Contacts of the strand formed by residues 9 - 24 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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315B ASN* 3.3 29.4 + - - +
350B TYR* 2.7 27.9 + - - -
352B PHE* 4.6 14.0 + - - +
4C TYR* 3.7 30.4 - - + -
5C ASN* 3.4 23.9 + - - -
6C LYS 3.3 14.0 + - - +
7C ASP* 3.4 4.8 + - - +
8C GLY* 1.3 80.0 - - - +
10C LYS* 1.3 62.1 + - - +
11C LEU* 5.0 2.5 - - - +
47C ASP 3.3 8.5 - - - +
48C THR* 4.4 0.4 - - - +
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Residues in contact with LYS 10 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B TYR* 4.1 0.7 + - - -
2C GLU* 3.0 46.5 + - - +
4C TYR 3.4 7.6 - - - +
5C ASN* 4.1 8.3 - - - +
9C ASN* 1.3 73.3 - - - +
11C LEU* 1.3 63.7 + - - +
12C ASP* 4.3 19.8 + - - +
45C LYS* 4.0 4.0 - - - +
46C GLY* 3.2 4.2 - - - -
47C ASP* 2.8 58.4 + - + +
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Residues in contact with LEU 11 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1B ALA* 6.0 2.2 - - + -
3B VAL* 6.6 0.2 - - + -
350B TYR* 4.2 2.2 - - - +
352B PHE* 3.6 55.9 - - + -
2C GLU* 3.8 4.4 - - - -
3C VAL* 2.9 38.6 + - + +
4C TYR* 3.1 37.0 + - + +
9C ASN* 5.0 2.5 - - - +
10C LYS* 1.3 75.3 - - - +
12C ASP* 1.3 62.7 + - - +
13C VAL* 5.1 7.0 - - + -
44C VAL* 5.5 4.0 - - + -
45C LYS 3.7 5.2 - - - +
46C GLY* 3.8 22.7 - - - +
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Residues in contact with ASP 12 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1C ALA 2.8 27.1 + - - -
2C GLU* 3.1 24.3 + - - +
10C LYS* 4.3 16.9 + - - -
11C LEU* 1.3 73.7 - - - +
13C VAL* 1.3 64.3 + - - +
14C TYR* 4.1 9.8 - - - +
44C VAL* 3.4 4.9 - - - +
45C LYS* 2.8 72.5 + - + +
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Residues in contact with VAL 13 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C ALA* 3.2 30.9 + - - +
3C VAL* 4.1 26.5 - - + +
11C LEU* 4.2 8.4 + - + -
12C ASP* 1.3 75.6 - - - +
14C TYR* 1.3 65.7 + - - +
43C GLY 3.5 7.6 - - - +
44C VAL* 3.8 21.5 - - + -
352C PHE* 4.1 20.4 - - + -
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Residues in contact with TYR 14 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1C ALA 4.6 3.6 - - - +
12C ASP* 4.1 19.1 - - - +
13C VAL* 1.3 78.4 - - - +
15C GLY* 1.3 61.1 + - - +
41C ARG* 4.7 8.7 - - - -
42C LEU* 3.6 2.8 - - - +
43C GLY* 2.8 63.0 + - - +
44C VAL 3.9 3.1 - - - -
45C LYS* 4.2 19.7 - - + -
59C ARG* 3.0 28.8 + - - -
60C PHE 4.0 0.9 + - - -
61C GLU* 2.6 42.4 + - + +
352C PHE* 3.5 24.4 - - - +
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Residues in contact with GLY 15 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14C TYR* 1.3 84.1 - - - +
16C LYS* 1.3 62.7 + - - +
41C ARG* 2.9 16.6 - - - -
42C LEU* 4.2 0.7 - - - -
351C GLN* 3.6 3.2 - - - +
352C PHE* 2.9 50.8 + - - +
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Residues in contact with LYS 16 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15C GLY* 1.3 75.8 - - - +
17C VAL* 1.3 62.5 - - - +
18C ASP* 3.1 32.3 + - + -
20C ARG* 4.8 3.4 - - - +
39C ARG* 5.1 6.3 - - - +
40C VAL* 3.4 7.2 - - - +
41C ARG* 2.7 84.2 + - + +
42C LEU* 6.1 0.2 - - - -
63C GLU* 4.5 3.3 + - - -
349C VAL* 4.2 15.7 - - + -
350C TYR 3.3 11.2 - - - +
351C GLN* 3.9 17.9 - - + +
352C PHE* 4.3 1.7 - - - -
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Residues in contact with VAL 17 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44A VAL* 6.0 2.2 - - + -
58A GLY* 4.3 5.6 - - - -
59A ARG* 4.0 26.7 - - - +
60A PHE* 4.6 9.0 - - + +
80A ALA* 4.2 3.1 - - + -
81A TYR 3.4 39.0 - - - +
82A ALA* 4.4 2.1 - - + +
16C LYS* 1.3 74.4 - - - +
18C ASP* 1.3 60.9 + - - +
19C VAL* 3.9 9.6 - - + -
39C ARG 4.1 1.8 - - - +
40C VAL* 4.3 12.6 - - + -
348C LEU 3.7 1.9 - - - +
349C VAL* 3.3 3.8 - - - -
350C TYR* 2.8 47.8 + - + +
352C PHE* 6.0 4.7 - - + -
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Residues in contact with ASP 18 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16C LYS* 3.1 31.0 + - + -
17C VAL* 1.3 73.1 - - - +
19C VAL* 1.3 60.9 + - - +
20C ARG* 2.8 39.9 + - - +
38C SER* 3.2 3.8 - - - -
39C ARG* 2.8 56.9 + - + +
113C LEU* 5.2 1.2 - - - +
319C VAL* 6.0 0.2 - - - +
347C GLY* 5.2 0.5 - - - -
348C LEU 3.8 3.0 + - - -
349C VAL* 3.5 24.8 - - + +
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Residues in contact with VAL 19 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A ALA* 3.9 17.5 - - + +
81A TYR* 4.0 1.3 - - - -
82A ALA* 4.0 15.5 - - + +
94A TYR* 3.6 45.3 - - + +
95A GLY* 4.1 0.9 - - - -
17C VAL* 4.0 11.2 - - + -
18C ASP* 1.3 75.7 - - - +
20C ARG* 1.3 61.5 + - - +
38C SER* 3.2 14.6 - - - +
347C GLY* 3.2 4.5 - - - -
348C LEU* 2.9 58.2 + - + +
401C LDA 4.8 0.8 - - + +
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Residues in contact with ARG 20 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 3.4 12.0 + - - -
16C LYS* 4.8 2.8 - - - +
18C ASP* 2.8 35.8 + - - +
19C VAL* 1.3 79.7 - - - +
21C HIS* 1.3 60.0 + - - +
22C TYR* 3.2 31.3 + - + -
36C ASP* 3.3 6.6 - - - +
37C ASP 3.0 29.4 + - - +
38C SER* 2.9 7.1 + - - -
39C ARG* 3.2 43.0 - - - +
112C PRO 4.8 4.2 + - - -
113C LEU* 3.5 48.4 + - + +
346C LEU 3.3 8.1 - - - +
347C GLY* 4.4 0.7 - - - -
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Residues in contact with HIS 21 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94A TYR* 3.3 8.5 + - - +
132A ASN* 3.0 37.5 + - - -
156A GLY* 4.5 2.5 - - - -
157A LYS 5.7 0.2 - - - -
20C ARG* 1.3 72.4 - - - +
22C TYR* 1.3 87.9 + - - +
23C PHE* 3.6 29.7 - + + -
34C ASP* 4.2 5.6 + - - -
35C GLY* 3.4 13.4 - - - -
344C LEU 3.9 0.9 - - - +
345C GLY* 3.5 0.5 - - - -
346C LEU* 2.9 34.6 + - + +
401C LDA 3.5 57.7 - - + +
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Residues in contact with TYR 22 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LYS* 4.0 13.5 - - + -
20C ARG* 3.2 44.4 + - + -
21C HIS* 1.3 88.8 - - - +
23C PHE* 1.3 60.3 + - - +
33C GLU* 3.2 31.0 - - - +
34C ASP* 2.9 5.9 - - - +
35C GLY 2.7 39.0 + - - +
37C ASP* 2.8 36.8 + - + -
39C ARG* 4.7 0.3 + - - -
113C LEU* 4.3 10.5 - - + -
114C TRP* 3.7 34.4 - + - -
343C VAL* 3.8 11.2 - - + -
344C LEU 3.4 2.7 - - - -
345C GLY* 3.8 9.4 - - - -
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Residues in contact with PHE 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C HIS* 3.6 23.3 - + - -
22C TYR* 1.3 72.6 - - - +
24C ALA* 1.3 64.0 + - - +
34C ASP* 3.6 5.6 - - - -
343C VAL* 3.6 2.0 - - - +
344C LEU* 2.7 61.0 + - + +
346C LEU* 3.6 32.3 - - + -
401C LDA 3.7 38.6 - - + -
402C LDA 4.2 18.8 - - + +
403C LDA 3.7 23.6 - - - -
437C LDA 3.7 30.1 - - - -
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Residues in contact with ALA 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LYS* 5.6 0.3 + - - -
23C PHE* 1.3 76.2 - - - +
25C SER* 1.3 71.8 + - - +
26C ALA* 3.4 4.0 + - - +
33C GLU* 4.2 6.5 - - + +
34C ASP* 3.4 37.1 + - - +
341C ASP* 5.5 2.7 - - + -
342C ASN 3.5 18.8 - - - +
343C VAL* 4.1 13.5 - - + -
402C LDA 5.0 8.0 + - - -
403C LDA 4.2 7.2 - - - -
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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
------------------------------------------------------------
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