Contacts of the strand formed by residues 33 - 38 (chain C) in PDB entry 3NPS
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 VAL 33 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23C CYS* 4.9 1.6 - - - -
28C ILE* 3.9 30.7 - - + -
31C ASN 4.7 1.3 - - - +
32C TYR* 1.3 79.0 - - - +
34C SER* 1.3 76.5 + - - +
35C TRP* 3.7 19.0 - - - +
48C ILE* 4.3 2.1 - - - +
49C TYR* 3.8 1.6 - - - -
50C ASP 3.6 4.0 + - - -
51C ASN* 2.9 42.2 + - - +
66C LYS* 4.7 2.0 - - + -
71C ALA* 3.8 27.1 - - + -
88C CYS* 4.2 11.9 - - + -
89C GLN 3.5 9.2 - - - +
90C SER* 4.6 1.3 - - - +
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Residues in contact with SER 34 (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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100B ASP* 2.6 37.2 + - - +
32C TYR 4.3 0.2 - - - -
33C VAL* 1.3 77.6 - - - +
35C TRP* 1.3 64.6 + - - +
36C TYR* 4.0 14.1 - - - -
46C LEU* 4.2 0.9 - - - -
48C ILE 3.1 11.4 - - - -
49C TYR* 3.4 15.9 - - - +
50C ASP 4.2 0.7 + - - -
88C CYS* 3.2 4.9 - - - -
89C GLN* 2.9 37.9 + - - -
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Residues in contact with TRP 35 (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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6C GLN* 4.0 5.4 - - - -
21C ILE* 3.3 36.1 - - + -
22C SER 4.2 0.4 - - - -
23C CYS* 3.6 31.4 - - + -
33C VAL* 3.7 12.8 - - + +
34C SER* 1.3 77.0 - - - +
36C TYR* 1.3 61.6 + - - +
46C LEU* 3.7 2.1 - - - +
47C LEU* 2.8 33.1 + - + -
48C ILE* 2.8 38.6 + - + +
51C ASN 4.9 2.7 + - - -
64C GLY* 4.9 2.1 - - - -
65C SER 5.1 0.2 + - - -
71C ALA* 4.0 3.4 - - + +
72C VAL* 3.7 20.7 + - - +
73C LEU* 3.5 53.2 - - + -
86C TYR 5.0 0.2 - - - -
87C TYR* 3.2 25.6 - - - -
88C CYS* 3.7 18.4 - - + -
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Residues in contact with TYR 36 (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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45B LEU* 4.6 4.0 - - + -
100B MET* 3.0 58.1 - - - +
103B TRP* 3.8 21.3 - + - -
34C SER* 4.0 9.9 - - - -
35C TRP* 1.3 76.8 - - - +
37C GLN* 1.3 61.4 + - - +
38C GLN 4.3 0.2 + - - -
44C PRO* 4.5 10.5 - - + -
45C LYS 3.2 9.4 - - - +
46C LEU* 3.6 26.0 - - + -
47C LEU* 4.0 4.5 - - - -
86C TYR* 3.3 7.1 - - - +
87C TYR* 2.8 44.1 + - + +
89C GLN* 3.0 39.2 + - + -
98C PHE* 3.9 16.6 - + - -
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Residues in contact with GLN 37 (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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36C TYR* 1.3 75.8 - - - +
38C GLN* 1.3 65.8 + - - +
39C LYS* 2.5 42.3 + - - +
43C ALA 4.5 0.3 - - - +
44C PRO* 3.3 2.7 - - - +
45C LYS* 2.8 47.5 + - + +
47C LEU* 3.8 24.4 - - + +
62C PHE* 4.0 12.1 - - - -
82C ASP* 4.4 9.3 + - - +
84C ALA* 3.7 19.8 - - + +
85C ASP 3.4 4.0 - - - -
86C TYR* 3.0 29.8 + - + -
87C TYR* 5.4 0.4 - - - -
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Residues in contact with GLN 38 (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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39B GLN* 3.1 34.5 + - - +
45B LEU* 4.0 3.8 - - - +
91B TYR* 3.4 22.2 + - - -
36C TYR 4.3 0.2 + - - -
37C GLN* 1.3 74.1 - - - +
39C LYS* 1.3 68.0 + - - +
40C PRO* 4.0 0.3 - - - +
41C GLY 6.0 0.2 - - - +
42C THR 3.0 28.9 + - - +
43C ALA 4.9 0.2 - - - -
44C PRO* 3.8 26.1 - - + +
84C ALA* 3.6 2.9 - - - +
85C ASP* 2.7 44.9 + - + +
87C TYR* 4.3 14.3 + - + -
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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