Contacts of the strand formed by residues 43 - 50 (chain C) in PDB entry 1AGQ
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 VAL 43 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C GLY* 3.8 19.5 - - - +
42C CYS* 1.3 79.7 - - - +
44C LEU* 1.3 69.6 + - - +
45C THR* 4.0 7.7 + - - +
68C TYR 3.7 0.3 - - - +
69C CYS* 3.5 2.6 - - - -
70C SER* 3.0 35.0 + - - +
132C CYS* 3.9 7.6 - - - -
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Residues in contact with LEU 44 (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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43C VAL* 1.3 79.8 - - - +
45C THR* 1.3 62.2 + - - +
46C ALA* 6.1 0.2 - - + -
67C ARG* 3.6 44.6 - - + +
68C TYR 3.4 9.2 - - - +
129C ALA* 3.6 31.0 - - + +
130C LYS 3.8 19.1 - - - +
131C ARG* 5.8 0.2 - - - -
132C CYS* 3.5 24.6 - - - +
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Residues in contact with THR 45 (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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43C VAL* 4.7 8.1 + - - +
44C LEU* 1.3 76.8 + - - +
46C ALA* 1.3 62.9 + - - +
47C ILE* 4.1 13.7 - - + -
67C ARG* 3.1 4.8 - - - -
68C TYR* 2.9 72.3 + - + +
70C SER* 4.6 5.7 + - - -
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Residues in contact with ALA 46 (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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44C LEU 4.3 0.2 - - - -
45C THR* 1.3 77.1 - - - +
47C ILE* 1.3 66.3 + - - +
65C ILE* 4.1 10.8 - - + -
66C PHE 3.6 4.0 - - - -
67C ARG* 3.7 26.9 - - + +
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Residues in contact with ILE 47 (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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45C THR* 4.1 16.2 - - + -
46C ALA* 1.3 80.1 - - - +
48C HIS* 1.3 62.5 + - - +
49C LEU* 3.8 32.2 + - + -
65C ILE* 3.4 6.8 - - - -
66C PHE* 2.9 48.8 + - + +
68C TYR* 4.0 21.5 - - + +
87D LEU* 5.3 0.2 - - + -
92D ARG 6.0 0.2 - - - +
93D LEU* 4.2 17.3 - - + -
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Residues in contact with HIS 48 (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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47C ILE* 1.3 72.7 - - - +
49C LEU* 1.3 77.5 + - - +
63C GLU* 2.8 36.2 + - + +
64C LEU 3.7 11.7 - - - -
65C ILE* 4.0 18.2 - - + +
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Residues in contact with LEU 49 (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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47C ILE* 3.8 24.7 + - + -
48C HIS* 1.3 85.5 - - - +
50C ASN* 1.3 67.2 + - - +
53C ASP* 3.7 19.1 - - + +
54C LEU* 4.0 19.7 - - + -
63C GLU* 3.2 7.5 - - - +
64C LEU* 2.9 40.4 + - + +
66C PHE* 3.9 25.1 - - + -
87D LEU* 4.1 26.2 - - + -
92D ARG* 5.8 4.0 - - + -
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Residues in contact with ASN 50 (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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49C LEU* 1.3 78.6 - - - +
51C VAL* 1.3 67.2 + - - +
52C THR* 3.5 20.3 + - - +
53C ASP* 2.8 39.4 + - - +
54C LEU 3.9 1.4 + - - -
60C THR 5.9 0.9 - - - +
61C LYS* 4.9 3.3 - - - +
62C GLU 3.8 6.7 - - - +
63C GLU* 3.7 22.2 - - - +
64C LEU* 4.0 2.1 - - - +
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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