Contacts of the strand formed by residues 63 - 70 (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 GLU 63 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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48A HIS* 2.7 34.2 + - - +
49A LEU 3.4 9.9 - - - +
50A ASN* 3.3 27.8 - - - +
51A VAL 4.2 0.2 - - - +
61A LYS 3.6 10.9 + - - +
62A GLU* 1.3 97.4 + - - +
64A LEU* 1.3 66.2 + - - +
112A LEU* 4.9 2.8 - - - +
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Residues in contact with LEU 64 (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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48A HIS* 3.7 5.4 - - - -
49A LEU* 2.9 48.9 + - + +
50A ASN 4.0 4.7 - - - +
51A VAL* 3.9 26.9 - - + +
54A LEU* 4.0 15.0 - - + -
63A GLU* 1.3 80.5 - - - +
65A ILE* 1.3 75.3 + - - +
66A PHE* 4.2 13.0 - - + +
112A LEU* 4.0 17.0 - - + -
127A HIS* 3.8 32.3 - - + +
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Residues in contact with ILE 65 (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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46A ALA* 3.7 25.6 - - + -
47A ILE 3.5 5.6 - - - +
48A HIS* 4.7 15.9 - - + +
64A LEU* 1.3 83.9 - - - +
66A PHE* 1.3 60.6 + - - +
67A ARG* 3.5 44.8 + - + +
109A ASP* 4.5 0.5 - - - +
127A HIS* 5.7 0.3 + - - -
128A SER* 3.7 8.8 + - - -
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Residues in contact with PHE 66 (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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45A THR 3.8 0.2 - - - +
46A ALA* 3.4 1.2 - - - -
47A ILE* 2.8 47.8 + - + +
49A LEU* 3.8 20.9 - - + -
54A LEU* 4.9 2.7 - - + -
64A LEU* 3.7 13.4 + - + -
65A ILE* 1.3 72.5 - - - +
67A ARG* 1.3 67.0 + - - +
68A TYR* 3.9 21.5 - + + -
127A HIS 3.0 27.8 - - - -
128A SER* 3.7 5.8 - - - -
80B TYR* 3.9 22.9 - + - -
83B ILE* 3.6 28.0 - - + -
84B LEU* 4.0 12.1 - - + -
87B LEU* 3.5 27.4 - - + -
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Residues in contact with ARG 67 (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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44A LEU* 3.7 21.5 - - + -
45A THR 3.1 7.0 - - - +
46A ALA* 3.9 16.8 - - + +
65A ILE* 3.5 42.3 + - + +
66A PHE* 1.3 81.9 - - - +
68A TYR* 1.3 62.1 + - - +
109A ASP* 3.0 27.0 + - - -
128A SER* 2.8 9.5 + - - +
129A ALA* 2.9 47.6 + - - +
130A LYS* 5.1 1.1 - - - +
80B TYR* 3.6 5.9 - - - -
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Residues in contact with TYR 68 (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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43A VAL 3.7 0.5 - - - +
44A LEU* 3.3 5.8 - - - +
45A THR* 2.9 72.7 + - + +
47A ILE* 4.3 17.5 - - + -
66A PHE* 3.9 22.9 - + + -
67A ARG* 1.3 75.0 - - - +
69A CYS* 1.3 71.5 + - - +
70A SER* 4.2 11.0 - - - -
129A ALA* 4.3 0.9 - - - -
80B TYR* 3.4 15.7 - - + +
84B LEU* 4.2 5.2 - - + -
93B LEU* 3.3 36.9 - - + +
98B VAL* 3.4 25.6 - - + -
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Residues in contact with CYS 69 (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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43A VAL 3.4 4.0 - - - -
68A TYR* 1.3 73.5 - - - +
70A SER* 1.3 62.5 + - - +
103A CYS* 3.8 11.4 - - - +
104A ARG* 3.9 13.7 - - - -
105A PRO* 3.5 26.0 - - - -
129A ALA* 3.8 11.0 - - - -
132A CYS* 2.0 49.6 - - + -
80B TYR* 2.9 9.7 + - - +
98B VAL* 3.5 7.1 - - - +
99B GLY* 3.0 22.3 + - - +
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Residues in contact with SER 70 (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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41A GLY 3.3 1.0 - - - +
43A VAL* 2.6 48.9 + - - +
45A THR* 4.3 4.3 + - - -
68A TYR* 4.2 15.0 - - - -
69A CYS* 1.3 76.5 - - - +
71A GLY* 1.3 56.3 + - - +
103A CYS* 3.4 8.6 - - - -
98B VAL* 3.8 22.7 - - - -
99B GLY 4.1 6.1 - - - +
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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