Contacts of the strand formed by residues 43 - 50 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40B ARG 3.5 19.1 - - - +
41B GLY* 3.5 7.9 - - - +
42B CYS* 1.3 79.3 - - - +
44B LEU* 1.3 67.9 - - - +
45B THR* 3.9 11.8 + - - +
68B TYR 3.7 0.7 - - - +
69B CYS* 3.4 3.6 - - - -
70B SER* 2.9 37.4 + - - +
103B CYS* 3.9 0.2 - - - -
132B CYS* 3.8 6.1 - - - -
44D LEU* 3.7 40.8 - - + +
46D ALA* 4.9 7.0 - - + +
67D ARG* 4.2 17.0 - - - +
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Residues in contact with LEU 44 (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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43B VAL* 1.3 75.5 - - - +
45B THR* 1.3 61.4 + - - +
67B ARG* 3.8 42.0 - - + +
68B TYR 3.5 4.9 - - - +
129B ALA* 3.6 28.0 - - + +
130B LYS 3.5 22.7 - - - +
131B ARG* 5.1 1.3 - - - -
132B CYS* 3.4 25.8 - - + +
44D LEU 4.7 2.6 + - - +
45D THR* 3.5 16.3 + - - +
46D ALA 3.1 22.0 + - - -
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Residues in contact with THR 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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43B VAL* 4.1 10.4 + - - +
44B LEU* 1.3 76.5 + - - +
46B ALA* 1.3 63.1 + - - +
67B ARG* 3.1 5.8 - - - -
68B TYR* 2.8 73.2 + - + +
70B SER* 4.4 4.2 + - - -
46D ALA* 3.4 29.6 - - + +
48D HIS* 3.5 20.2 - - + +
65D ILE* 4.3 5.7 - - + +
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Residues in contact with ALA 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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45B THR* 1.3 74.2 - - - +
47B ILE* 1.3 61.9 + - - +
65B ILE* 3.7 21.8 - - + -
66B PHE 3.4 4.5 - - - -
67B ARG* 3.8 13.2 - - + -
46D ALA 2.9 15.4 + - - +
47D ILE* 3.4 16.5 - - + +
48D HIS* 2.9 29.5 + - - -
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Residues in contact with ILE 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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87A LEU* 5.1 4.3 - - + -
91A ARG* 4.2 21.3 - - - +
46B ALA* 1.3 77.7 - - - +
48B HIS* 1.3 66.8 + - - +
49B LEU* 3.4 30.5 + - + -
65B ILE* 4.4 2.7 - - - -
66B PHE* 2.8 64.4 + - + +
68B TYR* 4.6 9.4 - - + -
47D ILE* 5.7 0.4 - - - -
48D HIS* 3.7 40.4 - - + +
63D GLU* 5.9 2.7 - - - +
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Residues in contact with HIS 48 (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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47B ILE* 1.3 76.3 - - - +
49B LEU* 1.3 70.3 + - - +
50B ASN* 5.1 2.5 - - - -
53B ASP* 5.1 0.2 - - - +
63B GLU* 2.8 45.6 + - - +
64B LEU* 3.4 23.6 - - - -
65B ILE* 3.9 21.6 - - + +
47D ILE* 6.2 0.8 - - - +
48D HIS 5.4 3.2 + - - -
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Residues in contact with LEU 49 (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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87A LEU* 3.9 25.4 - - + -
91A ARG* 4.1 15.9 - - - +
47B ILE* 3.7 28.7 - - + +
48B HIS* 1.3 83.9 - - - +
50B ASN* 1.3 71.2 + - - +
53B ASP* 3.6 18.6 - - + +
54B LEU* 3.6 24.0 - - + -
63B GLU* 3.3 5.4 - - - +
64B LEU* 2.8 38.9 + - + +
66B PHE* 3.7 20.0 - - + -
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Residues in contact with ASN 50 (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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48B HIS* 5.1 2.4 + - - -
49B LEU* 1.3 78.5 - - - +
51B VAL* 1.3 57.6 + - - +
52B THR* 3.5 20.0 + - - +
53B ASP* 2.6 51.7 + - - +
54B LEU* 3.7 2.6 + - - +
60B THR 5.8 1.1 - - - +
61B LYS* 5.0 2.5 + - - -
62B GLU 3.7 5.6 + - - +
63B GLU* 3.2 33.3 + - - +
64B LEU* 4.2 1.1 - - - -
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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