Contacts of the strand formed by residues 26 - 32 (chain F) in PDB entry 3HPN
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 ASP 26 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19B HIS* 4.4 18.8 + - - -
22F GLY 5.0 4.9 - - - +
23F LYS 5.0 4.6 - - - +
24F GLY 4.2 4.5 - - - +
25F TRP* 1.3 75.7 - - - +
27F LEU* 1.3 73.7 + - - +
28F MET* 3.5 25.0 + - + +
39F MET 3.4 2.6 - - - +
40F TYR* 3.5 6.0 - - - -
41F SER 2.9 34.4 + - - +
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Residues in contact with LEU 27 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B ASN* 3.3 41.1 + - + +
107B PHE 5.1 1.7 - - - +
108B GLN* 3.2 13.7 + - - +
7F PHE* 3.9 15.7 - - + -
13F GLU* 3.6 26.2 - - + +
26F ASP* 1.3 80.7 + - - +
28F MET* 1.3 59.9 + - - +
38F TYR* 4.0 16.2 - - + -
39F MET 3.4 15.5 - - - +
40F TYR* 3.6 41.8 - - + +
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Residues in contact with MET 28 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108B GLN* 3.6 5.4 - - - +
110B ARG* 5.7 4.5 - - - +
31E ILE* 5.0 27.1 - - + +
34E ASP* 5.0 10.3 - - - +
26F ASP* 3.5 31.0 - - + +
27F LEU* 1.3 78.8 - - - +
29F GLN* 1.3 60.8 - - - +
30F ASN* 4.0 3.8 - - - +
37F ILE 3.8 1.0 - - - +
38F TYR* 3.3 6.8 - - - -
39F MET* 3.0 43.2 + - + +
41F SER* 3.6 34.1 - - - +
42F VAL* 5.7 0.7 - - - -
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Residues in contact with GLN 29 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 4.9 1.2 + - - -
108B GLN* 2.9 21.7 + - + +
110B ARG* 4.7 16.0 + - - +
111B LEU* 3.4 32.5 - - + +
30E ASN* 4.7 1.0 - - - +
28F MET* 1.3 73.3 - - - +
30F ASN* 1.3 72.3 + - - +
31F ILE* 3.3 37.8 + - - +
36F PRO* 3.9 19.9 - - + +
37F ILE 3.9 2.7 - - - +
38F TYR* 3.0 40.5 + - + -
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Residues in contact with ASN 30 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ARG* 4.9 3.8 + - - -
30E ASN* 3.3 27.0 - - - +
31E ILE* 3.1 36.1 + - - +
32E MET* 3.9 9.9 - - - +
28F MET* 3.9 4.8 + - - +
29F GLN* 1.3 77.9 - - - +
31F ILE* 1.3 62.6 + - - +
36F PRO* 3.4 2.6 - - - +
37F ILE* 2.5 53.0 + - + +
39F MET* 2.8 30.6 - - + +
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Residues in contact with ILE 31 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B ARG* 6.5 0.9 - - + -
111B LEU* 4.7 8.7 - - + -
28E MET* 5.1 22.8 - - - +
30E ASN* 3.0 27.7 + - - +
39E MET* 4.0 9.7 - - - +
29F GLN* 3.3 35.2 - - - +
30F ASN* 1.3 75.6 - - - +
32F MET* 1.3 62.9 + - - +
34F ASP* 3.8 28.3 - - - +
35F MET 3.3 10.5 - - - +
36F PRO* 4.7 0.9 - - + -
37F ILE* 4.6 0.4 - - - -
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Residues in contact with MET 32 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30E ASN* 4.0 8.5 - - - +
37E ILE* 6.0 2.0 - - + -
39E MET* 3.7 26.7 - - + +
74E THR* 4.1 10.1 - - + -
129E PHE* 3.3 7.2 - - + -
134E VAL* 3.8 26.2 - - + -
163E ALA* 3.8 27.4 - - - -
165E LEU* 4.3 10.5 - - + -
31F ILE* 1.3 72.0 - - - +
33F ASN* 1.3 74.8 + - - +
34F ASP 3.2 0.7 - - - -
35F MET* 2.7 37.7 + - - +
37F ILE* 4.2 14.5 - - + +
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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