Contacts of the strand formed by residues 73 - 79 (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 VAL 73 (chain R).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10R ALA* 5.5 4.3 - - + -
11R ILE 3.2 14.1 - - - +
12R LYS* 4.0 2.7 - - - -
13R PRO* 3.6 30.3 - - + -
16R VAL* 4.2 0.9 - - - -
39R LYS 3.9 0.3 - - - +
40R PHE* 3.3 8.2 - - - -
41R LEU* 2.8 53.8 + - + +
43R ALA* 4.7 4.9 - - + +
68R MET* 4.2 19.7 - - + +
71R GLY 4.1 3.1 - - - +
72R PRO* 1.3 77.8 - - - +
74R VAL* 1.3 64.9 + - - +
75R ALA* 4.6 3.1 - - + +
133R TRP* 3.9 21.3 - - + -
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Residues in contact with VAL 74 (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* 4.9 0.4 - - + -
38L MET* 3.7 28.3 - - + -
9R ILE 3.7 1.2 - - - +
10R ALA* 3.3 4.0 - - - -
11R ILE* 2.8 45.1 + - + +
16R VAL* 4.1 11.0 - - + -
21R VAL* 4.3 17.3 - - + -
38R MET* 4.0 4.0 - - + -
39R LYS 3.5 3.8 - - - +
40R PHE* 3.4 29.4 - - + -
73R VAL* 1.3 74.4 - - - +
75R ALA* 1.3 58.8 + - - +
76R MET* 3.8 29.7 + - + +
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Residues in contact with ALA 75 (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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8R PHE* 3.6 21.1 - - + -
9R ILE 3.7 3.4 - - - -
10R ALA* 4.4 1.3 - - - +
38R MET* 3.2 1.7 - - - -
39R LYS* 2.8 43.9 + - + +
41R LEU* 4.2 3.1 - - + +
73R VAL* 4.0 2.5 - - + -
74R VAL* 1.3 71.7 - - - +
76R MET* 1.3 62.9 + - - +
133R TRP* 3.9 20.2 - - + -
134R PHE* 3.2 18.8 - - + -
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Residues in contact with MET 76 (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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8R PHE* 3.4 9.6 - - - -
9R ILE* 2.8 68.2 + - + +
11R ILE* 3.8 27.1 - - + -
24R ILE* 5.0 3.6 - - + -
25R ILE* 4.2 20.4 - - + -
28R PHE* 6.0 0.4 - - + -
35R LEU* 4.3 2.0 - - + -
37R ALA 3.1 9.9 - - - +
38R MET* 3.6 22.2 - - + +
74R VAL* 3.8 14.1 - - + +
75R ALA* 1.3 81.1 - - - +
77R VAL* 1.3 64.9 + - - +
78R TRP* 3.6 25.1 - - + +
134R PHE* 3.5 2.8 - - - -
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Residues in contact with VAL 77 (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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6R ARG* 3.2 41.1 - - + -
7R THR 3.2 8.1 - - - +
8R PHE* 4.8 0.4 - - + -
35R LEU* 3.5 9.0 - - - +
36R VAL* 2.8 38.9 + - + -
37R ALA* 2.9 10.5 + - + +
76R MET* 1.3 73.5 - - - +
78R TRP* 1.3 61.1 - - - +
130R ILE* 4.0 17.5 - - + -
134R PHE* 3.4 35.9 - - + -
139R LEU* 4.0 13.7 - - + -
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Residues in contact with TRP 78 (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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6R ARG* 3.2 4.1 - - - -
7R THR* 2.8 40.0 + - + -
9R ILE* 3.7 26.7 - - + +
25R ILE* 4.0 19.9 - - + +
28R PHE* 3.7 37.9 - + + -
29R GLU* 3.9 22.4 - - + -
33R PHE* 3.0 38.8 - - + -
34R ARG 3.4 14.4 - - - -
35R LEU* 3.4 34.8 - - + -
76R MET* 3.6 27.9 - - + +
77R VAL* 1.3 76.8 - - - +
79R GLU* 1.3 59.3 + - - +
83R VAL* 3.3 20.7 - - + +
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Residues in contact with GLU 79 (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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4R LEU* 4.2 18.4 - - + +
5R GLU 3.6 19.7 - - - +
6R ARG* 4.0 6.4 - - + +
32R GLY 4.9 0.2 - - - +
33R PHE* 3.5 8.3 - - - +
34R ARG* 2.6 70.8 + - + +
36R VAL* 3.5 21.8 - - + +
78R TRP* 1.3 72.9 - - - +
80R GLY* 1.3 63.2 + - - +
83R VAL* 3.7 2.5 - - - -
142R TYR 5.3 0.2 - - - +
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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