Contacts of the strand formed by residues 56 - 62 (chain N) in PDB entry 3CMA
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 ASP 56 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1179 G 5.0 2.3 + - - -
1189 C 3.5 26.0 - - - +
48N VAL* 3.2 4.5 - - - -
49N THR* 2.6 60.5 + - + +
50N LEU 3.9 0.9 - - - +
51N GLY* 3.9 15.6 - - - -
52N PRO* 5.1 2.3 - - - +
54N GLY 4.5 3.2 - - - +
55N ASP* 1.3 79.7 - - - +
57N THR* 1.3 61.5 + - - +
58N LEU* 3.3 9.0 - - + +
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Residues in contact with THR 57 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59 G 3.0 24.9 + - - -
69 C 5.3 0.5 + - - -
1189 C 3.1 9.7 + - - +
1199 C 3.4 50.1 - - - +
46N GLN* 4.0 11.1 + - + -
47N LEU 3.4 6.5 - - - +
48N VAL* 4.0 9.7 - - - +
55N ASP 4.3 0.4 - - - -
56N ASP* 1.3 72.1 - - - +
58N LEU* 1.3 62.0 + - - +
59N ALA* 3.6 22.2 - - - +
60N SER* 3.9 9.4 - - - -
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Residues in contact with LEU 58 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32N PRO* 5.6 6.3 - - + -
47N LEU* 2.9 11.8 + - + +
48N VAL 4.7 0.4 - - - -
49N THR* 3.5 33.9 - - + +
56N ASP* 3.3 23.3 - - + +
57N THR* 1.3 75.5 - - - +
59N ALA* 1.3 61.9 + - - +
95N ALA* 4.2 18.4 - - + +
97N VAL* 3.7 31.9 - - + -
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Residues in contact with ALA 59 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46N GLN* 3.5 0.2 - - - -
47N LEU* 2.7 39.3 + - + +
57N THR* 3.5 4.2 - - - +
58N LEU* 1.3 82.0 - - + +
60N SER* 1.3 61.1 + - - +
88N ALA 4.3 1.8 - - - +
91N ARG* 3.8 11.7 - - + +
92N ALA* 3.4 42.0 - - + +
95N ALA* 5.0 1.3 - - + -
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Residues in contact with SER 60 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1199 C 3.4 17.3 + - - -
1209 A 4.2 14.0 + - - +
44N ARG* 5.7 2.4 - - - -
45N ALA 3.1 15.7 - - - -
46N GLN* 3.6 18.6 - - - -
57N THR* 3.9 5.2 - - - -
59N ALA* 1.3 78.0 - - - +
61N ALA* 1.3 62.4 + - - +
88N ALA* 3.9 8.0 - - - +
91N ARG* 3.0 25.2 + - - +
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Residues in contact with ALA 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44N ARG* 3.7 5.0 - - - +
45N ALA 2.8 30.7 + - - +
60N SER* 1.3 75.3 - - - +
62N HIS* 1.3 61.5 + - - +
84N THR* 3.2 17.3 - - + +
87N LEU* 3.7 18.4 - - + -
88N ALA* 3.1 33.8 - - + +
91N ARG* 3.5 6.3 - - - +
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Residues in contact with HIS 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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269 C 5.3 2.4 + - - -
279 C 5.0 2.6 + - - -
1209 A 5.0 8.7 - - - +
42N HIS* 3.4 44.1 - + + +
43N VAL 3.8 5.6 + - - -
44N ARG* 3.7 47.8 + - + +
61N ALA* 1.3 75.1 - - - +
63N SER* 1.3 66.2 + - - +
64N SER* 2.7 39.8 + - - +
65N ASP* 3.0 35.1 + - - +
66N LEU* 3.6 5.2 + - - +
84N THR* 4.1 5.2 + - - +
87N LEU* 4.9 2.6 - - - +
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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