Contacts of the strand formed by residues 21 - 26 (chain C) in PDB entry 3NSH
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
---------------------------
Residue Dist Surf HB Arom Phob DC
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11C ASN 3.9 0.5 - - - +
12C LEU* 3.4 8.7 - - - -
13C ARG* 2.9 51.5 + - + +
14C GLY* 3.4 23.7 + - - -
15C LYS* 5.9 0.7 - - + +
19C GLY 4.6 0.4 - - - -
20C TYR* 1.3 73.7 - - - +
22C VAL* 1.3 63.4 + - - +
23C GLU 5.1 0.2 - - - -
34C ASN* 3.4 36.4 + - + -
35C ILE 3.0 23.8 - - - +
36C LEU* 3.9 2.5 - - - +
37C VAL 4.3 0.4 - - - +
119C SER 3.7 16.6 - - - -
120C ASN* 3.6 21.6 - - + +
121C TRP* 3.9 24.0 - + + -
174C ALA* 5.0 8.5 + - - -
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Residues in contact with VAL 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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11C ASN* 3.7 32.8 - - + +
12C LEU* 3.7 12.3 - - + -
21C TYR* 1.3 75.8 - - - +
23C GLU* 1.3 71.1 + - - +
24C MET* 3.5 23.5 + - + -
34C ASN* 4.4 2.5 - - - -
35C ILE* 2.8 36.3 + - + +
37C VAL* 3.8 5.8 - - + +
93C ILE* 4.0 11.2 - - + -
95C HIS* 5.8 1.3 - - + -
125C LEU* 4.8 2.2 - - + -
180C MET* 3.7 27.8 - - + -
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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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11C ASN 4.5 2.8 + - - -
21C TYR* 4.4 0.8 + - - -
22C VAL* 1.3 77.6 - - - +
24C MET* 1.3 68.0 - - - +
32C THR* 4.1 28.6 + - + +
33C LEU 3.7 4.7 - - - +
34C ASN* 3.7 13.5 + - - +
56C ARG* 5.8 0.3 + - - -
93C ILE* 3.6 18.9 - - - +
94C PRO* 3.3 33.8 - - + +
95C HIS* 4.9 17.9 + - + -
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Residues in contact with MET 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 VAL* 4.0 13.5 - - + -
23C GLU* 1.3 79.9 - - - +
25C THR* 1.3 69.5 + - - +
26C VAL* 6.2 0.7 - - + -
32C THR* 3.4 7.4 - - - +
33C LEU* 2.7 34.6 + - + -
35C ILE* 3.5 43.1 - - + -
44C PHE* 3.9 11.9 - - + -
91C VAL* 3.6 26.2 - - + -
92C SER 3.4 6.1 - - - +
93C ILE* 3.9 26.2 - - + -
94C PRO* 4.0 1.6 - - - -
125C LEU* 4.0 24.5 - - + -
142C PHE* 4.3 5.2 - - + -
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Residues in contact with THR 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* 5.4 0.2 - - - +
24C MET* 1.3 80.9 - - - +
26C VAL* 1.3 63.8 + - - +
27C GLY 4.4 1.1 + - - -
30C PRO* 3.9 25.2 - - + +
31C GLN 3.1 7.4 - - - -
32C THR* 4.2 14.8 - - - +
90C LEU 5.4 0.2 + - - -
91C VAL* 3.3 9.6 - - - +
92C SER* 2.8 51.7 + - - +
94C PRO* 3.8 23.6 - - + -
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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 MET* 5.7 0.9 - - + -
25C THR* 1.3 77.9 - - - +
27C GLY* 1.3 61.9 + - - +
31C GLN* 2.8 44.1 + - + +
33C LEU* 4.1 18.4 - - + -
44C PHE* 4.3 14.1 - - + -
46C VAL* 5.3 1.8 - - + -
58C TYR* 3.6 33.8 - - + -
89C ASP* 4.7 0.4 - - - -
90C LEU 3.4 2.0 - - - +
91C VAL* 4.1 10.8 - - + -
105C ILE* 3.5 33.7 - - + -
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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