Contacts of the strand formed by residues 21 - 28 (chain C) in PDB entry 3RZW
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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77B ASP 5.0 5.5 + - - -
78B ASN* 4.3 10.6 + - - +
79B TYR* 3.5 49.9 + + + +
20C GLU* 1.3 106.5 + - - +
22C ILE* 1.3 71.2 + - - +
37C LYS* 3.4 33.3 + - + -
38C VAL 3.2 8.5 - - - +
39C LYS* 3.4 55.2 + - + +
84C GLU* 4.2 2.3 - - - +
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Residues in contact with ILE 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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21C TYR* 1.3 82.2 - - - +
23C LYS* 1.3 60.4 - - - +
24C LEU* 3.8 29.9 + - + +
36C PHE 3.4 1.4 - - - +
37C LYS* 3.4 6.8 - - - +
38C VAL* 2.8 39.9 + - - +
40C MET* 3.7 33.0 - - + -
77C PRO* 4.2 6.7 - - + -
82C MET* 3.9 14.4 - - + -
83C GLU* 3.8 17.7 - - - -
84C GLU* 3.1 30.3 - - + +
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Residues in contact with LYS 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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27B TRP* 3.6 35.4 - - + -
22C ILE* 1.3 71.1 - - - +
24C LEU* 1.3 67.7 + - - +
25C LYS* 3.8 12.1 - - - +
35C HIS* 2.9 42.8 + - + -
36C PHE 3.2 6.3 - - - -
37C LYS* 4.6 4.0 - - - +
84C GLU* 2.7 22.6 + - - +
85C GLU* 2.8 63.8 + - - +
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Residues in contact with LEU 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 ILE* 3.8 28.0 - - + +
23C LYS* 1.3 78.3 - - - +
25C LYS* 1.3 63.1 + - - +
26C VAL* 3.8 1.4 + - - +
34C ILE 3.9 0.2 - - - +
35C HIS* 3.4 3.0 - - - -
36C PHE* 2.8 38.7 + - - +
38C VAL* 4.3 14.6 - - + -
44C LEU* 4.3 6.7 - - + -
47C LEU* 4.0 18.4 - - + -
77C PRO* 4.5 4.9 - - + -
82C MET* 4.0 22.7 - - + -
83C GLU 4.2 0.2 - - - +
86C ASP* 3.4 28.5 - - + +
88C ILE* 3.9 29.4 - - + -
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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 LYS* 3.8 12.8 - - - +
24C LEU* 1.3 71.5 - - - +
26C VAL* 1.3 61.9 + - - +
27C ILE* 3.8 6.8 + - + -
33C GLU* 3.4 21.9 + - - +
34C ILE 3.9 2.9 - - - -
35C HIS* 3.5 24.3 + - + +
85C GLU* 3.4 46.1 + - + +
86C ASP 2.8 12.2 + - - +
87C VAL* 3.3 18.0 - - + +
88C ILE* 2.8 28.6 + - - +
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Residues in contact with VAL 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 LEU 4.3 2.5 - - - +
25C LYS* 1.3 76.3 - - - +
27C ILE* 1.3 58.5 + - - +
28C GLY 4.0 0.2 + - - -
32C SER 3.8 0.5 - - - +
33C GLU* 3.4 3.8 - - - -
34C ILE 2.8 37.5 + - - +
36C PHE* 3.5 29.4 - - + -
47C LEU* 4.0 19.5 - - + -
51C TYR* 3.7 26.5 - - + -
64C PHE* 4.6 4.0 - - + -
88C ILE* 3.4 17.9 - - + +
90C VAL* 3.3 30.1 - - + -
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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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25C LYS* 4.5 6.7 - - + +
26C VAL* 1.3 75.6 - - - +
28C GLY* 1.3 71.2 + - - +
29C GLN* 3.2 18.4 + - - +
31C SER* 4.4 11.7 - - - +
32C SER 3.3 8.1 - - - +
33C GLU* 4.1 29.4 - - + +
87C VAL* 3.7 35.9 - - + -
88C ILE 3.0 10.3 + - - +
89C GLU* 3.6 1.4 - - + -
90C VAL* 3.0 25.0 + - - -
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Residues in contact with GLY 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 VAL 4.0 0.2 + - - -
27C ILE* 1.3 78.8 - - - +
29C GLN* 1.3 60.6 + - - -
30C ASP* 3.0 10.3 - - - -
31C SER* 2.6 23.7 + - - -
32C SER* 3.0 18.7 + - - -
51C TYR* 3.7 21.2 + - - -
90C VAL* 4.0 8.1 - - - -
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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