Contacts of the strand formed by residues 34 - 41 (chain R) 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 R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4R LEU* 6.2 1.1 - - - -
32R GLY 5.2 4.0 - - - +
33R PHE* 1.3 73.0 - - - +
35R LEU* 1.3 62.1 + - - +
36R VAL* 3.1 12.2 + - - +
78R TRP* 3.4 5.4 - - - -
79R GLU* 2.6 75.1 + - + +
140R VAL 3.4 11.7 + - - -
141R ASP* 4.1 1.8 + - - +
142R TYR* 3.0 89.4 + - + +
143R LYS* 5.7 0.4 - - - +
144R SER* 4.0 25.8 - - - +
147R HIS* 5.7 6.5 - - - -
151R TYR* 6.6 0.2 - - + -
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Residues in contact with LEU 35 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16L VAL* 5.8 1.1 - - + -
21L VAL* 5.2 10.8 - - + -
40L PHE* 3.1 39.4 - - + -
74L VAL* 4.8 3.1 - - + -
25R ILE* 5.5 1.1 - - + -
34R ARG* 1.3 67.9 - - - +
36R VAL* 1.3 60.9 + - - +
37R ALA* 3.0 32.1 - - - +
38R MET* 3.8 29.4 - - + -
76R MET* 4.3 8.7 - - + -
77R VAL 3.5 9.4 - - - +
78R TRP* 3.4 32.4 - - + -
142R TYR* 2.6 31.5 + - - +
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Residues in contact with VAL 36 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40L PHE* 3.5 9.3 - - - -
6R ARG* 4.5 8.1 - - - +
34R ARG* 3.6 13.0 - - - +
35R LEU* 1.3 73.0 - - - +
37R ALA* 1.3 57.5 + - - +
77R VAL* 2.8 23.0 + - + +
79R GLU* 3.5 38.6 - - + +
139R LEU* 3.6 33.9 - - + -
140R VAL 2.8 45.9 + - - +
141R ASP* 5.1 4.0 - - - +
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Residues in contact with ALA 37 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40L PHE* 3.8 7.0 - - - -
35R LEU* 3.0 11.2 - - - +
36R VAL* 1.3 79.6 - - - +
38R MET* 1.3 62.5 + - - +
76R MET* 3.1 1.9 - - - -
77R VAL* 2.9 29.2 + - + +
134R PHE* 4.0 13.5 - - + -
138R GLU* 3.2 22.9 - - + +
139R LEU* 3.4 23.1 - - + -
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Residues in contact with MET 38 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21L VAL* 4.6 7.4 - - + -
38L MET* 3.5 45.5 - - + -
39L LYS* 3.4 3.7 - - - +
40L PHE* 2.9 39.7 + - + +
74L VAL* 3.7 31.2 - - + -
25R ILE* 3.9 18.6 - - + -
35R LEU* 3.8 22.2 - - + -
37R ALA* 1.3 79.3 - - - +
39R LYS* 1.3 65.2 + - - +
74R VAL* 4.0 1.6 - - + -
75R ALA 3.2 6.3 - - - +
76R MET* 3.6 20.2 - - + +
134R PHE* 4.1 2.3 - - - -
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Residues in contact with LYS 39 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38L MET* 3.4 9.4 - - - +
39L LYS* 5.2 3.6 - - + -
38R MET* 1.3 78.3 - - - +
40R PHE* 1.3 60.6 + - - +
41R LEU* 3.8 31.9 - - + +
74R VAL* 3.5 4.4 - - - +
75R ALA* 2.8 37.1 + - + -
133R TRP* 3.2 23.8 + - + +
134R PHE* 3.6 17.2 - - + +
135R LYS* 5.0 5.9 - - - +
138R GLU* 3.0 39.7 + - - -
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Residues in contact with PHE 40 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35L LEU* 3.1 44.2 - - + -
36L VAL 3.6 19.5 - - - -
37L ALA* 3.9 8.1 - - - -
38L MET* 3.0 33.4 + - + +
138L GLU* 4.5 7.6 - - - +
140L VAL* 3.8 13.3 - - + +
142L TYR* 3.6 13.2 - + - -
16R VAL* 3.9 15.0 - - + -
39R LYS* 1.3 73.8 - - - +
41R LEU* 1.3 63.1 + - - +
72R PRO* 3.4 33.4 - - + -
73R VAL 3.3 13.9 - - - -
74R VAL* 3.4 19.7 - - + +
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Residues in contact with LEU 41 (chain R).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140L VAL* 4.0 8.7 - - - -
39R LYS* 3.8 40.4 - - + +
40R PHE* 1.3 79.6 - - - +
42R ARG* 1.3 57.2 + - - +
43R ALA* 4.3 13.0 - - - +
47R HIS* 5.2 5.4 - - + +
72R PRO* 3.9 3.6 - - - -
73R VAL* 2.8 53.0 + - + +
75R ALA* 4.2 3.6 - - + -
133R TRP* 4.1 22.0 - - + +
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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