Contacts of the strand formed by residues 44 - 47 (chain B) in PDB entry 1MGV
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 ARG 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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33B GLU* 2.6 36.8 + - - +
36B GLU* 3.0 41.6 + - - +
37B LEU 3.4 6.1 - - - +
38B ILE* 3.4 30.8 - - + +
42B GLY 3.4 12.8 + - - +
43B ARG* 1.3 73.8 - - - +
45B LEU* 1.3 66.7 + - - +
387B GLY* 3.9 10.0 - - - +
412B ARG* 4.9 4.7 + - - -
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Residues in contact with LEU 45 (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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27B TYR* 5.9 0.2 - - + -
36B GLU* 3.1 7.0 - - - -
37B LEU* 2.8 46.4 + - + +
39B LEU* 3.7 39.5 - - + -
43B ARG* 5.1 4.3 - - + -
44B ARG* 1.3 80.3 - - - +
46B VAL* 1.3 63.5 + - - +
47B ASP 3.3 0.2 + - - -
384B VAL* 3.5 36.1 - - + +
387B GLY* 3.6 16.6 - - - -
388B VAL 3.7 17.7 - - - +
389B TRP* 4.1 26.9 - - + +
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Residues in contact with VAL 46 (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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35B CYS 3.6 7.4 - - - +
36B GLU* 4.7 6.5 - - + +
44B ARG 4.3 0.2 + - - -
45B LEU* 1.3 69.9 - - - +
47B ASP* 1.3 61.0 + - - +
48B GLY 3.3 1.4 + - - -
387B GLY 3.0 16.7 + - - +
388B VAL* 3.4 8.0 - - + -
389B TRP 2.7 29.3 + - - -
405B ILE* 4.0 12.3 - - + -
408B GLN* 6.0 0.2 - - - +
409B GLN* 3.8 45.3 - - + +
412B ARG* 4.0 22.7 - - - +
413B LEU* 3.8 19.2 - - + +
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Residues in contact with ASP 47 (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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35B CYS 2.9 19.3 + - - +
37B LEU* 4.1 13.5 - - + -
45B LEU 3.3 1.8 + - - -
46B VAL* 1.3 74.0 - - - +
48B GLY* 1.3 57.5 + - - +
49B MET* 3.1 14.6 + - - +
50B SER* 2.7 27.9 + - - -
51B SER 4.2 1.0 + - - -
59B TYR* 2.8 36.5 + - + -
389B TRP* 3.5 25.6 - - - -
401B PRO* 4.1 2.4 - - - +
402B PRO* 3.6 20.6 - - + +
405B ILE* 4.3 1.7 - - - +
413B LEU* 4.2 3.1 - - - +
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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