Contacts of the strand formed by residues 21 - 28 (chain Q) 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 ARG 21 (chain Q).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Q THR 3.5 0.7 - - - +
11Q ALA* 3.0 8.0 - - - +
12Q MET* 2.7 81.2 + - + +
14Q ARG* 3.5 28.2 - - - +
19Q GLU 4.1 0.9 - - - -
20Q PRO* 1.3 74.6 - - - +
22Q PHE* 1.3 61.6 + - - +
23Q ILE* 3.5 33.1 - - - +
37Q ASP* 3.6 22.1 + - - -
38Q SER* 3.7 2.7 - - - -
39Q ASP* 3.1 33.8 + - - +
34R ASP* 5.3 0.8 + - - -
54R LEU* 5.2 3.2 - - - +
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Residues in contact with PHE 22 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9Q TYR* 3.7 35.9 - + + -
10Q THR 3.7 1.3 - - - -
11Q ALA* 4.2 9.2 - - + -
20Q PRO 4.2 0.2 + - - -
21Q ARG* 1.3 73.8 - - - +
23Q ILE* 1.3 67.0 + - - +
24Q ALA* 3.7 21.5 - - + -
36Q PHE* 4.2 13.9 - + - -
37Q ASP* 3.5 3.5 - - - +
38Q SER* 2.9 37.9 + - - +
67Q PHE* 4.2 18.8 - + - -
70Q ASN* 3.9 20.9 - - + -
71Q THR* 4.1 25.6 - - + +
74Q TYR* 3.4 43.5 - + + -
75Q ARG* 6.5 0.2 - - + -
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Residues in contact with ILE 23 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q PHE 3.7 1.2 - - - +
9Q TYR* 3.6 2.6 - - - -
10Q THR* 3.1 50.2 + - + +
12Q MET* 3.9 11.2 - - + -
21Q ARG* 3.5 30.1 - - - +
22Q PHE* 1.3 81.0 - - - +
24Q ALA* 1.3 63.7 + - - +
25Q VAL* 5.5 3.8 - - + -
36Q PHE 3.3 10.8 - - - +
37Q ASP* 4.2 16.6 - - + +
53R ASP* 5.7 2.9 - - + -
54R LEU* 3.7 54.9 - - + +
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Residues in contact with ALA 24 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8Q PHE 3.4 4.0 - - - -
9Q TYR* 3.6 29.4 - - + -
22Q PHE* 3.7 14.1 - - + -
23Q ILE* 1.3 74.9 - - - +
25Q VAL* 1.3 65.5 + - - +
35Q ARG* 3.3 3.3 - - - -
36Q PHE* 2.7 44.7 + - + +
67Q PHE* 3.8 17.9 - - + -
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Residues in contact with VAL 25 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7Q TYR* 3.3 11.6 - - - -
8Q PHE* 3.1 45.1 + - + +
23Q ILE* 5.5 3.4 - - + -
24Q ALA* 1.3 80.7 - - - +
26Q GLY* 1.3 58.9 + - - +
27Q TYR* 3.5 25.9 - - + -
32Q GLN* 3.5 25.4 - - - +
34Q VAL* 3.5 7.4 - - - +
35Q ARG* 4.2 5.2 - - + -
53R ASP* 3.7 19.1 - - + +
54R LEU 4.4 11.9 - - - +
55R SER* 4.1 11.4 - - - +
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Residues in contact with GLY 26 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Q ARG 3.3 8.5 - - - -
7Q TYR* 3.6 16.6 - - - -
25Q VAL* 1.3 75.1 - - - +
27Q TYR* 1.3 61.5 + - - -
32Q GLN* 3.3 5.4 - - - +
33Q PHE* 2.9 34.5 + - - -
34Q VAL* 3.1 17.9 + - - +
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Residues in contact with TYR 27 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5Q MET* 3.2 5.5 - - - -
6Q ARG* 2.8 46.7 + - + -
8Q PHE* 4.0 22.7 - + - -
25Q VAL* 3.5 27.1 - - + +
26Q GLY* 1.3 76.2 - - - -
28Q VAL* 1.3 58.9 + - - +
29Q ASP 4.1 11.4 - - - +
30Q ASP* 4.1 16.4 - - - -
31Q THR 3.3 6.7 - - - -
32Q GLN* 3.5 37.6 + - + +
33Q PHE* 3.3 11.3 - - - -
53R ASP 5.1 1.4 + - - -
55R SER* 3.2 20.2 + - - -
63R TYR* 3.1 27.9 + - - -
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Residues in contact with VAL 28 (chain Q).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Q SER 3.2 3.1 - - - +
5Q MET* 4.4 3.6 - - + -
27Q TYR* 1.3 70.3 - - - +
29Q ASP* 1.3 70.2 + - - +
31Q THR* 2.7 33.5 + - - +
33Q PHE* 3.5 24.9 - - + -
51Q TRP* 3.9 17.7 - - + -
168Q LEU* 4.0 29.8 - - + -
171Q TYR* 4.4 6.7 - - + -
172Q LEU* 4.1 7.9 - - + -
179Q LEU* 3.6 31.5 - - + +
209Q TYR* 3.0 7.6 + - - -
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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