Contacts of the strand formed by residues 35 - 43 (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 MET 35 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76C ARG* 3.4 36.3 - - - +
126C SER 5.9 1.3 - - - +
129C PHE* 3.6 50.0 - - + -
130C GLU* 6.0 4.0 - - - +
31D ILE* 3.4 2.4 - - - -
32D MET 2.8 31.5 + - - +
33D ASN 3.0 1.0 + - - -
34D ASP* 1.3 79.4 - - - +
36D PRO* 1.3 83.9 - - + +
37D ILE* 3.3 4.3 + - - +
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Residues in contact with PRO 36 (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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129C PHE* 5.8 1.9 - - - +
132C ARG* 4.4 3.8 + - - -
29D GLN* 3.8 29.2 - - + +
30D ASN 3.5 6.1 - - - +
31D ILE* 4.6 2.4 - - + -
34D ASP 3.4 9.6 - - - +
35D MET* 1.3 101.4 - - + +
37D ILE* 1.3 59.6 + - - +
38D TYR* 3.9 20.0 + - + +
111F LEU* 4.7 9.2 - - + -
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Residues in contact with ILE 37 (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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32C MET* 6.3 0.9 - - + -
129C PHE* 4.9 13.5 - - + +
132C ARG* 3.5 45.1 - - + +
134C VAL* 5.4 9.4 - - + -
29D GLN* 4.4 0.2 - - - -
30D ASN* 2.6 60.5 + - + +
32D MET* 4.2 17.0 - - + +
35D MET 3.6 11.4 - - - +
36D PRO* 1.3 72.5 - - - +
38D TYR* 1.3 60.1 + - - +
39D MET* 4.0 10.7 - - + +
165D LEU* 4.4 8.5 - - + -
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Residues in contact with TYR 38 (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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132C ARG* 2.7 33.8 + - - +
7D PHE* 3.3 22.5 - - + +
8D ALA* 6.4 0.7 - - - -
13D GLU* 3.8 35.1 + - + -
27D LEU* 4.0 8.1 - - + -
28D MET 3.3 13.7 - - - -
29D GLN* 2.9 24.9 + - + -
36D PRO* 3.9 25.1 - - + -
37D ILE* 1.3 74.8 - - - +
39D MET* 1.3 63.6 + - - +
165D LEU* 3.8 1.7 - - - +
103F TYR* 5.9 0.2 - - - -
106F ASN* 5.2 0.2 + - - -
108F GLN* 2.3 57.3 - - - +
111F LEU* 3.5 13.0 - - - +
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Residues in contact with MET 39 (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 4.5 6.1 - - - +
32C MET* 3.7 16.4 - - + +
7D PHE* 3.7 3.1 - - - -
26D ASP 3.4 0.7 - - - +
27D LEU* 3.4 10.5 - - - +
28D MET* 2.9 49.4 + - + +
30D ASN* 3.0 37.5 - - + +
37D ILE* 4.0 16.2 - - + +
38D TYR* 1.3 74.5 - - - +
40D TYR* 1.3 59.8 + - - +
41D SER* 4.2 13.2 - - - -
163D ALA* 4.2 11.2 - - + -
164D LEU 3.4 15.3 - - - +
165D LEU* 3.3 26.9 - - + -
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Residues in contact with TYR 40 (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* 3.6 26.9 - + - -
13D GLU 4.0 5.3 + - - -
16D TRP* 3.5 38.5 + + + +
18D THR* 4.1 12.4 - - + +
25D TRP* 3.6 12.3 - - + -
26D ASP* 3.5 19.3 - - - -
27D LEU* 3.6 44.0 - - + +
39D MET* 1.3 71.6 - - - +
41D SER* 1.3 59.8 + - - +
54D LEU* 3.6 45.3 - - + -
163D ALA* 3.6 0.2 - - - -
164D LEU* 2.7 47.0 + - + +
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Residues in contact with SER 41 (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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33C ASN* 5.0 10.6 + - - -
24D GLY 3.9 0.2 - - - +
25D TRP* 3.6 3.1 - - - -
26D ASP* 2.9 36.4 + - - +
28D MET* 3.6 31.2 - - - +
39D MET* 4.2 11.5 - - - -
40D TYR* 1.3 77.3 - - - +
42D VAL* 1.3 66.8 + - - +
43D CYS* 5.8 0.9 - - - +
162D VAL 3.4 11.4 + - - -
163D ALA* 4.1 8.9 - - - +
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Residues in contact with VAL 42 (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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24D GLY* 3.6 34.1 - - - +
25D TRP* 3.8 23.1 - - + +
28D MET* 5.7 1.1 - - - -
41D SER* 1.3 78.1 + - - +
43D CYS* 1.3 65.6 + - - +
44D ASN* 4.1 14.6 - - - +
52D ASN* 4.2 0.2 - - - +
157D ASP* 3.3 46.4 - - + +
160D ALA 3.3 1.5 - - - +
161D CYS* 3.3 2.3 - - - -
162D VAL* 2.9 35.2 + - + +
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Residues in contact with CYS 43 (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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33C ASN* 5.1 0.7 - - - -
34C ASP* 4.0 33.4 - - - +
41D SER* 5.8 1.1 - - - +
42D VAL* 1.3 74.2 - - - +
44D ASN* 1.3 70.3 + - - +
45D VAL* 3.3 10.5 + - - +
81D PHE* 3.6 21.3 - - - -
160D ALA 3.7 4.9 - - - -
161D CYS* 2.1 47.3 - - - -
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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