Contacts of the strand formed by residues 74 - 79 (chain P) in PDB entry 2NX5
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 ASP 74 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22P ARG* 3.4 24.6 + - - +
23P CYS 3.1 2.7 - - - +
24P HIS* 3.2 21.7 - - - +
32P MET* 4.3 0.4 - - - -
68P SER 3.8 1.0 - - - +
69P ARG* 3.6 18.0 - - - -
70P SER* 4.1 12.2 + - - +
71P LYS* 3.2 34.7 + - + +
72P THR 3.4 0.4 - - - -
73P GLU* 1.3 93.8 - - - +
75P PHE* 1.3 61.2 + - - +
76P LEU* 4.0 15.0 - - + -
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Residues in contact with PHE 75 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23P CYS* 2.8 33.1 + - + +
32P MET* 3.4 58.1 - - + +
33P TYR 3.8 10.8 - - - -
34P TRP* 3.1 35.4 + + - -
47P HIS 3.8 2.2 - - - -
48P TYR* 3.8 20.9 - - - -
49P SER* 3.9 10.8 - - - -
55P THR* 4.2 5.4 - - + -
67P VAL* 3.5 38.1 - - + -
68P SER 3.6 12.1 - - - -
69P ARG* 4.2 8.7 - - - -
74P ASP* 1.3 73.9 - - - +
76P LEU* 1.3 61.1 + - - +
92P CYS* 5.5 0.2 - - + -
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Residues in contact with LEU 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20P THR* 4.4 21.1 - - + -
21P LEU 3.3 5.8 - - - +
22P ARG* 3.5 37.5 - - + -
34P TRP* 4.1 1.6 - - - -
66P SER 3.9 0.2 - - - +
67P VAL* 3.1 7.7 - - - +
68P SER* 2.9 51.0 + - - +
70P SER* 5.4 7.0 - - - +
74P ASP* 4.0 19.1 - - + -
75P PHE* 1.3 77.5 - - - +
77P LEU* 1.3 61.8 + - - +
78P THR* 5.0 1.6 + - - +
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Residues in contact with LEU 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19P VAL 4.1 0.2 - - - +
20P THR* 3.5 0.5 - - - +
21P LEU* 2.8 50.7 + - + +
34P TRP* 3.6 35.6 - - + +
46P ILE* 3.9 13.5 - - + -
65P TYR* 3.7 32.3 - - + -
66P SER 3.5 8.5 - - - +
67P VAL* 3.6 19.3 - - + -
76P LEU* 1.3 73.2 - - - +
78P THR* 1.3 62.9 + - - +
79P LEU* 4.2 3.9 - - + +
90P TYR* 3.7 34.5 - - + -
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Residues in contact with THR 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18P PRO* 5.9 2.7 - - + -
19P VAL 3.4 10.5 - - - +
20P THR* 3.2 32.7 + - - +
65P TYR* 3.5 6.2 - - - +
66P SER* 2.8 44.1 + - - -
76P LEU* 4.1 3.2 + - - +
77P LEU* 1.3 71.8 + - - +
79P LEU* 1.3 76.2 + - - +
80P GLU* 4.0 23.7 + - - +
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Residues in contact with LEU 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17P THR 3.7 1.9 - - - +
18P PRO* 3.4 1.0 - - - +
19P VAL* 3.0 42.0 + - + +
21P LEU* 5.0 8.3 - - + -
64P GLY 3.7 15.5 - - - +
65P TYR* 3.5 26.7 - - + -
77P LEU* 4.2 13.2 - - + +
78P THR* 1.3 85.2 - - - +
80P GLU* 1.3 64.0 + - - +
81P SER 3.5 0.7 - - - -
82P ALA* 4.5 8.3 - - + -
86P GLN* 3.4 38.8 - - + +
90P TYR* 4.1 0.7 - - - +
114P LEU* 4.1 18.8 - - + -
116P ILE* 4.3 6.7 - - + -
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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