Contacts of the strand formed by residues 35 - 43 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76E ARG* 3.2 36.8 - - - +
126E SER 6.0 0.7 - - - +
129E PHE* 3.4 52.5 - - + -
130E GLU* 6.4 2.2 - - - -
31F ILE* 3.3 3.9 - - - -
32F MET 2.7 39.1 + - - +
33F ASN 3.1 1.0 + - - -
34F ASP* 1.3 73.4 - - - +
36F PRO* 1.3 82.9 - - + +
37F ILE* 3.4 3.1 + - + +
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Residues in contact with PRO 36 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129E PHE* 6.1 0.7 - - - +
132E ARG* 5.0 1.6 + - - -
29F GLN* 3.9 27.4 - - - +
30F ASN 3.5 6.1 - - - +
31F ILE* 4.6 1.8 - - + -
34F ASP 3.4 9.0 - - - +
35F MET* 1.3 98.5 - - + +
37F ILE* 1.3 59.9 + - - +
38F TYR* 4.0 20.7 + - + +
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Residues in contact with ILE 37 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E MET* 6.1 1.6 - - + -
129E PHE* 5.1 7.4 - - + +
132E ARG* 3.3 44.4 - - + +
134E VAL* 5.6 9.4 - - + -
28F MET 3.8 0.5 - - - +
29F GLN* 4.4 0.4 - - - +
30F ASN* 2.5 58.3 + - + +
32F MET* 4.2 17.5 - - + +
35F MET* 3.7 11.4 - - + +
36F PRO* 1.3 74.3 - - - +
38F TYR* 1.3 63.5 + - - +
39F MET* 3.9 9.4 - - + +
165F LEU* 4.4 11.0 - - + -
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Residues in contact with TYR 38 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B TYR* 3.9 21.1 + - - -
106B ASN* 3.6 18.7 + - - -
108B GLN* 3.8 5.8 - - - -
111B LEU* 4.8 0.7 - - - +
132E ARG* 3.3 24.3 + - - +
7F PHE* 3.3 21.8 - - + +
13F GLU* 3.7 43.2 + - + -
27F LEU* 4.0 11.9 - - + -
28F MET 3.3 14.6 - - - -
29F GLN* 3.0 33.1 + - + -
36F PRO* 4.0 24.4 - - + +
37F ILE* 1.3 78.1 - - - +
39F MET* 1.3 63.4 + - - +
165F LEU* 3.8 4.0 - - - +
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Residues in contact with MET 39 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31E ILE 4.1 10.5 - - - +
32E MET* 3.7 12.6 - - + +
33E ASN 5.9 0.2 - - - -
7F PHE* 3.7 8.3 - - - -
26F ASP 3.4 0.7 - - - +
27F LEU* 3.4 5.4 - - - +
28F MET* 3.0 48.0 + - + +
30F ASN* 2.8 37.0 - - + +
37F ILE* 3.9 15.0 - - + +
38F TYR* 1.3 74.7 - - - +
40F TYR* 1.3 60.1 + - - +
41F SER* 4.3 14.1 - - - -
163F ALA* 4.2 11.2 - - - -
164F LEU 3.3 16.8 - - - +
165F LEU* 3.3 27.6 - - + -
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Residues in contact with TYR 40 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F PHE* 3.7 26.3 - + - -
13F GLU 4.2 5.6 + - - -
16F TRP* 3.6 33.9 + + + +
18F THR* 4.0 13.8 - - + +
25F TRP* 3.5 12.2 - - + -
26F ASP 3.6 10.8 - - - -
27F LEU* 3.6 52.4 - - + +
39F MET* 1.3 70.3 - - - +
41F SER* 1.3 59.8 + - - +
54F LEU* 3.6 49.6 - - + -
163F ALA 3.6 0.2 - - - -
164F LEU* 2.7 47.7 + - + +
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Residues in contact with SER 41 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ASN* 5.0 10.2 + - - -
34E ASP* 5.3 4.0 + - - -
24F GLY 3.9 0.7 - - - +
25F TRP* 3.6 4.1 - - - -
26F ASP* 2.9 37.3 + - - +
28F MET* 3.6 26.9 - - - +
39F MET* 4.3 16.7 - - - -
40F TYR* 1.3 76.5 - - - +
42F VAL* 1.3 65.5 + - - +
43F CYS* 5.7 0.3 - - - +
162F VAL 3.4 11.8 + - - -
163F ALA* 4.2 8.6 - - - +
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Residues in contact with VAL 42 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24F GLY* 3.6 33.4 - - - +
25F TRP* 4.0 22.4 - - + +
28F MET* 5.7 0.9 - - - -
41F SER* 1.3 78.3 + - - +
43F CYS* 1.3 65.1 + - - +
44F ASN* 4.2 12.8 - - - +
52F ASN* 4.1 3.1 - - - +
157F ASP* 3.4 46.4 - - + +
160F ALA 3.2 3.9 - - - +
161F CYS* 3.3 0.7 - - - -
162F VAL* 3.0 33.6 + - + +
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Residues in contact with CYS 43 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33E ASN* 5.2 0.4 - - - -
34E ASP* 3.4 37.2 - - - +
41F SER* 5.7 0.7 - - - +
42F VAL* 1.3 74.7 - - - +
44F ASN* 1.3 67.7 + - - +
45F VAL* 3.3 10.9 + - - +
81F PHE* 3.6 22.2 - - - -
160F ALA 3.6 5.6 - - - -
161F CYS* 2.1 46.4 - - - -
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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