Contacts of the strand formed by residues 66 - 73 (chain E) in PDB entry 1PPF
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 66 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E VAL* 3.6 23.8 - - + -
32E SER 3.9 3.1 - - - -
33E LEU* 3.5 19.7 - - + -
52E VAL* 4.2 9.4 - - + -
64E VAL* 4.2 0.9 - - + -
65E ARG* 1.3 74.7 - - - +
67E VAL* 1.3 57.8 + - - +
68E LEU* 3.9 12.6 - - + -
81E GLN 3.6 1.4 - - - +
82E VAL* 3.3 5.9 - - - +
83E PHE* 2.7 40.5 + - + +
85E VAL* 4.0 26.5 - - + -
106E LEU* 4.8 0.2 - - + -
108E LEU* 3.8 31.4 - - + -
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Residues in contact with VAL 67 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E MET 4.6 0.2 - - - +
31E VAL* 3.5 5.1 - - - -
32E SER* 3.0 43.4 + - - +
34E GLN* 3.9 30.1 - - + +
65E ARG* 4.4 6.7 - - + +
66E VAL* 1.3 78.3 - - - +
68E LEU* 1.3 67.9 + - - +
70E ALA* 4.1 12.7 - - + +
80E ARG* 3.4 41.5 - - + +
81E GLN 3.5 4.0 - - - +
82E VAL* 4.5 15.9 - - + -
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Residues in contact with LEU 68 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E MET 4.8 4.7 - - - -
31E VAL* 3.6 32.3 - - + -
46E LEU* 4.5 8.3 - - + -
52E VAL* 4.4 6.7 - - + -
66E VAL* 3.9 13.0 - - + -
67E VAL* 1.3 74.3 - - - +
69E GLY* 1.3 67.3 + - - +
70E ALA 3.1 4.8 + - - -
80E ARG* 3.3 5.4 - - - +
81E GLN* 2.8 35.0 + - + +
83E PHE* 3.3 35.7 - - + -
108E LEU* 4.5 4.7 - - + -
112E ALA* 3.7 21.8 - - + -
118E VAL* 3.8 20.9 - - + -
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Residues in contact with GLY 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E HIS* 3.3 7.1 - - - -
28E PRO 5.2 2.0 + - - -
30E MET 4.6 6.3 + - - -
68E LEU* 1.3 75.9 - - - +
70E ALA* 1.3 63.1 + - - +
77E GLU* 4.3 0.7 - - - +
79E THR* 2.8 39.4 - - - +
80E ARG* 4.0 4.7 - - - +
117E ASN 3.8 9.4 + - - -
118E VAL* 3.6 20.3 - - - +
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Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25E HIS* 4.0 7.4 + - - -
30E MET* 5.2 4.8 + - - +
32E SER* 5.1 0.7 - - - -
67E VAL* 4.1 16.3 + - + +
68E LEU 3.1 2.8 - - - -
69E GLY* 1.3 81.4 - - - +
71E HIS* 1.3 62.0 + - - +
73E LEU* 3.9 25.8 - - + -
77E GLU* 3.3 11.2 - - - +
80E ARG* 4.0 10.5 - - - +
141E TRP* 3.9 21.0 - - + -
155E LEU* 5.2 4.0 - - - +
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Residues in contact with HIS 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22E ALA* 3.2 31.0 + - + +
23E ARG 3.8 4.6 + - - -
24E PRO* 3.4 37.4 - - + +
25E HIS* 3.7 21.5 + - + +
70E ALA* 1.3 75.8 - - - +
72E ASN* 1.3 63.6 + - + +
73E LEU 4.1 0.2 - - - -
77E GLU* 2.8 19.2 + - - +
141E TRP* 3.1 25.0 + - - -
154E VAL* 3.2 28.0 - - + +
155E LEU* 3.2 23.3 + - - +
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Residues in contact with ASN 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71E HIS* 1.3 77.8 - - + +
73E LEU* 1.3 61.7 + - - +
74E SER* 2.7 32.5 + - - -
75E ARG* 3.3 45.7 + - + +
77E GLU* 2.9 18.4 + - - +
80E ARG* 3.1 13.7 + - - -
153E SER* 3.1 13.5 - - - -
154E VAL* 3.8 24.9 - - + +
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Residues in contact with LEU 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E SER* 4.1 5.2 - - - +
34E GLN* 3.8 21.8 + - - +
40E HIS* 3.7 32.1 - - + +
70E ALA* 3.9 28.0 - - + -
72E ASN* 1.3 73.1 - - - +
74E SER* 1.3 59.5 + - - +
75E ARG 3.3 1.2 - - - +
80E ARG* 3.6 16.5 + - - +
141E TRP* 3.6 43.5 - - + +
151E ILE* 5.9 1.8 - - + -
152E ALA 4.6 3.8 - - - +
153E SER* 2.8 16.4 + - - +
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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