Contacts of the strand formed by residues 26 - 32 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLY 5.3 3.6 - - - +
23A LYS 4.9 3.9 - - - +
24A GLY 4.1 5.2 - - - +
25A TRP* 1.3 76.2 - - - +
27A LEU* 1.3 80.9 + - - +
28A MET* 3.5 22.9 - - + +
39A MET 3.5 2.9 - - - +
40A TYR* 3.7 5.6 - - - -
41A SER 2.9 34.6 + - - +
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Residues in contact with LEU 27 (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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7A PHE* 3.9 12.3 - - + -
13A GLU* 3.6 34.3 - - + +
14A LEU* 5.6 3.1 - - + -
26A ASP* 1.3 83.1 + - - +
28A MET* 1.3 60.0 + - - +
38A TYR* 3.9 24.7 - - + -
39A MET 3.4 15.7 - - - +
40A TYR* 3.7 39.2 - - + +
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Residues in contact with MET 28 (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 ASP* 3.5 30.5 - - + +
27A LEU* 1.3 79.3 - - - +
29A GLN* 1.3 62.4 + - - +
30A ASN* 4.1 2.9 - - - +
38A TYR* 3.3 8.9 - - - -
39A MET* 3.0 44.1 + - + +
41A SER* 3.7 33.2 - - - +
42A VAL* 5.9 0.7 - - - -
31B ILE* 5.1 26.9 - - + +
34B ASP* 4.8 13.0 - - - +
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Residues in contact with GLN 29 (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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28A MET* 1.3 72.3 - - - +
30A ASN* 1.3 74.4 + - - +
31A ILE* 3.4 22.2 - - - +
36A PRO* 3.8 20.9 - - + +
37A ILE 3.7 3.4 - - - +
38A TYR* 2.9 40.5 + - + -
110D ARG* 2.6 55.5 + - - +
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Residues in contact with ASN 30 (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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28A MET* 4.1 3.7 + - - +
29A GLN* 1.3 79.3 - - - +
31A ILE* 1.3 64.1 + - - +
36A PRO* 3.5 1.7 - - - +
37A ILE* 2.6 54.8 + - + +
39A MET* 3.0 23.1 - - + +
29B GLN 4.9 0.3 - - - +
30B ASN* 3.5 25.2 - - - +
31B ILE* 2.9 42.6 + - - +
32B MET* 3.8 9.7 - - - +
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Residues in contact with ILE 31 (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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29A GLN* 3.4 24.2 - - - +
30A ASN* 1.3 77.6 - - - +
32A MET* 1.3 63.9 + - - +
33A ASN 4.3 0.2 - - - -
34A ASP* 3.9 27.6 - - - +
35A MET 3.4 10.1 - - - +
36A PRO* 4.7 1.3 - - + -
37A ILE* 4.5 0.2 - - - -
28B MET* 5.1 20.1 - - + +
30B ASN* 2.8 28.5 + - - +
39B MET* 4.0 8.1 - - - +
110D ARG* 2.5 35.7 - - - +
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Residues in contact with MET 32 (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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30A ASN 4.2 0.2 - - - -
31A ILE* 1.3 74.0 - - - +
33A ASN* 1.3 73.7 + - - +
34A ASP 3.2 0.2 - - - -
35A MET* 2.8 38.0 + - - +
37A ILE* 4.3 14.1 - - + +
30B ASN* 3.9 7.2 - - - +
37B ILE* 6.0 2.2 - - + -
39B MET* 3.6 30.3 - - + +
74B THR* 3.8 9.9 - - + -
129B PHE* 3.5 9.2 - - + -
134B VAL* 4.0 23.6 - - + -
163B ALA* 3.7 28.9 - - - -
165B LEU* 4.1 13.7 - - + -
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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