Contacts of the strand formed by residues 9 - 23 (chain B) in PDB entry 5NXR
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 ASN 9 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315A ASN* 3.3 27.3 + - - +
350A TYR* 5.0 2.7 - - - +
4B TYR* 3.4 28.5 - - - -
5B ASN* 3.5 21.4 + - - +
6B LYS 3.0 26.6 + - - +
7B ASP* 3.8 10.5 + - - +
8B GLY* 1.3 81.9 - - - +
10B LYS* 1.3 74.1 + - - +
11B LEU* 5.6 0.5 - - - +
47B ASP* 3.0 17.5 - - - +
48B THR* 4.1 1.6 - - - +
49B GLN 4.6 0.7 - - - +
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Residues in contact with LYS 10 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A TYR* 4.1 1.6 + - - -
2B GLU* 4.2 21.1 - - + +
4B TYR 3.5 8.3 - - - +
5B ASN* 4.2 12.8 - - - +
9B ASN* 1.3 90.7 - - - +
11B LEU* 1.3 62.2 + - - +
12B ASP* 4.2 0.4 - - + -
45B LYS 4.0 0.5 - - - +
46B GLY* 3.3 4.3 - - - -
47B ASP* 2.8 55.6 + - + +
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Residues in contact with LEU 11 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350A TYR* 4.8 6.1 - - - +
352A PHE* 3.3 44.9 - - + -
2B GLU* 3.7 4.2 + - - -
3B VAL* 2.9 30.8 + - + +
4B TYR* 3.1 38.9 + - + +
9B ASN* 6.0 0.2 - - - +
10B LYS* 1.3 73.1 - - - +
12B ASP* 1.3 60.2 + - - +
13B VAL* 3.9 17.3 - - + -
44B VAL* 3.7 26.2 - - + -
45B LYS 3.7 5.4 - - - +
46B GLY* 4.7 2.2 - - - -
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Residues in contact with ASP 12 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ALA 2.9 40.8 + - - -
2B GLU* 3.2 12.3 + - + +
10B LYS* 4.2 0.4 - - + -
11B LEU* 1.3 73.4 - - - +
13B VAL* 1.3 61.2 + - - +
14B TYR* 3.6 20.4 - - - +
43B GLY 4.0 0.2 - - - +
44B VAL* 3.4 7.4 - - - +
45B LYS* 2.8 65.1 + - + +
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Residues in contact with VAL 13 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ALA* 3.2 31.0 + - - +
3B VAL* 4.0 19.3 - - + +
11B LEU* 3.9 19.5 - - + -
12B ASP* 1.3 76.6 + - - +
14B TYR* 1.3 66.2 + - - +
43B GLY 3.5 8.7 - - - +
44B VAL* 4.5 8.3 - - + -
352B PHE* 4.1 21.9 - - + -
11C LEU* 6.3 0.2 - - + -
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Residues in contact with TYR 14 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ALA 4.7 3.1 - - - +
12B ASP* 3.6 20.4 - - - +
13B VAL* 1.3 77.3 - - - +
15B GLY* 1.3 60.7 + - - +
41B ARG* 4.6 9.2 - - - -
42B LEU* 3.6 2.4 - - - +
43B GLY* 2.8 63.1 + - - +
44B VAL 3.9 2.5 - - - -
45B LYS* 4.2 24.9 - - + -
59B ARG* 3.0 21.7 + - - -
60B PHE 4.0 1.0 + - - -
61B GLU* 2.6 43.1 + - + +
352B PHE* 3.7 27.1 - - - +
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Residues in contact with GLY 15 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14B TYR* 1.3 83.4 - - - +
16B LYS* 1.3 63.1 + - - +
41B ARG* 2.9 16.6 - - - -
42B LEU* 4.2 0.9 - - - -
351B GLN* 3.6 3.2 - - - +
352B PHE* 2.9 49.1 + - - +
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Residues in contact with LYS 16 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B GLY* 1.3 74.9 - - - +
17B VAL* 1.3 63.3 + - - +
18B ASP* 3.1 35.5 + - + -
20B ARG* 4.7 4.2 - - - +
39B ARG* 5.0 6.3 - - - +
40B VAL* 3.4 7.4 - - - +
41B ARG* 2.7 85.9 + - + +
42B LEU* 6.0 0.2 - - - -
63B GLU* 4.5 2.9 + - - -
349B VAL* 4.2 12.3 - - + -
350B TYR 3.3 10.5 - - - +
351B GLN* 3.9 16.8 - - + -
352B PHE* 4.6 2.2 - - - -
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Residues in contact with VAL 17 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 1.3 74.8 - - - +
18B ASP* 1.3 59.9 + - - +
19B VAL* 3.9 9.4 - - + -
39B ARG 4.1 1.6 - - - +
40B VAL* 4.4 12.6 - - + -
348B LEU 3.7 1.9 - - - +
349B VAL* 3.3 4.0 - - - +
350B TYR* 2.8 46.5 + - + +
352B PHE* 6.2 3.6 - - + -
44C VAL* 5.8 3.1 - - + -
58C GLY* 4.4 4.9 - - - -
59C ARG* 4.0 26.9 - - - +
60C PHE* 4.5 9.9 - - + +
80C ALA* 4.1 3.8 - - + -
81C TYR 3.5 38.8 - - - +
82C ALA* 4.4 2.1 - - + +
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Residues in contact with ASP 18 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 3.1 31.7 + - + -
17B VAL* 1.3 72.8 - - - +
19B VAL* 1.3 62.0 + - - +
20B ARG* 2.8 41.1 + - - +
38B SER* 3.2 3.5 - - - -
39B ARG* 2.8 57.7 + - + +
113B LEU* 5.2 1.2 - - - +
347B GLY* 5.2 0.5 - - - -
348B LEU 3.8 2.4 + - - -
349B VAL* 3.4 24.4 - - + +
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Residues in contact with VAL 19 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B VAL* 4.0 10.5 - - + -
18B ASP* 1.3 76.4 - - - +
20B ARG* 1.3 61.3 + - - +
38B SER* 3.2 15.3 - - - +
39B ARG 5.6 0.2 - - - +
347B GLY* 3.2 4.5 - - - -
348B LEU* 2.9 57.3 + - + +
80C ALA* 3.9 18.8 - - + +
81C TYR* 4.0 1.1 - - - -
82C ALA* 4.0 16.4 - - + +
94C TYR* 3.6 44.4 - - + +
95C GLY* 4.1 0.9 - - - -
407C LDA 4.2 0.8 - - + +
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Residues in contact with ARG 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LYS* 4.7 3.0 - - - +
18B ASP* 2.8 36.3 + - - +
19B VAL* 1.3 81.4 - - - +
21B HIS* 1.3 60.8 + - - +
22B TYR* 3.2 35.8 + - + -
36B ASP* 3.3 9.2 - - - +
37B ASP 3.0 41.5 + - - +
38B SER* 2.9 6.9 + - - -
39B ARG* 3.4 28.7 - - - +
112B PRO 4.8 4.0 + - - -
113B LEU* 3.5 45.6 + - + +
346B LEU 3.3 7.6 - - - +
347B GLY* 4.4 0.4 - - - -
94C TYR* 3.4 8.6 + - - -
407C LDA 4.9 0.2 - - - -
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Residues in contact with HIS 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B ARG* 1.3 72.7 - - - +
22B TYR* 1.3 90.8 + - - +
23B PHE* 3.9 22.0 + + + -
34B ASP* 4.1 8.5 - - - -
35B GLY* 3.4 11.1 - - - -
344B LEU 4.0 0.9 - - - +
345B GLY* 3.5 0.5 - - - -
346B LEU* 2.9 35.6 + - - +
94C TYR* 3.2 11.2 - + - +
132C ASN* 2.8 38.4 + - - -
156C GLY* 4.5 3.4 - - - -
407C LDA 3.6 57.8 - - + +
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Residues in contact with TYR 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B ARG* 3.2 45.0 + - + -
21B HIS* 1.3 88.2 + - - +
23B PHE* 1.3 58.9 + - - +
33B GLU* 3.3 29.4 - - + +
34B ASP* 3.0 6.3 - - - +
35B GLY 2.8 38.1 + - - +
37B ASP* 2.9 37.1 + - + -
39B ARG* 4.0 0.2 + - - -
113B LEU* 4.2 10.3 + - + -
114B TRP* 3.7 34.2 - + - -
343B VAL* 3.8 11.0 - - + -
344B LEU 3.4 3.4 - - - -
345B GLY* 3.8 10.1 - - - -
163C LYS* 3.9 16.4 - - + -
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Residues in contact with PHE 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B HIS* 3.9 30.3 - + - -
22B TYR* 1.3 72.8 - - - +
24B ALA* 1.3 63.8 + - - +
34B ASP* 3.7 5.2 - - - -
343B VAL* 3.6 1.9 - - - +
344B LEU* 2.7 61.9 + - + +
346B LEU* 3.8 28.9 - - + -
409B LDA 3.8 25.6 + - - -
407C LDA 3.9 45.1 - - + -
409C LDA 5.4 5.6 - - + -
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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
------------------------------------------------------------
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