Contacts of the strand formed by residues 68 - 72 (chain C) in PDB entry 2AG1
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 68 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57C ALA* 3.6 24.2 - - - -
60C TYR* 4.1 8.7 - - - -
61C ALA* 3.7 4.1 - - - +
67C LEU* 1.3 75.6 - - - +
69C VAL* 1.3 63.8 + - - +
94C PRO 3.0 11.6 + - - -
95C VAL* 3.2 8.4 - - - -
96C LEU 2.9 24.8 + - - -
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Residues in contact with VAL 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14C LEU* 4.4 4.7 - - + -
19C VAL* 4.1 21.8 - - + -
21C HIS 4.4 8.6 + - - +
22C LEU* 3.6 25.0 - - + -
23C PHE* 3.0 31.2 + - - -
57C ALA* 3.9 4.4 - - - +
60C TYR* 5.4 0.2 - - - -
67C LEU* 3.9 24.7 + - + +
68C GLY* 1.3 79.3 - - - +
70C ALA* 1.3 62.6 + - - +
96C LEU* 3.5 17.7 - - + +
98C LEU* 3.8 29.8 - - + -
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Residues in contact with ALA 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C PHE 3.2 8.3 - - - +
53C ALA 4.8 0.2 - - - -
54C GLY* 4.2 10.3 - - - +
57C ALA* 3.8 17.4 - - + +
69C VAL* 1.3 74.6 - - - +
71C LEU* 1.3 57.4 + - - +
72C VAL* 5.1 5.4 - - + -
95C VAL* 4.2 0.4 - - + +
96C LEU 2.8 7.9 + - - +
97C PHE* 3.7 31.9 - - + -
98C LEU* 2.7 36.9 + - - +
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Residues in contact with LEU 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C LEU* 4.1 18.8 - - + -
23C PHE 2.8 13.6 + - - +
24C GLY* 3.0 22.2 - - - -
25C LEU 3.4 6.8 + - - +
30C ILE* 3.4 28.3 - - + +
33C ILE* 3.8 44.2 - - + -
34C PHE* 3.7 29.8 - - + -
44C ILE* 3.9 17.0 - - + -
70C ALA* 1.3 75.5 - - - +
72C VAL* 1.3 65.4 + - - +
98C LEU* 3.3 14.1 - - + +
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Residues in contact with VAL 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C LEU 4.5 2.9 - - - +
30C ILE* 3.6 11.0 - - - +
50C GLU* 3.6 32.8 - - + +
53C ALA* 5.2 5.8 - - + -
54C GLY* 5.9 0.7 - - - +
70C ALA* 5.1 5.4 - - + -
71C LEU* 1.3 83.3 - - - +
73C THR* 1.3 59.1 + - - +
77C GLY 3.6 21.8 - - - +
78C PHE* 3.9 5.8 - - + -
81C ALA* 4.3 15.3 - - + -
97C PHE* 6.0 3.8 - - + -
98C LEU 2.8 11.4 + - - +
99C THR* 3.2 26.8 - - - +
100C GLY 2.8 23.7 + - - -
158C LEU* 6.0 0.9 - - + -
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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