Contacts of the strand formed by residues 46 - 51 (chain A) in PDB entry 1PIC
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 46 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A VAL* 4.6 1.8 - - - -
37A ARG* 3.1 72.2 + - - +
41A LYS* 4.1 7.8 - - - +
45A TYR* 1.3 80.5 - - - +
47A CYS* 1.3 61.1 + - - +
48A SER 3.5 0.4 + - - -
57A HIS* 4.9 0.9 - - - +
58A CYS 2.8 16.6 - - - +
59A VAL* 4.0 0.4 - - - +
201B PTR 4.1 7.6 - - + -
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Residues in contact with CYS 47 (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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34A PHE* 3.6 35.2 - - - -
35A LEU 3.0 21.3 - - - -
36A VAL* 3.8 8.5 - - - +
46A ALA* 1.3 71.8 - - - +
48A SER* 1.3 60.0 + - - +
49A VAL* 3.0 11.7 + - - +
58A CYS* 2.7 29.5 + - - +
59A VAL* 4.5 2.2 - - - +
60A ILE* 4.2 10.7 - - + +
69A PHE* 3.7 35.4 - - + -
83A VAL* 5.1 0.7 - - - -
102A LEU* 4.5 0.9 - - - -
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Residues in contact with SER 48 (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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22A ALA* 4.6 0.4 - - - -
26A LEU* 2.8 38.3 - - - +
34A PHE* 3.4 0.7 - - - -
35A LEU* 2.8 46.9 + - - +
37A ARG* 3.9 3.8 + - - -
46A ALA 3.5 0.6 + - - -
47A CYS* 1.3 67.8 - - - +
49A VAL* 1.3 59.1 + - - +
55A VAL* 4.4 1.1 - - - -
56A LYS 3.2 10.5 - - - -
57A HIS* 2.7 39.3 + - - -
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Residues in contact with VAL 49 (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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32A GLY 4.8 0.2 - - - -
33A THR 3.0 15.9 - - - +
34A PHE* 4.0 11.7 - - + +
47A CYS* 3.0 5.6 + - + +
48A SER* 1.3 75.6 - - - +
50A VAL* 1.3 78.4 + - - +
51A VAL* 3.6 12.7 + - + +
55A VAL* 4.2 0.7 - - - -
56A LYS* 3.0 25.5 + - + +
58A CYS* 3.7 28.0 - - - -
69A PHE* 6.2 0.7 - - + -
91A LEU* 5.2 0.7 - - + -
100A VAL* 4.1 17.3 - - + -
101A THR 4.7 4.3 - - - +
102A LEU* 4.6 10.3 - - + -
204B MET* 4.3 11.2 - - + -
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Residues in contact with VAL 50 (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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26A LEU* 3.3 43.7 - - + +
29A LYS* 4.7 4.0 - - + +
30A ARG 4.0 3.1 - - - +
31A ASP* 2.8 30.8 - - - +
32A GLY 3.3 7.1 + - - -
33A THR* 3.0 29.8 + - - +
49A VAL* 1.3 77.3 - - - +
51A VAL* 1.3 59.9 + - - +
53A GLY* 3.8 31.4 - - - +
55A VAL* 3.8 11.2 - - + +
100A VAL* 3.4 6.6 - - - +
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Residues in contact with VAL 51 (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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49A VAL* 4.1 15.5 - - + +
50A VAL* 1.3 75.7 - - - +
52A ASP* 1.3 69.9 + - + +
53A GLY 2.9 8.7 + - - -
54A GLU* 3.0 27.6 + - - +
56A LYS* 5.6 6.3 - - + -
97A SER 3.2 26.9 - - - +
98A LEU* 3.3 31.4 - - + +
100A VAL* 3.0 34.1 - - + -
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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