Contacts of the strand formed by residues 26 - 32 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22D GLY 5.2 5.9 - - - +
23D LYS 5.2 1.4 - - - +
24D GLY 4.1 5.5 - - - +
25D TRP* 1.3 77.7 - - - +
27D LEU* 1.3 76.2 + - - +
28D MET* 3.4 22.8 - - + +
39D MET 3.4 2.9 - - - +
40D TYR* 3.7 5.0 - - - -
41D SER 2.9 35.3 + - - +
19F HIS* 5.5 7.8 + - - -
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Residues in contact with LEU 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D PHE* 3.9 17.9 - - + -
13D GLU* 3.6 22.2 - - + +
26D ASP* 1.3 82.3 + - - +
28D MET* 1.3 59.1 + - - +
38D TYR* 4.0 15.9 - - + -
39D MET 3.4 15.5 - - - +
40D TYR* 3.6 37.9 - - + +
106F ASN* 4.0 8.7 - - - +
107F PHE 5.7 0.9 - - - +
108F GLN* 3.4 29.9 + - - +
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Residues in contact with MET 28 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ILE* 5.7 17.5 - - + +
34C ASP* 5.4 7.9 - - - +
26D ASP* 3.4 35.0 - - + +
27D LEU* 1.3 76.9 - - - +
29D GLN* 1.3 60.7 + - - +
30D ASN* 4.0 0.9 - - - +
37D ILE 4.0 0.2 - - - +
38D TYR* 3.3 7.5 - - - -
39D MET* 2.9 45.3 + - + +
41D SER* 3.6 35.0 - - - +
42D VAL* 5.7 0.4 - - - -
108F GLN* 4.8 0.7 - - - -
110F ARG* 4.1 9.6 - - - +
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Residues in contact with GLN 29 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28D MET* 1.3 71.7 - - - +
30D ASN* 1.3 61.7 + - - +
31D ILE* 3.3 32.1 - - - +
36D PRO* 3.8 15.9 - - + +
37D ILE 3.8 3.1 - - - +
38D TYR* 2.9 39.8 + - + -
108F GLN* 3.8 7.7 + - - +
110F ARG* 1.6 77.9 + - + +
111F LEU* 3.0 28.3 - - - +
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Residues in contact with ASN 30 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ASN* 3.4 25.7 - - - +
31C ILE* 3.4 34.2 + - - +
32C MET* 3.7 11.1 - - - +
28D MET* 4.0 2.0 + - - +
29D GLN* 1.3 76.0 - - - +
31D ILE* 1.3 63.6 + - - +
37D ILE* 2.6 53.5 + - + +
39D MET* 3.0 29.1 - - + +
110F ARG* 3.5 12.9 + - - -
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Residues in contact with ILE 31 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C MET* 5.5 17.0 - - - +
30C ASN* 3.3 25.1 + - - +
39C MET* 4.4 6.1 - - - +
29D GLN* 3.3 31.4 - - - +
30D ASN* 1.3 77.2 - - - +
32D MET* 1.3 64.8 + - - +
34D ASP* 3.8 28.3 - - - +
35D MET 3.4 10.1 - - - +
36D PRO* 4.6 1.8 - - + -
37D ILE* 4.5 0.2 - - - -
110F ARG* 3.7 27.8 - - + +
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Residues in contact with MET 32 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C ASN* 3.8 10.1 - - - +
37C ILE* 6.1 1.3 - - + -
39C MET* 3.7 29.8 - - + +
74C THR* 3.9 11.9 - - + -
129C PHE* 3.4 9.1 - - + -
134C VAL* 4.0 22.4 - - + -
163C ALA* 3.7 28.3 - - - -
165C LEU* 4.4 8.7 - - + -
31D ILE* 1.3 72.7 - - - +
33D ASN* 1.3 74.5 + - - +
34D ASP 3.2 0.4 - - - -
35D MET* 2.8 34.0 + - - +
37D ILE* 4.2 13.9 - - + +
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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