Contacts of the strand formed by residues 343 - 352 (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 VAL 343 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22B TYR* 3.8 24.0 - - + -
23B PHE 3.6 6.3 - - - +
24B ALA* 4.1 3.6 - - + -
33B GLU* 3.7 33.4 - - + -
114B TRP* 3.5 30.6 - - + -
321B ASP 3.4 2.9 - - - +
322B TYR* 3.4 4.9 - - - -
323B LYS* 2.7 48.2 + - + +
339B ASN* 4.2 5.6 - - - +
341B ASP* 3.9 10.7 + - + +
342B ASN* 1.3 82.3 - - - +
344B LEU* 1.3 62.2 + - - +
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Residues in contact with LEU 344 (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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22B TYR* 3.4 0.9 - - - -
23B PHE* 2.7 67.3 + - + +
320B VAL* 3.8 28.5 - - + -
321B ASP 4.1 0.2 - - - +
322B TYR* 4.1 22.8 - - + -
343B VAL* 1.3 74.2 - - - +
345B GLY* 1.3 62.2 + - - +
346B LEU* 5.1 6.1 - - + -
409B LDA 4.0 49.6 + - + -
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Residues in contact with GLY 345 (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 3.5 6.3 - - - -
22B TYR* 3.8 10.1 - - - -
113B LEU* 3.4 20.6 - - - -
114B TRP* 4.1 3.0 - - - -
320B VAL* 3.3 7.1 - - - +
321B ASP 2.8 35.8 + - - -
343B VAL 4.0 0.8 + - - -
344B LEU* 1.3 75.9 - - - +
346B LEU* 1.3 65.6 + - - +
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Residues in contact with LEU 346 (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* 3.3 4.9 - - - +
21B HIS 2.9 34.2 + - - +
23B PHE* 3.8 29.4 - - + -
113B LEU* 4.2 4.8 - - - +
319B VAL 3.4 3.6 - - - +
320B VAL* 3.7 31.2 - - + -
344B LEU* 5.1 7.4 - - + -
345B GLY* 1.3 80.8 - - - +
347B GLY* 1.3 58.5 + - - +
406B LDA 5.4 10.5 - - + -
407C LDA 4.0 28.6 - - + +
409C LDA 4.6 17.3 - - + -
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Residues in contact with GLY 347 (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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18B ASP* 5.2 1.3 - - - -
19B VAL 3.2 11.4 - - - -
20B ARG* 4.3 6.7 - - - -
113B LEU* 4.8 0.2 - - - -
318B ALA* 3.4 5.0 - - - +
319B VAL* 2.8 49.8 + - - +
346B LEU* 1.3 75.6 - - - +
348B LEU* 1.3 60.8 + - - +
349B VAL* 5.0 0.4 - - - -
406B LDA 4.6 3.3 - - - +
407C LDA 4.1 4.7 - - - +
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Residues in contact with LEU 348 (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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17B VAL 3.7 1.7 - - - +
19B VAL* 2.9 43.5 + - + +
312B PHE* 4.2 5.4 - - + -
316B MET* 3.7 20.4 - - + -
317B SER 3.5 15.9 - - - +
318B ALA* 4.0 14.6 - - + -
347B GLY* 1.3 74.5 - - - -
349B VAL* 1.3 62.8 + - - +
350B TYR 4.2 0.2 - - - -
406B LDA 5.0 7.2 - - + -
82C ALA* 3.7 12.9 - - + +
83C GLY* 3.6 33.7 - - - +
84C LEU* 4.2 16.4 - - + -
94C TYR 5.4 0.4 - - - +
406C LDA 4.4 13.5 - - + -
407C LDA 4.0 8.7 - - + +
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Residues in contact with VAL 349 (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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16B LYS* 4.2 25.8 - - + +
17B VAL 3.3 8.3 - - - +
18B ASP* 3.4 28.5 - - + +
315B ASN 3.8 0.5 - - - +
316B MET* 3.5 9.3 - - - +
317B SER* 2.8 48.0 + - - +
319B VAL* 5.2 11.0 - - + -
347B GLY 5.0 2.7 - - - -
348B LEU* 1.3 80.2 - - - +
350B TYR* 1.3 61.6 + - - +
351B GLN* 3.9 20.5 + - - +
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Residues in contact with TYR 350 (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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16B LYS* 3.3 2.4 - - - -
17B VAL* 2.8 44.8 + - + +
315B ASN* 3.5 9.2 - - + -
316B MET* 3.9 21.1 - - - -
348B LEU 4.2 0.6 - - - -
349B VAL* 1.3 72.8 - - - +
351B GLN* 1.3 76.1 + - - +
352B PHE* 4.2 15.8 - + + +
9C ASN* 2.7 24.7 + - - -
10C LYS 4.1 0.3 + - - -
11C LEU* 4.2 3.5 - - - +
46C GLY* 3.2 41.9 - - - -
47C ASP 3.5 0.3 + - - -
48C THR* 3.9 24.2 - - + -
56C GLY 4.4 0.4 - - - -
57C PHE* 4.0 3.8 - - - +
58C GLY* 3.8 31.6 - - - -
82C ALA* 4.3 7.4 - - + +
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Residues in contact with GLN 351 (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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15B GLY 3.6 6.7 - - - +
16B LYS* 3.9 22.7 - - + -
314B LYS 4.3 15.4 + - - +
315B ASN* 2.7 40.5 + - - +
317B SER* 4.1 12.5 + - - -
349B VAL* 3.9 17.4 + - - +
350B TYR* 1.3 82.5 - - - +
352B PHE* 1.3 64.1 + - - +
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Residues in contact with PHE 352 (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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1B ALA* 3.5 32.5 + - + +
13B VAL* 4.1 24.5 - - + -
14B TYR* 3.7 26.8 - - - +
15B GLY* 2.9 55.5 + - - +
16B LYS* 4.6 2.0 - - - -
17B VAL* 6.2 2.9 - - + -
42B LEU* 4.3 16.6 - - + -
315B ASN* 4.2 7.0 - - - +
350B TYR* 4.2 16.6 - + + +
351B GLN* 1.3 80.4 - - - +
9C ASN* 4.6 10.4 + - - +
11C LEU* 3.6 44.6 - - + -
44C VAL* 4.6 21.8 - - + -
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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