Contacts of the strand formed by residues 35 - 43 (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 MET 35 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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31E ILE* 3.3 3.6 - - - -
32E MET 2.8 33.1 + - - +
33E ASN 3.0 1.6 + - - -
34E ASP* 1.3 79.6 - - - +
36E PRO* 1.3 81.0 - - + +
37E ILE* 3.4 2.8 + - + +
76F ARG* 3.1 37.2 - - - +
129F PHE* 3.6 49.6 - - + -
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Residues in contact with PRO 36 (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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29E GLN* 3.9 19.5 - - + +
30E ASN 3.5 6.3 - - - +
31E ILE* 4.6 2.2 - - + -
34E ASP 3.4 9.4 - - - +
35E MET* 1.3 98.2 - - + +
37E ILE* 1.3 60.9 + - - +
38E TYR* 3.9 26.8 + - + +
132F ARG* 4.7 3.8 + - - -
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Residues in contact with ILE 37 (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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28E MET 4.0 0.5 - - - +
29E GLN* 3.8 0.8 - - - +
30E ASN* 2.6 58.2 + - + +
31E ILE 4.3 0.2 - - - +
32E MET* 4.1 18.4 - - + +
35E MET* 3.7 11.4 - - + +
36E PRO* 1.3 74.1 - - - +
38E TYR* 1.3 62.9 + - - +
39E MET* 4.2 6.2 - - + +
165E LEU* 4.5 13.9 - - + -
32F MET* 6.0 2.0 - - + -
129F PHE* 5.2 8.5 - - + +
132F ARG* 3.8 42.6 - - + +
134F VAL* 5.7 8.5 - - + -
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Residues in contact with TYR 38 (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* 3.3 21.5 - - + +
8E ALA* 6.4 0.9 - - - -
13E GLU* 3.7 48.5 + - + -
27E LEU* 4.0 18.4 - - + -
28E MET 3.3 15.0 - - - -
29E GLN* 2.9 33.5 + - + -
36E PRO* 3.9 25.9 - - + +
37E ILE* 1.3 75.8 - - - +
39E MET* 1.3 63.4 + - - +
165E LEU* 3.8 0.9 - - - +
132F ARG* 3.1 25.8 + - - +
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Residues in contact with MET 39 (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* 3.7 7.8 - - - -
26E ASP 3.5 0.2 - - - +
27E LEU* 3.4 5.2 - - - +
28E MET* 2.9 50.4 + - + +
30E ASN* 3.1 34.8 - - + +
37E ILE* 4.2 14.4 - - + +
38E TYR* 1.3 74.2 - - - +
40E TYR* 1.3 60.7 + - - +
41E SER* 4.3 12.6 - - - -
163E ALA* 4.2 16.4 - - + -
164E LEU 3.4 17.0 - - - +
165E LEU* 3.2 29.2 - - + -
31F ILE 4.0 10.5 - - - +
32F MET* 3.7 8.5 - - + +
33F ASN 6.0 0.2 - - - -
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Residues in contact with TYR 40 (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* 3.6 26.7 - + + -
13E GLU 4.2 5.4 + - - -
16E TRP* 3.6 32.6 + + + +
18E THR* 4.0 12.5 - - + +
25E TRP* 3.5 12.8 - - + -
26E ASP 3.5 9.6 - - - -
27E LEU* 3.5 52.1 - - + +
39E MET* 1.3 71.1 - - - +
41E SER* 1.3 60.4 + - - +
54E LEU* 3.6 50.0 - - + -
164E LEU* 2.7 44.3 + - + +
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Residues in contact with SER 41 (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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24E GLY 3.8 0.7 - - - +
25E TRP* 3.5 3.2 - - - -
26E ASP* 2.8 37.7 + - - +
28E MET* 3.7 30.9 - - - +
39E MET* 4.3 9.8 - - - -
40E TYR* 1.3 76.9 - - - +
42E VAL* 1.3 66.9 + - - +
43E CYS* 5.7 0.5 - - - +
161E CYS* 6.1 0.3 - - - -
162E VAL 3.3 12.4 + - - -
163E ALA* 4.1 11.1 - - - +
33F ASN* 4.9 9.9 + - - -
34F ASP* 5.2 4.2 + - - -
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Residues in contact with VAL 42 (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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24E GLY* 3.6 34.5 - - - +
25E TRP* 3.8 23.3 - - + +
28E MET* 5.8 0.7 - - - -
41E SER* 1.3 79.8 + - - +
43E CYS* 1.3 64.5 - - - +
44E ASN* 4.1 11.9 - - - +
52E ASN* 4.1 2.9 - - - +
157E ASP* 3.4 46.4 - - + +
160E ALA 3.2 3.3 - - - +
161E CYS* 3.3 1.0 - - - -
162E VAL* 3.0 32.4 + - + +
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Residues in contact with CYS 43 (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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41E SER* 5.7 0.4 - - - +
42E VAL* 1.3 72.9 - - - +
44E ASN* 1.3 69.0 + - - +
45E VAL* 3.2 11.3 + - - +
81E PHE* 3.7 20.0 - - - -
160E ALA 3.7 5.6 - - - -
161E CYS* 2.1 46.7 - - - -
33F ASN* 5.7 0.2 - - - -
34F ASP* 3.3 37.0 - - - +
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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