Contacts of the strand formed by residues 26 - 32 (chain E) 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 E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22E GLY 5.1 4.5 - - - +
23E LYS 4.9 4.2 - - - +
24E GLY 4.1 5.2 - - - +
25E TRP* 1.3 75.7 - - - +
27E LEU* 1.3 76.1 + - - +
28E MET* 3.5 23.3 + - + +
40E TYR* 3.5 6.2 - - - -
41E SER 2.8 36.9 + - - +
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Residues in contact with LEU 27 (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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7E PHE* 3.9 16.4 - - + -
13E GLU* 3.6 31.0 - - + +
14E LEU* 5.5 3.1 - - + -
26E ASP* 1.3 82.1 + - - +
28E MET* 1.3 60.0 + - - +
38E TYR* 4.0 22.7 - - + -
39E MET 3.4 15.3 - - - +
40E TYR* 3.5 42.5 - - + +
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Residues in contact with MET 28 (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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26E ASP* 3.5 30.5 - - + +
27E LEU* 1.3 79.0 - - - +
29E GLN* 1.3 62.4 + - - +
30E ASN* 4.1 2.5 - - - +
37E ILE 4.0 0.3 - - - +
38E TYR* 3.3 8.1 - - - -
39E MET* 2.9 45.6 + - + +
41E SER* 3.7 33.9 - - - +
42E VAL* 5.8 0.4 - - - -
31F ILE* 5.1 26.2 - - + +
34F ASP* 5.1 9.2 - - - +
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Residues in contact with GLN 29 (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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110B ARG* 3.0 48.2 + - - +
28E MET* 1.3 74.3 - - - +
30E ASN* 1.3 73.0 + - - +
31E ILE* 3.3 22.2 - - - +
36E PRO* 3.9 16.9 - - + +
37E ILE 3.8 3.1 - - - +
38E TYR* 2.9 42.8 + - + -
29F GLN 5.8 0.2 - - - +
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Residues in contact with ASN 30 (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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110B ARG* 4.9 0.2 - - - +
28E MET* 4.0 3.4 + - - +
29E GLN* 1.3 77.7 - - - +
31E ILE* 1.3 62.8 + - - +
36E PRO* 3.5 1.6 - - - +
37E ILE* 2.6 54.0 + - + +
39E MET* 3.1 23.4 - - + +
29F GLN 4.7 0.7 - - - +
30F ASN* 3.3 28.2 - - - +
31F ILE* 3.0 42.3 + - - +
32F MET* 4.0 9.1 - - - +
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Residues in contact with ILE 31 (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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110B ARG* 2.5 33.9 - - - +
29E GLN* 3.3 24.2 - - - +
30E ASN* 1.3 80.3 - - - +
32E MET* 1.3 62.6 + - - +
34E ASP* 3.8 27.8 - - - +
35E MET 3.3 11.2 - - - +
36E PRO* 4.7 1.1 - - + -
37E ILE* 4.4 0.4 - - - -
28F MET* 5.0 21.7 - - + +
30F ASN* 3.1 24.4 + - - +
39F MET* 4.1 8.3 - - - +
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Residues in contact with MET 32 (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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31E ILE* 1.3 73.8 - - - +
33E ASN* 1.3 73.2 + - - +
34E ASP 3.2 0.4 - - - -
35E MET* 2.8 35.6 + - - +
37E ILE* 4.1 14.7 - - + +
30F ASN* 3.9 7.6 - - - +
37F ILE* 6.1 1.8 - - + -
39F MET* 3.7 28.5 - - + +
74F THR* 3.8 12.8 - - + -
129F PHE* 3.3 8.2 - - + -
134F VAL* 3.9 22.9 - - + -
163F ALA* 3.7 28.0 - - - -
165F LEU* 4.1 11.9 - - + -
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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