Contacts of the strand formed by residues 21 - 27 (chain C) in PDB entry 3UDB
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 TYR 21 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15C MET* 3.2 16.6 - - + +
16C HIS* 4.7 2.2 - + - +
17C ASP* 2.8 18.9 + - + +
18C SER* 3.4 15.8 - - - +
20C ARG* 1.3 112.6 + - + +
22C GLU* 1.3 59.9 + - - +
38C MET* 3.6 34.8 - - + -
39C ARG 3.3 2.5 - - - +
40C ASP* 3.0 45.2 + - + +
41C LYS* 3.9 4.0 - - - -
47C VAL* 4.6 13.9 - - + -
81C LYS* 6.0 1.0 - - - +
82C GLU* 2.5 27.7 + - - +
84C ILE* 3.9 14.6 - - + -
93C VAL* 4.2 13.3 - - + +
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Residues in contact with GLU 22 (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 MET* 4.1 1.3 - - - -
21C TYR* 1.3 72.8 - - - +
23C LEU* 1.3 73.6 + - - +
24C VAL* 3.9 3.0 - - + +
38C MET* 3.2 3.5 - - - -
39C ARG* 2.7 78.2 + - + +
41C LYS* 3.8 18.4 - - + +
111D ARG* 4.2 18.8 + - - +
243D TYR 5.0 4.7 - - - +
245D HIS* 5.1 11.9 - - + +
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Residues in contact with LEU 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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15C MET* 3.6 37.2 - - + +
22C GLU* 1.3 77.5 - - - +
24C VAL* 1.3 59.9 + - - +
25C LYS* 3.7 11.0 - - - +
26C ASP* 3.8 6.7 - - - +
36C ARG* 3.4 51.8 - - + +
37C LEU 3.6 3.8 - - - +
38C MET* 4.3 1.6 - - - -
111D ARG* 2.7 24.1 + - - -
243D TYR* 3.7 48.4 - - + +
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Residues in contact with VAL 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 GLU* 3.9 4.7 - - - +
23C LEU* 1.3 76.7 - - - +
25C LYS* 1.3 60.5 + - - +
37C LEU* 2.9 26.8 + - + +
38C MET 3.8 3.6 - - - -
39C ARG* 3.7 32.1 - - + +
46C LEU* 3.9 12.8 - - + -
109D ALA 3.6 24.2 - - - +
110D GLY* 4.2 2.5 - - - -
111D ARG* 2.8 55.4 + - + +
243D TYR* 3.9 5.2 - - - -
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Residues in contact with LYS 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 LEU* 3.7 5.0 - - - +
24C VAL* 1.3 84.8 - - + +
26C ASP* 1.3 77.3 + - - +
27C ILE* 3.2 17.9 + - + +
37C LEU* 3.0 25.5 + - + +
110D GLY* 4.1 29.6 - - - +
111D ARG* 5.0 0.2 - - - -
212D VAL* 3.2 26.6 + - - +
213D GLY 3.4 20.2 + - - +
214D ALA* 3.9 12.1 - - - +
243D TYR* 4.2 19.6 + - + -
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Residues in contact with ASP 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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12C LEU* 4.0 19.0 - - + +
23C LEU* 3.8 6.1 - - - +
25C LYS* 1.3 84.5 - - - +
27C ILE* 1.3 61.6 + - - +
35C ALA 3.8 4.3 - - - +
36C ARG* 2.6 51.2 + - - +
243D TYR* 4.9 13.6 + - - +
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Residues in contact with ILE 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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12C LEU* 5.7 1.2 - - - +
25C LYS* 3.2 23.8 + - + +
26C ASP* 1.3 78.3 - - - +
28C GLY* 1.3 75.5 + - - +
34C VAL* 3.8 6.0 - - - +
35C ALA* 2.7 46.0 + - + +
37C LEU* 3.6 32.5 - - + -
96C TYR* 5.4 9.4 - - + +
107D CYS 5.9 1.6 - - - +
110D GLY* 5.5 1.1 - - - -
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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