Contacts of the strand formed by residues 34 - 41 (chain U) in PDB entry 1NSK
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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4U LEU* 6.2 0.9 - - - -
32U GLY 5.4 1.3 - - - +
33U PHE* 1.3 73.9 - - - +
35U LEU* 1.3 60.6 + - - +
36U VAL* 3.2 15.1 + - - +
78U TRP* 3.2 6.6 - - - -
79U GLU* 2.7 75.1 + - + +
140U VAL 3.3 11.7 + - - -
141U ASP* 3.9 3.6 + - - +
142U TYR* 2.7 87.9 + - + +
143U LYS* 5.8 0.2 - - - +
144U SER* 4.0 26.5 - - - +
147U HIS* 5.8 5.4 - - - -
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Residues in contact with LEU 35 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16N VAL* 5.7 2.0 - - + -
21N VAL* 5.2 10.5 - - + -
40N PHE* 3.1 40.9 - - + -
74N VAL* 4.9 2.7 - - + -
25U ILE* 5.4 1.6 - - + -
34U ARG* 1.3 68.8 - - - +
36U VAL* 1.3 61.8 + - - +
37U ALA 3.1 33.7 - - - +
38U MET* 3.8 26.9 - - + -
76U MET* 4.3 10.3 - - + -
77U VAL 3.7 4.9 - - - +
78U TRP* 3.3 33.5 - - + -
142U TYR* 2.7 29.8 + - - +
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Residues in contact with VAL 36 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40N PHE* 3.5 8.9 - - - -
6U ARG* 4.6 7.6 - - + +
34U ARG* 3.7 14.1 - - - +
35U LEU* 1.3 73.9 - - - +
37U ALA* 1.3 59.3 + - - +
77U VAL* 2.8 21.7 + - + +
79U GLU* 3.5 37.7 - - + +
139U LEU* 3.6 36.6 - - + -
140U VAL* 2.8 42.0 + - - +
141U ASP* 4.6 5.8 - - - +
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Residues in contact with ALA 37 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40N PHE* 3.9 6.3 - - - -
35U LEU* 3.1 9.0 - - - +
36U VAL* 1.3 83.4 - - - +
38U MET* 1.3 62.0 + - - +
76U MET* 3.0 4.5 - - - -
77U VAL* 2.9 28.3 + - + +
134U PHE* 3.7 16.6 - - + -
138U GLU* 3.4 18.4 - - + +
139U LEU* 3.5 24.2 - - + -
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Residues in contact with MET 38 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21N VAL* 4.5 7.2 - - + -
38N MET* 3.8 29.6 - - + -
39N LYS* 3.3 3.2 - - - +
40N PHE* 2.8 44.2 + - + +
74N VAL* 3.7 34.8 - - + -
25U ILE* 3.7 25.6 - - - -
35U LEU* 3.8 25.8 - - + -
37U ALA* 1.3 77.9 - - - +
39U LYS* 1.3 64.9 + - - +
74U VAL* 4.0 2.7 - - + -
75U ALA 3.2 6.3 - - - +
76U MET* 3.8 20.0 - - + +
134U PHE* 3.9 2.4 - - - -
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Residues in contact with LYS 39 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38N MET* 3.2 9.6 - - - +
39N LYS* 5.0 4.7 - - + -
38U MET* 1.3 79.8 - - - +
40U PHE* 1.3 60.9 + - - +
41U LEU* 3.7 34.1 - - + +
74U VAL* 3.6 3.7 - - - +
75U ALA* 2.9 38.4 + - + +
133U TRP 3.2 22.1 + - - +
134U PHE* 3.8 15.9 - - + +
135U LYS* 5.0 6.5 - - - +
138U GLU* 3.0 41.0 + - - -
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Residues in contact with PHE 40 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35N LEU* 3.0 48.2 - - + -
36N VAL 3.5 20.2 - - - -
37N ALA* 3.8 6.7 - - - -
38N MET* 2.8 31.6 + - + +
138N GLU* 4.3 9.2 - - - +
140N VAL* 3.7 16.9 - - + +
142N TYR* 3.6 13.7 - + - -
16U VAL* 3.9 13.7 - - + -
39U LYS* 1.3 73.6 - - - +
41U LEU* 1.3 64.5 + - - +
72U PRO* 3.4 31.6 - - + -
73U VAL 3.5 6.1 - - - -
74U VAL* 3.5 26.5 - - + +
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Residues in contact with LEU 41 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140N VAL* 3.9 8.3 - - - -
39U LYS* 3.7 43.3 - - + +
40U PHE* 1.3 80.3 - - - +
42U ARG* 1.3 56.5 + - - +
43U ALA* 4.3 12.1 - - - +
47U HIS* 5.2 5.8 - - + +
72U PRO* 3.9 5.4 - - - -
73U VAL* 2.7 59.8 + - + +
75U ALA* 4.2 8.5 - - + -
133U TRP* 4.2 15.9 - - + +
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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