Contacts of the strand formed by residues 343 - 352 (chain A) 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 VAL 343 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A TYR* 3.8 25.1 - - + -
23A PHE 3.6 6.1 - - - +
24A ALA* 4.1 4.3 - - + -
33A GLU* 3.7 33.7 - - + +
114A TRP* 3.5 31.1 - - + -
321A ASP 3.4 2.8 - - - +
322A TYR* 3.5 4.6 - - - -
323A LYS* 2.7 48.4 + - + +
339A ASN* 4.1 3.1 - - - +
341A ASP* 3.9 9.6 + - + +
342A ASN* 1.3 81.9 - - - +
344A LEU* 1.3 62.6 + - - +
403A LDA 4.2 0.2 - - - -
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Residues in contact with LEU 344 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A TYR* 3.4 0.5 - - - -
23A PHE* 2.7 51.0 + - + +
320A VAL* 3.9 24.2 - - + -
321A ASP 3.6 4.7 - - - +
322A TYR* 4.1 20.2 - - + -
343A VAL* 1.3 75.6 - - - +
345A GLY* 1.3 63.5 + - - +
346A LEU* 5.1 2.2 - - + -
403A LDA 3.7 59.9 - - + -
404A LDA 3.8 33.2 - - + -
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Residues in contact with GLY 345 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A HIS 3.5 6.3 - - - -
22A TYR* 3.8 10.3 - - - -
113A LEU* 3.3 20.4 - - - -
114A TRP* 4.0 3.3 - - - -
320A VAL* 3.3 6.8 - - - +
321A ASP 2.8 36.5 + - - -
343A VAL 4.0 0.4 - - - -
344A LEU* 1.3 74.9 - - - +
346A LEU* 1.3 64.7 + - - +
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Residues in contact with LEU 346 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A ARG* 3.3 5.9 - - - +
21A HIS 2.8 33.9 + - - +
23A PHE* 3.6 30.3 - - + -
113A LEU* 4.2 3.5 - - - +
319A VAL 3.4 3.4 - - - +
320A VAL* 3.7 31.0 - - + -
344A LEU* 5.1 3.1 - - + -
345A GLY* 1.3 83.0 - - - +
347A GLY* 1.3 59.0 + - - +
402A LDA 4.0 28.5 - - + +
403A LDA 4.5 17.5 - - + -
404A LDA 4.9 9.9 - - + -
410A LDA 4.2 15.9 - - + -
411A LDA 5.8 0.2 - - + -
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Residues in contact with GLY 347 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A ASP* 5.2 1.1 - - - -
19A VAL 3.2 10.1 - - - -
20A ARG* 4.3 7.0 - - - -
113A LEU* 4.8 0.2 - - - -
318A ALA* 3.4 5.2 - - - +
319A VAL* 2.8 49.6 + - - +
346A LEU* 1.3 76.4 - - - +
348A LEU* 1.3 60.6 + - - +
349A VAL* 5.0 0.9 - - - -
402A LDA 3.8 4.7 - - - -
410A LDA 4.4 3.5 - - - +
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Residues in contact with LEU 348 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A VAL 3.7 1.6 - - - +
19A VAL* 2.9 43.3 + - + +
312A PHE* 4.2 4.5 - - + -
316A MET* 3.7 23.1 - - + -
317A SER 3.4 16.2 - - - +
318A ALA* 4.0 14.8 - - + -
347A GLY* 1.3 74.6 - - - +
349A VAL* 1.3 63.1 + - - +
350A TYR 4.2 0.2 - - - -
402A LDA 3.7 12.1 - - + +
410A LDA 5.2 5.6 - - + -
82B ALA* 3.7 14.2 - - + +
83B GLY* 3.7 31.0 - - - +
84B LEU* 4.1 16.2 - - + -
93B ASP* 5.8 0.2 - - - -
94B TYR* 5.4 1.8 - - + +
416B LDA 5.2 7.6 - - + -
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Residues in contact with VAL 349 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16A LYS* 4.2 17.0 - - + -
17A VAL 3.3 8.3 - - - +
18A ASP* 3.5 28.0 - - + +
315A ASN 3.8 0.3 - - - +
316A MET* 3.5 8.5 - - - +
317A SER* 2.8 47.5 + - - +
319A VAL* 5.3 10.3 - - + -
347A GLY 5.0 2.2 - - - -
348A LEU* 1.3 80.1 - - - +
350A TYR* 1.3 61.8 + - - +
351A GLN* 3.8 30.6 - - + +
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Residues in contact with TYR 350 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A LYS* 3.3 2.6 - - - -
17A VAL* 2.8 43.8 + - + +
315A ASN* 3.4 17.9 + - + -
316A MET* 3.9 16.8 - - - -
348A LEU 4.2 0.6 - - - -
349A VAL* 1.3 72.8 - - - +
351A GLN* 1.3 68.7 + - - +
352A PHE* 3.7 31.4 - + - +
9B ASN* 5.0 2.4 - - - +
10B LYS 4.1 1.9 + - - -
11B LEU* 4.8 2.3 - - - +
46B GLY* 3.2 43.3 - - - -
47B ASP 3.3 9.2 + - - -
48B THR* 3.8 25.3 - - + -
56B GLY 4.6 0.4 - - - -
57B PHE 4.1 6.3 - - - +
58B GLY* 3.7 32.3 - - - -
82B ALA* 4.3 6.0 - - + +
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Residues in contact with GLN 351 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A GLY 3.7 5.2 - - - +
16A LYS* 4.0 14.3 - - + +
311A TYR* 6.3 1.2 - - - -
314A LYS 4.3 13.5 + - - +
315A ASN* 2.7 43.3 + - - +
317A SER* 4.5 9.8 + - - +
349A VAL* 3.8 26.4 - - + +
350A TYR* 1.3 79.0 - - - +
352A PHE* 1.4 66.1 + - - +
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Residues in contact with PHE 352 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ALA* 3.9 22.2 + - - +
13A VAL* 4.3 11.8 - - + +
14A TYR* 3.7 17.0 - - - +
15A GLY* 2.9 59.8 + - - +
16A LYS* 4.6 2.9 - - - -
17A VAL* 5.0 7.4 - - + -
42A LEU* 4.1 10.1 - - + -
315A ASN* 4.9 6.1 - - - +
350A TYR* 3.7 29.2 - + + +
351A GLN* 1.4 76.8 - - - +
11B LEU* 3.3 34.1 - - + -
44B VAL* 3.9 37.9 - - + -
46B GLY 5.9 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