Contacts of the strand formed by residues 32 - 39 (chain F) in PDB entry 1H4O
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 LYS 32 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113E ASP* 4.3 16.8 + - - -
115E SER* 5.3 3.6 + - - -
145E ASP* 3.7 14.7 - - - +
27F GLU 5.7 0.9 - - - -
28F LEU* 3.9 19.9 + - - +
29F PHE* 3.3 10.9 - - - +
30F LYS 3.9 12.8 - - - +
31F GLY* 1.3 80.9 - - - +
33F LYS* 1.3 67.6 + - - +
34F GLY 3.9 0.2 + - - -
68F GLN* 4.0 29.8 + - + -
69F VAL* 4.3 14.9 - - + +
132F VAL 3.7 1.0 - - - +
133F GLN* 3.7 0.9 - - - -
134F ASP* 2.8 22.9 + - - +
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Residues in contact with LYS 33 (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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145E ASP* 3.7 23.5 + - - +
147E THR* 5.3 2.9 + - - -
32F LYS* 1.3 77.2 - - - +
34F GLY* 1.3 60.0 + - - +
65F LYS 3.0 27.4 + - - -
66F GLY* 3.9 17.7 + - - +
67F VAL* 3.5 7.3 - - + -
68F GLN* 2.8 30.8 + - - +
69F VAL 3.8 0.9 + - - -
131F VAL* 4.3 14.8 - - + -
132F VAL 3.5 7.6 - - - +
133F GLN* 4.3 23.3 - - + +
161F LEU* 3.9 36.9 + - + +
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Residues in contact with GLY 34 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29F PHE* 3.8 16.5 - - - -
32F LYS 3.9 0.6 + - - -
33F LYS* 1.3 77.6 - - - +
35F VAL* 1.3 62.9 + - - +
67F VAL* 4.1 4.0 - - - -
69F VAL* 3.1 14.8 - - - -
131F VAL* 3.5 7.1 - - - +
132F VAL 2.8 37.2 + - - +
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Residues in contact with VAL 35 (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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29F PHE* 3.6 8.8 - - - -
34F GLY* 1.3 80.3 - - - +
36F LEU* 1.3 70.9 + - - +
37F PHE* 4.5 1.1 - - + +
55F PHE* 3.9 25.6 - - + -
62F LEU* 4.5 13.5 - - + -
67F VAL* 4.0 23.1 - - + -
69F VAL 3.0 8.9 + - - +
70F VAL* 3.3 14.5 - - + -
71F ALA 2.9 24.9 + - - -
130F MET 3.2 13.2 - - - +
131F VAL* 4.6 4.7 - - + -
157F ILE* 4.1 18.8 - - + -
161F LEU* 5.1 0.7 - - + -
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Residues in contact with LEU 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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9F ILE* 3.8 26.5 - - + -
25F LEU* 4.5 13.2 - - + -
29F PHE* 3.8 17.7 - - + -
35F VAL* 1.3 76.8 - - - +
37F PHE* 1.3 59.5 + - - +
71F ALA* 3.4 28.9 - - + +
73F LEU* 4.3 21.3 - - + -
97F LEU* 4.8 0.7 - - + -
104F PHE* 3.9 20.2 - - + -
128F PHE* 3.9 12.4 - - + -
129F SER* 3.4 1.0 - - - -
130F MET* 2.7 54.4 + - + +
132F VAL* 4.5 2.1 - - + +
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Residues in contact with PHE 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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35F VAL* 4.6 0.4 - - + -
36F LEU* 1.3 75.4 - - - +
38F GLY* 1.3 56.8 + - - +
39F VAL* 4.1 11.2 - - + -
51F HIS* 3.5 25.8 - + - +
52F LEU* 3.9 23.6 - - + -
55F PHE* 3.4 51.8 - + + -
70F VAL* 4.0 7.2 - - + -
71F ALA 2.9 15.8 + - - +
72F CYS* 3.3 39.7 - - + -
73F LEU* 2.8 26.7 + - - +
94F VAL* 4.0 8.7 - - + -
128F PHE* 3.2 20.9 - - - +
129F SER* 4.0 11.0 - - - -
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Residues in contact with GLY 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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37F PHE* 1.3 74.8 - - - +
39F VAL* 1.3 61.0 + - - -
51F HIS* 3.5 9.9 - - - -
73F LEU 3.3 9.9 - - - -
125F LEU* 4.5 3.1 - - - -
126F LYS 4.2 4.3 - - - -
127F ARG* 3.4 5.0 - - - -
128F PHE* 2.9 51.3 + - - -
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Residues in contact with VAL 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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37F PHE* 4.1 4.9 - - + -
38F GLY* 1.3 73.8 - - - -
40F PRO* 1.3 69.1 - - - +
41F GLY 4.0 7.2 - - - +
47F CYS* 3.6 17.3 - - + +
51F HIS* 3.3 30.3 - - + +
72F CYS* 3.9 20.0 - - - -
73F LEU 3.0 10.4 + - - +
74F SER* 3.5 32.7 - - - -
75F VAL 4.6 0.2 + - - -
84F TRP* 3.9 22.2 - - + -
125F LEU* 3.9 11.5 - - - +
127F ARG* 4.0 3.1 - - - +
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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