 81.1 - - - +
418A GLU* 1.3 60.2 + - + +
419A ARG 4.9 0.6 - - - -
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Residues in contact with GLU 418 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A ARG* 4.6 4.9 + - - -
76A ARG* 3.7 13.7 + - - +
414A ARG* 3.1 43.3 + - + +
415A VAL* 3.2 24.1 + - - +
417A ALA* 1.3 82.2 - - + +
419A ARG* 1.3 64.6 + - + +
420A PRO* 3.9 5.2 - - - +
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Residues in contact with ARG 419 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A ARG* 4.2 6.7 - - - +
73A GLY* 3.1 33.8 + - - -
74A GLU 3.6 15.3 - - - +
75A PRO* 3.6 9.1 - - - +
76A ARG* 3.7 22.2 - - + +
80A ASP* 3.4 34.6 + - - +
83A ASP* 4.3 1.8 + - - +
84A ASP* 2.9 41.2 + - - -
411A TYR* 3.8 3.4 + - - -
412A ARG* 4.6 0.2 - - - +
415A VAL* 2.9 39.2 + - - +
416A ALA* 3.3 15.4 - - - +
417A ALA 5.1 0.4 - - - -
418A GLU* 1.3 86.4 + - + +
420A PRO* 1.3 66.7 - - - +
421A ALA 3.7 1.0 + - - -
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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