Contacts of the strand formed by residues 34 - 41 (chain C) in PDB entry 1NUE
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 ARG 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3C ASN* 4.7 1.0 + - - -
6C ARG* 3.4 6.3 - - - +
32C GLY 3.9 0.8 + - - +
33C PHE* 1.3 73.4 - - - +
35C LEU* 1.3 62.9 + - - +
36C VAL* 3.4 10.6 + - - +
78C TRP* 3.3 5.4 - - - -
79C GLU* 2.8 81.2 + - + +
140C VAL 2.8 24.0 + - - -
141C ASP* 3.0 24.6 + - - -
142C TYR* 3.1 66.6 + - + +
143C LYS* 4.9 0.4 - - - +
144C SER* 3.8 24.9 - - - +
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Residues in contact with LEU 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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25C ILE* 5.5 1.8 - - + -
29C GLU* 6.2 0.2 - - + -
34C ARG* 1.3 71.5 - - - +
36C VAL* 1.3 59.7 + - - +
37C ALA 3.5 22.9 - - - +
38C MET* 3.9 29.4 - - + -
76C MET* 4.2 7.9 - - + -
77C VAL 3.7 8.3 - - - +
78C TRP* 3.6 44.1 - - + +
142C TYR* 2.8 38.8 + - - +
16F VAL* 5.8 2.7 - - + -
21F VAL* 5.1 14.1 - - + -
40F PHE* 3.4 28.2 - - + -
74F VAL* 5.1 0.4 - - + -
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Residues in contact with VAL 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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6C ARG* 3.9 22.0 - - - +
34C ARG* 3.6 20.6 - - - +
35C LEU* 1.3 74.8 - - - +
37C ALA* 1.3 56.7 + - - +
77C VAL* 2.8 21.6 + - + +
78C TRP 4.4 1.6 - - - -
79C GLU* 3.5 34.8 - - + +
138C GLU 3.9 0.2 - - - +
139C LEU* 3.8 26.5 - - + -
140C VAL* 2.8 48.2 + - - +
40F PHE* 3.8 5.3 - - - -
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Residues in contact with ALA 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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35C LEU* 3.5 6.9 - - - +
36C VAL* 1.3 81.2 - - - +
38C MET* 1.3 65.0 + - - +
76C MET* 3.2 2.6 - - - -
77C VAL* 3.0 28.3 + - + -
134C PHE* 3.6 21.1 - - + -
138C GLU 3.7 10.8 - - - +
139C LEU* 3.5 28.0 - - + -
40F PHE* 4.0 7.1 - - - -
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Residues in contact with MET 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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25C ILE* 4.0 16.4 - - + -
35C LEU* 3.9 25.1 - - + -
37C ALA* 1.3 79.6 - - - +
39C LYS* 1.3 69.1 + - - +
74C VAL* 4.1 8.1 - - + -
75C ALA 3.2 12.6 - - - +
76C MET* 3.9 17.9 - - + +
134C PHE* 3.8 4.7 - - - -
138C GLU 5.2 0.2 + - - -
21F VAL* 4.6 7.6 - - + -
38F MET* 3.8 28.0 - - + -
39F LYS* 3.3 2.4 - - - +
40F PHE* 3.0 40.9 + - + +
74F VAL* 3.8 33.4 - - + -
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Residues in contact with LYS 39 (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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38C MET* 1.3 79.3 - - - +
40C PHE* 1.3 61.5 + - - +
41C LEU* 4.1 26.2 - - + +
73C VAL 3.8 0.3 - - - +
74C VAL* 3.6 4.0 - - - +
75C ALA* 2.9 36.1 + - + +
133C TRP* 2.7 30.8 + - - -
134C PHE* 3.7 22.0 - - + +
135C LYS* 6.1 0.6 - - - +
138C GLU* 3.0 33.8 + - - +
38F MET* 3.3 11.9 - - - +
39F LYS* 4.8 5.2 - - + -
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Residues in contact with PHE 40 (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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16C VAL* 4.0 15.7 - - + -
39C LYS* 1.3 75.0 - - - +
41C LEU* 1.3 64.6 + - - +
72C PRO* 3.4 35.4 - - + -
73C VAL 3.3 13.0 - - - -
74C VAL* 3.7 20.9 - - + -
35F LEU* 3.4 42.6 - - + -
36F VAL 3.6 24.5 - - - -
37F ALA* 4.0 4.3 - - - -
38F MET* 3.0 29.4 + - + +
138F GLU* 4.6 8.0 - - - +
140F VAL* 4.0 16.1 - - + +
142F TYR* 3.8 7.2 - + - -
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Residues in contact with LEU 41 (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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39C LYS* 4.1 32.3 - - + +
40C PHE* 1.3 79.1 - - - +
42C ARG* 1.3 68.3 + - - +
43C ALA* 4.3 11.2 - - + +
47C HIS* 5.6 4.3 - - + +
72C PRO* 4.0 5.6 - - - -
73C VAL* 2.7 48.1 + - + +
75C ALA* 4.1 13.0 - - + -
133C TRP* 4.2 22.0 - - + -
140F VAL* 4.0 9.2 - - - -
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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