Contacts of the strand formed by residues 53 - 59 (chain C) in PDB entry 5HVO
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 THR 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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11C HIS* 2.8 19.7 + - + +
12C ARG* 3.4 30.5 + - + +
13C LEU* 2.7 33.4 + - - +
50C LYS* 5.9 2.5 - - - +
52C THR* 1.3 73.5 - - - +
54C PHE* 1.3 65.3 + - - +
81C ASN* 6.2 0.2 - - - -
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Residues in contact with PHE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ARG* 5.2 1.7 + - - -
13C LEU* 3.2 24.2 - - + -
15C ILE* 3.7 17.9 - - + -
47C GLY 4.0 19.7 - - - -
48C LEU* 5.7 0.2 - - - -
49C SER* 3.6 26.5 - - - -
50C LYS* 4.5 16.4 - - + -
52C THR* 3.6 29.2 - - - -
53C THR* 1.3 84.8 + - - +
55C GLN* 1.3 60.9 + - - +
56C TRP* 4.2 20.5 + + + +
81C ASN* 3.8 19.8 + - - +
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Residues in contact with GLN 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ARG* 3.8 29.1 + - - +
13C LEU 3.0 6.9 + - - +
14C LEU* 3.5 4.0 - - + -
15C ILE* 3.1 25.3 + - - +
54C PHE* 1.3 75.6 - - - +
56C TRP* 1.3 63.7 + - - +
57C TYR* 3.5 27.2 - - + +
77C LYS* 4.7 14.8 - - - +
81C ASN* 3.1 44.3 + - - +
82C ALA 3.8 4.6 + - - +
83C THR* 2.9 21.7 + - - +
139C GLU* 3.7 7.0 + - - +
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Residues in contact with TRP 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C ILE* 3.7 46.2 - - + -
17C SER* 5.7 3.8 - - - -
20C LEU* 3.7 15.9 - - + +
21C PRO* 3.8 35.0 - - + -
36C MET* 5.5 10.2 - - + +
45C LEU* 4.1 39.0 - - + -
54C PHE* 4.2 21.6 + + + +
55C GLN* 1.3 74.8 - - - +
57C TYR* 1.3 64.7 + - - +
80C PHE 3.8 14.5 + - - -
81C ASN* 2.9 21.5 + - + +
82C ALA* 4.0 5.8 - - + -
83C THR* 2.6 33.4 + - - +
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Residues in contact with TYR 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12C ARG* 4.0 6.8 + - - -
14C LEU* 3.5 34.5 - - + +
15C ILE 2.7 19.7 + - - +
16C VAL* 3.4 8.5 - - + -
17C SER* 3.1 27.8 + - - +
19C ARG 4.8 0.3 - - - +
20C LEU* 3.4 3.7 - - - +
55C GLN* 3.5 28.2 - - + +
56C TRP* 1.3 75.6 - - - +
58C GLY* 1.3 58.2 + - - +
83C THR* 3.4 32.1 - - + +
85C VAL* 5.1 4.0 - - + -
132C PHE* 4.6 2.0 - - - -
135C THR* 4.3 7.0 - - + -
136C ILE* 3.8 42.2 - - + -
139C GLU* 2.7 36.6 + - - +
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Residues in contact with GLY 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C SER 3.2 15.3 - - - -
20C LEU* 3.0 31.9 - - - +
57C TYR* 1.3 75.1 - - - +
59C TRP* 1.3 66.8 + - - -
83C THR 3.4 2.8 + - - -
84C PRO* 3.4 0.2 - - - +
85C VAL* 2.9 23.1 + - - +
132C PHE* 4.0 4.5 - - - -
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Residues in contact with TRP 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18C ASN* 2.9 27.9 + - - +
19C ARG* 3.2 53.5 - - + +
20C LEU 3.1 18.4 + - - -
58C GLY* 1.3 69.8 - - - -
60C PRO* 1.3 77.3 - - + +
61C GLY* 3.1 37.7 + - - -
62C LEU* 3.5 19.2 + - - -
85C VAL* 3.2 24.9 - - + +
87C MET* 3.5 44.7 + - + +
89C ASP* 4.9 6.3 - - - -
92C ALA* 4.0 22.2 - - + +
96C TYR* 5.6 7.0 - + + -
132C PHE* 3.9 6.7 - - + -
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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