Contacts of the helix formed by residues 11 - 16 (chain M) in PDB entry 3J7Y
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 11 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M ALA* 1.3 71.1 - - - +
12M ALA* 1.3 60.5 + - - +
14M ASP* 3.2 9.1 + - - +
15M LEU* 2.9 39.2 + - + +
88o ILE* 6.5 0.2 - - + -
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Residues in contact with ALA 12 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90F ALA* 5.9 0.2 - - + -
91F PRO* 3.4 32.5 - - + -
10M ALA* 3.4 5.7 - - + +
11M ARG* 1.3 78.8 - - - +
13M LEU* 1.3 57.6 + - - +
15M LEU* 3.2 7.7 + - - +
16M LEU* 2.9 31.5 + - - +
88o ILE* 3.7 32.2 - - + +
92o LEU* 3.8 9.3 - - + +
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Residues in contact with LEU 13 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59F ARG* 6.0 0.2 - - - +
87F PHE 5.8 0.2 - - - +
88F ALA* 4.0 32.3 - - + +
89F THR 3.7 17.9 - - - +
91F PRO* 4.5 14.6 - - + -
179F THR* 4.6 13.9 - - - +
183F ALA* 4.1 24.9 - - + +
10M ALA* 3.7 31.5 + - + +
11M ARG 3.2 0.2 - - - -
12M ALA* 1.3 78.0 - - - +
14M ASP* 1.3 66.1 + - - +
16M LEU* 3.2 22.3 + - + +
17M ARG* 3.4 9.2 + - - +
118h HIS* 6.1 7.0 - - + +
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Residues in contact with ASP 14 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10M ALA 3.0 19.4 + - - +
11M ARG* 3.2 12.2 + - - +
13M LEU* 1.3 79.3 - - - +
15M LEU* 1.3 58.7 + - + +
17M ARG* 3.0 72.3 + - - +
18M GLY 4.1 0.5 + - - -
118h HIS* 4.4 8.8 + - - -
119h GLN* 4.3 5.4 + - - +
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Residues in contact with LEU 15 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11M ARG* 2.9 23.3 + - + +
12M ALA* 3.2 11.4 + - - +
14M ASP* 1.3 77.1 - - + +
16M LEU* 1.3 53.4 - - - +
17M ARG 3.0 0.2 - - - -
18M GLY* 2.8 33.6 + - - +
19M LEU* 3.8 9.4 - - + +
88o ILE* 5.2 3.1 - - + -
89o ALA* 5.5 8.7 - - + -
92o LEU* 3.4 26.7 - - + -
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Residues in contact with LEU 16 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91F PRO* 3.5 33.9 - - + -
93F LEU* 5.1 2.2 - - + -
180F VAL* 4.7 14.4 - - + -
183F ALA* 4.2 19.5 - - + -
184F GLN* 2.8 39.9 + - - +
12M ALA 2.9 13.6 + - - +
13M LEU* 3.2 18.6 + - + +
15M LEU* 1.3 74.8 - - - +
17M ARG* 1.3 55.9 + - - +
18M GLY 2.8 6.5 - - - +
19M LEU* 4.4 3.1 - - + -
22M VAL* 4.8 4.5 - - + -
92o LEU* 3.6 18.4 - - + -
95o LEU* 3.6 31.0 - - + -
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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