Contacts of the strand formed by residues 26 - 32 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B GLY 5.1 4.5 - - - +
23B LYS 5.0 4.6 - - - +
24B GLY 4.2 4.9 - - - +
25B TRP* 1.3 76.6 - - - +
27B LEU* 1.3 76.5 + - - +
28B MET* 3.4 23.9 + - + +
39B MET 3.3 3.5 - - - +
40B TYR* 3.6 4.9 - - - -
41B SER 2.9 37.6 + - - +
19D HIS* 4.5 20.0 - - - -
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Residues in contact with LEU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B PHE* 3.9 15.7 - - + -
13B GLU* 3.7 26.5 - - + +
14B LEU* 5.5 0.4 - - + -
26B ASP* 1.3 81.7 + - - +
28B MET* 1.3 58.4 + - - +
38B TYR* 3.9 18.2 - - + -
39B MET 3.4 14.8 - - - +
40B TYR* 3.6 40.3 - - + +
106D ASN* 3.6 37.5 + - + +
107D PHE 5.0 2.1 - - - +
108D GLN* 3.4 13.2 + - - +
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Residues in contact with MET 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A ILE* 5.1 23.1 - - + +
34A ASP* 5.0 10.5 - - - +
26B ASP* 3.5 35.7 - - + +
27B LEU* 1.3 75.8 - - - +
29B GLN* 1.3 62.6 + - - +
30B ASN* 3.9 3.1 + - - +
38B TYR* 3.2 7.8 - - - -
39B MET* 2.9 44.7 + - + +
41B SER* 3.6 34.3 - - - +
42B VAL* 5.7 0.9 - - - -
108D GLN* 3.8 5.2 - - - +
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Residues in contact with GLN 29 (chain B).
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* 4.9 0.3 - - - +
28B MET* 1.3 72.5 - - - +
30B ASN* 1.3 74.5 + - - +
31B ILE* 3.3 26.0 - - - +
36B PRO* 3.7 20.9 - - + +
37B ILE 4.0 2.5 - - - +
38B TYR* 2.8 37.0 + - + -
103D TYR* 4.8 1.6 + - - -
108D GLN* 2.8 29.7 + - + +
110D ARG* 4.8 14.6 + - - +
111D LEU* 3.2 43.3 - - + +
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Residues in contact with ASN 30 (chain B).
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 4.8 0.2 - - - +
30A ASN* 3.5 24.4 - - - +
31A ILE* 2.8 45.0 + - - +
32A MET* 3.9 8.1 - - - +
28B MET* 3.9 4.7 + - - +
29B GLN* 1.3 81.6 - - - +
31B ILE* 1.3 64.1 + - - +
37B ILE* 2.6 52.6 + - + +
39B MET* 2.9 24.7 - - + +
110D ARG* 4.6 3.8 + - - -
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Residues in contact with ILE 31 (chain B).
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* 5.1 21.2 - - - +
30A ASN* 2.9 27.2 + - - +
39A MET* 4.2 6.9 - - - +
29B GLN* 3.3 36.1 - - + +
30B ASN* 1.3 78.7 - - - +
32B MET* 1.3 64.5 + - - +
34B ASP* 3.9 27.6 - - - +
35B MET 3.3 9.9 - - - +
36B PRO* 4.6 1.1 - - + -
110D ARG* 5.8 7.9 - - + +
111D LEU* 4.0 14.1 - - + -
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Residues in contact with MET 32 (chain B).
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* 3.8 8.1 - - - +
37A ILE* 5.8 2.7 - - + -
39A MET* 3.5 30.7 - - + +
74A THR* 3.9 9.9 - - + -
129A PHE* 3.5 8.8 - - + -
134A VAL* 4.1 21.1 - - + -
163A ALA* 3.6 29.2 - - - -
165A LEU* 4.1 13.5 - - + -
31B ILE* 1.3 73.7 - - - +
33B ASN* 1.3 81.6 + - - +
35B MET* 2.9 25.6 + - - +
37B ILE* 4.1 13.6 - - + +
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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