Contacts of the strand formed by residues 22 - 30 (chain C) in PDB entry 5CYP
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 PHE 22 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C LYS* 4.1 24.7 - - - -
20C GLN 4.9 0.2 - - - -
21C GLY* 1.3 86.0 - - - -
23C GLU* 1.3 64.1 + - - +
24C PHE* 4.8 0.2 - - - +
79C VAL* 3.7 26.7 - - + -
80C ARG 2.9 10.0 + - - +
81C MET* 3.3 12.5 - - + +
82C LYS* 2.8 23.9 + - - +
270C MET* 4.4 24.9 - - + -
271C GLN* 5.3 5.8 - - - -
274C LYS* 4.5 13.7 - - - +
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Residues in contact with GLU 23 (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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21C GLY 4.3 2.2 + - - +
22C PHE* 1.3 74.7 - - - +
24C PHE* 1.3 61.5 + - - +
25C ASN* 5.3 1.1 - - - +
82C LYS* 3.6 40.2 + - + +
127C ARG* 5.7 5.2 - - - -
128C ILE 4.7 1.7 - - - +
129C PRO* 3.8 11.2 - - - +
130C ASP* 2.8 55.7 + - + +
134C HIS* 4.0 2.1 - - + -
270C MET* 4.7 0.3 - - - +
274C LYS* 3.0 33.0 + - - +
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Residues in contact with PHE 24 (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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22C PHE 3.8 0.2 + - - -
23C GLU* 1.3 76.3 - - - +
25C ASN* 1.3 63.2 + - - +
26C ILE* 3.6 33.9 - - + -
81C MET* 4.1 24.5 - - + -
82C LYS 3.5 6.8 + - - +
83C LEU* 3.6 11.3 - - + +
84C THR 2.9 24.9 + - - -
134C HIS* 3.6 31.0 - - + -
135C CYS* 4.2 10.3 - - + -
265C LEU* 3.4 27.8 - - + -
266C ILE* 4.9 1.6 - - + -
270C MET* 3.6 32.8 - - + -
273C ILE* 4.0 20.2 - - + -
274C LYS* 3.7 8.5 - - + -
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Residues in contact with ASN 25 (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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23C GLU* 5.3 1.2 - - - +
24C PHE* 1.3 80.0 + - - +
26C ILE* 1.3 63.5 + - - +
82C LYS* 4.8 2.1 + - - +
84C THR* 3.2 31.2 + - - +
86C ILE* 4.5 9.6 - - + -
130C ASP 3.0 27.7 + - - +
131C THR* 3.3 13.2 - - - +
132C ARG 2.6 29.8 + - - +
133C VAL* 4.1 6.2 - - - -
134C HIS* 3.1 17.4 + - - +
135C CYS* 3.1 25.1 + - - +
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Residues in contact with ILE 26 (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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24C PHE* 3.6 31.0 - - + -
25C ASN* 1.3 77.9 - - - +
27C MET* 1.3 64.3 + - - +
28C VAL* 4.2 3.8 - - + -
43C LEU* 4.6 18.8 - - + -
83C LEU* 3.9 18.2 - - + -
84C THR 2.8 10.9 + - - +
85C VAL* 3.1 15.2 - - + +
86C ILE* 2.8 25.5 + - - +
135C CYS* 3.3 16.4 - - + +
137C LEU* 4.2 29.2 - - + -
265C LEU* 4.5 17.7 - - + -
266C ILE* 5.2 5.4 - - + -
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Residues in contact with MET 27 (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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26C ILE* 1.3 74.4 - - - +
28C VAL* 1.3 66.5 + - - +
29C VAL* 3.7 26.9 - - + -
67C ILE* 5.2 0.4 - - + -
86C ILE* 3.6 28.5 - - + +
88C THR* 4.1 7.9 - - + -
104C ILE* 3.9 17.7 - - + -
107C PHE* 3.5 34.5 - - + -
108C ILE* 4.4 15.3 - - + -
133C VAL* 3.7 24.0 - - + +
135C CYS 2.8 10.0 + - - +
136C CYS* 3.2 9.4 - - + -
137C LEU 2.8 27.5 + - - +
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Residues in contact with VAL 28 (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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26C ILE* 4.2 2.6 + - + -
27C MET* 1.3 73.0 - - - +
29C VAL* 1.3 57.8 + - - +
36C LYS* 4.2 11.7 - - + +
39C LEU* 5.1 3.4 - - + -
40C ILE* 3.7 27.1 - - + -
85C VAL* 4.6 7.0 - - + -
86C ILE 3.2 12.0 + - - +
87C ASP* 3.4 25.1 - - - +
88C THR* 2.5 30.5 + - - +
137C LEU* 3.7 19.1 - - + -
139C PHE* 3.9 26.5 - - + -
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Residues in contact with VAL 29 (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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27C MET* 3.7 26.0 - - + -
28C VAL* 1.3 79.4 - - - +
30C GLY* 1.3 55.2 + - - +
36C LYS* 3.5 5.4 - - - +
88C THR* 3.6 4.5 - - - +
91C PHE* 3.5 20.4 - - + -
104C ILE* 3.8 20.2 - - + -
136C CYS* 3.7 14.1 - - - -
137C LEU 2.8 14.4 + - - +
138C TYR* 3.3 22.2 - - + -
139C PHE* 2.7 33.6 + - - -
154C PHE* 4.1 4.9 - - + -
158C LEU* 4.0 9.2 - - + -
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Residues in contact with GLY 30 (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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29C VAL* 1.3 81.6 - - - +
31C GLN* 1.3 68.7 + - - -
36C LYS* 3.1 19.6 + - - +
88C THR* 4.6 0.6 + - - -
89C PRO 4.5 0.5 - - - +
90C GLY* 3.3 11.6 - - - -
91C PHE* 3.5 21.9 + - - -
138C TYR* 5.1 1.1 - - - -
139C PHE* 4.0 15.3 - - - -
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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