Contacts of the strand formed by residues 68 - 74 (chain A) in PDB entry 8ATC
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 ALA 68 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39A LEU* 3.1 31.3 + - + +
42A LYS* 3.4 9.4 - - + +
44A ILE* 4.0 23.1 - - + -
63A MET* 3.1 22.8 + - + +
64A HIS* 3.8 16.3 - - - -
66A LEU 3.5 0.8 + - - -
67A GLY* 1.3 78.0 - - - +
69A SER* 1.3 62.8 + - - +
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Residues in contact with SER 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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41A HIS* 6.1 0.3 - - - -
42A LYS 2.8 13.9 + - - -
43A VAL* 3.4 18.6 - - - +
44A ILE* 2.8 32.4 + - - +
64A HIS* 4.9 3.6 - - - -
67A GLY 5.1 0.9 + - - -
68A ALA* 1.3 73.6 - - - +
70A VAL* 1.3 64.5 - - - +
71A VAL* 5.9 0.7 - - - -
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Residues in contact with VAL 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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44A ILE 3.2 8.5 - - - +
46A SER* 3.9 20.4 - - - -
60A GLN* 4.0 19.1 - - + +
63A MET* 3.3 36.3 - - + -
64A HIS* 4.0 26.8 + - + +
69A SER* 1.3 81.6 - - - +
71A VAL* 1.3 82.7 + - - +
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Residues in contact with VAL 71 (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* 3.8 17.7 - - + -
44A ILE 2.9 8.5 + - - +
45A ALA* 3.1 9.5 - - + -
46A SER 2.9 21.1 + - - -
69A SER* 5.9 0.9 - - - -
70A VAL* 1.3 84.9 - - - +
72A GLY* 1.3 60.0 + - - +
95A ILE* 6.3 0.2 - - + -
98A TYR* 6.1 2.5 - - + -
99A VAL* 3.9 27.8 - - + -
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Residues in contact with GLY 72 (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 ALA* 5.0 0.7 - - - -
46A SER* 3.2 13.7 - - - -
47A CYS* 4.8 4.0 - - - -
60A GLN* 6.1 0.7 - - - -
71A VAL* 1.3 78.1 - - - +
73A PHE* 1.3 73.1 + - - +
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Residues in contact with PHE 73 (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 SER 2.9 9.4 + - - +
47A CYS* 3.8 26.5 - - + -
48A PHE* 3.0 36.8 + - - +
49A PHE* 3.4 49.4 - + - -
56A ARG* 4.6 2.2 - - - -
60A GLN* 6.1 0.4 - - - -
72A GLY* 1.3 79.5 - - - +
74A SER* 1.3 62.2 + - - +
75A ASP 3.4 16.8 - - - +
76A SER* 4.4 0.2 - - - -
79A THR* 3.8 29.4 - - + -
91A THR* 4.8 3.8 - - + -
95A ILE* 4.2 15.5 - - + -
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Residues in contact with SER 74 (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 PHE* 3.4 20.6 - - - +
49A PHE 5.5 0.3 - - - -
50A GLU 4.8 7.1 + - - +
51A ALA* 5.5 2.3 - - - -
56A ARG* 3.4 36.6 + - - -
73A PHE* 1.3 75.1 - - - +
75A ASP* 1.3 62.6 - - - +
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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