Contacts of the strand formed by residues 73 - 78 (chain A) in PDB entry 1P9K
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 HIS 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32A TRP* 2.7 76.3 + + + -
41A ILE* 5.3 6.5 - - + +
70A PHE* 2.6 35.3 + + - +
71A ALA* 5.5 3.6 - - + -
72A GLY* 1.3 79.8 + - - -
74A SER* 1.3 55.0 + - - +
75A VAL* 5.5 1.8 - - + -
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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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11A ALA* 4.1 6.8 - - - +
67A THR* 5.1 4.0 - - - -
68A VAL 3.7 3.6 - - - -
69A SER* 3.5 21.9 + - - -
70A PHE 5.0 0.2 + - - -
72A GLY 3.4 8.9 + - - -
73A HIS* 1.3 72.1 - - - +
75A VAL* 1.3 68.7 + - - +
76A GLN* 5.8 1.1 + - - -
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Residues in contact with VAL 75 (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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11A ALA* 3.2 30.7 - - + +
26A LEU* 5.6 1.3 - - + -
30A GLU* 3.2 35.2 - - + +
32A TRP* 3.1 33.1 - - + +
67A THR* 2.8 24.6 - - - +
68A VAL* 2.8 21.5 + - - +
73A HIS* 4.8 1.6 - - + -
74A SER* 1.3 83.0 - - - +
76A GLN* 1.3 68.4 + - - +
77A VAL* 5.1 2.3 - - + +
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Residues in contact with GLN 76 (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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10A MET* 5.6 0.5 - - - +
11A ALA 3.2 20.1 + - - +
12A THR* 3.3 18.9 - - + +
13A PHE 2.7 30.5 + - - -
65A GLY 6.2 0.2 - - - -
66A GLN 3.6 5.4 - - - +
67A THR* 3.0 29.2 - - + +
74A SER 5.8 1.2 + - - -
75A VAL* 1.3 79.9 - - - +
77A VAL* 1.3 61.0 + - - +
78A VAL* 6.1 0.9 - - + -
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Residues in contact with VAL 77 (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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13A PHE* 3.2 33.9 - - + +
15A LEU* 3.4 38.8 - - + -
26A LEU* 3.0 37.5 - - + -
64A ALA 3.3 2.7 - - - +
65A GLY* 2.9 5.4 - - - -
66A GLN* 2.5 40.3 + - + +
67A THR* 5.4 0.4 - - - -
75A VAL* 5.1 2.9 - - + +
76A GLN* 1.3 79.5 - - - +
78A VAL* 1.3 71.2 + - - +
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Residues in contact with VAL 78 (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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12A THR* 4.8 18.4 - - + -
13A PHE 2.8 18.6 + - - +
14A SER* 3.7 7.4 - - - -
15A LEU* 2.8 27.0 + - - +
16A GLY 4.0 0.3 + - - -
64A ALA 3.2 5.8 - - - -
65A GLY* 4.0 6.7 - - - -
76A GLN* 6.1 0.9 - - + -
77A VAL* 1.3 79.6 - - - +
79A ALA* 1.3 62.9 + - - +
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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