Contacts of the strand formed by residues 102 - 107 (chain A) 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 CYS 102 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A CYS* 3.5 7.0 - - - -
100A GLN* 3.9 10.3 + - - -
101A ALA* 1.3 80.8 - - - +
103A CYS* 1.3 65.0 + - - +
104A ARG* 3.3 18.7 + - + +
134A CYS* 3.4 0.2 - - - -
135A ILE 2.9 32.3 + - - +
99B GLY* 5.8 2.5 - - - -
100B GLN 4.2 6.1 - - - +
102B CYS* 2.0 52.5 - - + -
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Residues in contact with CYS 103 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A CYS* 2.0 58.1 - - + -
43A VAL 3.9 0.2 - - - -
69A CYS* 3.8 9.9 - - - +
70A SER* 3.4 28.7 - - - -
71A GLY 3.2 23.2 + - - +
73A CYS* 3.3 7.2 - - - -
102A CYS* 1.3 69.7 - - - +
104A ARG* 1.3 67.8 + - - +
133A GLY 3.6 0.9 - - - -
99B GLY* 3.7 19.0 - - - +
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Residues in contact with ARG 104 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A CYS* 3.6 8.7 - - - -
102A CYS* 3.7 15.9 - - + +
103A CYS* 1.3 82.1 - - - +
105A PRO* 1.4 76.0 - - + +
106A VAL* 3.9 1.3 - - - +
108A PHE* 6.0 1.8 - - - -
132A CYS* 3.5 1.0 - - - -
133A GLY 2.9 32.1 + - - +
135A ILE* 3.7 23.1 - - + -
78B THR* 4.5 2.8 - - - +
80B TYR* 3.7 16.9 - - - -
81B ASP* 2.8 43.6 + - - -
84B LEU* 4.4 0.2 - - - +
99B GLY 3.0 20.2 + - - -
100B GLN 3.4 18.2 - - - -
101B ALA* 3.4 12.2 - - - +
135B ILE* 2.7 36.1 + - - +
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Residues in contact with PRO 105 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A CYS* 3.5 3.8 - - - -
104A ARG* 1.4 100.1 - - + +
106A VAL* 1.3 61.6 + - - +
107A ALA 4.0 4.7 - - - +
108A PHE* 3.6 33.2 - - + -
129A ALA* 3.9 15.0 - - + -
131A ARG 3.4 8.1 - - - +
135A ILE* 4.2 7.3 - - - +
80B TYR* 3.4 50.7 - - + +
135B ILE* 5.2 1.4 - - - +
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Residues in contact with VAL 106 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104A ARG 3.9 0.9 - - - +
105A PRO* 1.3 76.9 - - - +
107A ALA* 1.3 61.4 + - - +
108A PHE* 5.4 3.1 - - - -
131A ARG* 2.9 50.6 + - + +
132A CYS 3.9 7.6 - - - +
133A GLY* 3.8 17.7 - - - +
135A ILE* 3.7 30.7 - - + -
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Residues in contact with ALA 107 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105A PRO* 3.4 3.2 - - - +
106A VAL* 1.3 81.2 - - - +
108A PHE* 1.3 68.4 + - - +
129A ALA* 3.7 4.3 - - - -
130A LYS* 2.8 31.7 + - + +
131A ARG* 3.4 50.0 + - + +
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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