Contacts of the strand formed by residues 316 - 325 (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 MET 316 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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312B PHE* 3.0 46.9 + - + -
313B ASN* 3.0 22.1 + - - +
314B LYS 3.6 0.6 + - - -
315B ASN* 1.3 77.9 - - - +
317B SER* 1.3 63.8 + - - +
348B LEU* 3.7 35.4 - - + -
349B VAL 3.5 8.1 - - - +
350B TYR* 3.9 24.5 - - - -
351B GLN* 5.9 0.2 - - - -
48C THR* 4.0 8.7 - - + -
50C ILE* 4.6 1.1 - - + -
56C GLY* 4.0 10.3 - - - -
57C PHE 4.2 2.7 - - - +
82C ALA* 4.6 2.9 - - + -
83C GLY 3.3 29.4 - - - +
84C LEU* 3.8 12.6 - - + -
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Residues in contact with SER 317 (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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309B TYR* 5.5 1.7 - - - -
310B TYR 3.2 12.8 - - - -
311B TYR* 4.0 25.0 - - - -
312B PHE* 3.9 5.4 - - - -
313B ASN 5.3 0.2 - - - -
316B MET* 1.3 77.0 - - - +
318B ALA* 1.3 62.9 + - - +
319B VAL* 5.5 5.1 - - - +
348B LEU* 3.5 5.5 - - - +
349B VAL* 2.8 47.3 + - - +
351B GLN* 4.1 13.2 + - - -
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Residues in contact with ALA 318 (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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309B TYR* 4.3 0.2 - - - +
310B TYR* 2.7 40.3 + - + +
312B PHE* 3.8 18.1 - - + -
317B SER* 1.3 76.3 - - - +
319B VAL* 1.3 68.4 + - - +
347B GLY 3.4 10.5 - - - +
348B LEU* 4.0 5.8 - - + -
406B LDA 3.9 25.8 - - + -
417B LDA 4.8 4.9 - - + -
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Residues in contact with VAL 319 (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* 5.9 0.2 - - - +
112B PRO* 3.9 13.7 - - + +
113B LEU* 3.8 29.6 - - + -
308B SER 3.2 10.3 - - - +
309B TYR* 3.5 34.8 - - + -
317B SER* 5.5 4.0 - - - +
318B ALA* 1.3 82.2 - - - +
320B VAL* 1.3 67.2 + - - +
346B LEU* 3.4 5.0 - - - +
347B GLY* 2.8 48.2 + - - +
349B VAL* 5.2 11.4 - - + -
406B LDA 5.6 1.9 - - - +
417B LDA 5.7 0.4 - - - -
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Residues in contact with VAL 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112B PRO* 3.6 5.0 - - - +
113B LEU* 4.7 0.2 - - - -
307B GLY* 3.0 3.0 - - - -
308B SER* 2.9 39.1 + - - +
319B VAL* 1.3 78.5 - - - +
321B ASP* 1.3 67.9 + - - +
322B TYR 5.0 0.4 - - - +
344B LEU* 3.8 20.9 - - + -
345B GLY 3.3 10.5 - - - +
346B LEU* 3.7 17.7 - - + -
406B LDA 6.4 0.9 - - + -
409B LDA 4.5 21.3 - - + -
417B LDA 3.4 33.7 - - + -
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Residues in contact with ASP 321 (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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111B PHE* 3.9 0.9 - - - +
112B PRO* 3.3 18.6 - - + +
113B LEU* 2.6 43.0 + - + +
114B TRP* 3.0 36.8 + - - +
305B SER* 2.8 23.3 + - - -
306B VAL 3.7 8.7 - - - +
307B GLY* 4.0 0.2 - - - -
320B VAL* 1.3 73.9 - - - +
322B TYR* 1.3 62.4 + - - +
343B VAL 3.4 1.2 - - - +
344B LEU* 4.4 2.5 - - - -
345B GLY 2.8 36.9 + - - -
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Residues in contact with TYR 322 (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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114B TRP* 4.0 1.6 - - - -
304B ILE 3.6 1.0 - - - +
305B SER* 3.5 4.5 - - - -
306B VAL* 2.8 55.6 + - + +
320B VAL* 5.0 0.4 - - - +
321B ASP* 1.3 71.4 + - - +
323B LYS* 1.3 69.3 + - - +
324B ILE* 3.6 13.8 + - + +
342B ASN* 3.5 24.5 + - + +
343B VAL 3.4 14.6 - - - -
344B LEU* 4.1 10.1 - - + +
409B LDA 3.6 68.0 - - + +
410B LDA 3.4 46.6 - - + -
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Residues in contact with LYS 323 (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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33B GLU* 5.7 5.5 + - - +
114B TRP* 3.4 53.0 - - + +
117B ASP* 4.9 4.0 + - - -
303B TYR* 3.8 45.0 - - + -
304B ILE 3.6 4.0 - - - -
305B SER* 4.8 0.2 - - - +
322B TYR* 1.3 72.5 - - - +
324B ILE* 1.3 62.9 + - - +
325B ASN* 4.4 9.2 - - + +
339B ASN* 5.0 6.4 - - - +
341B ASP 4.7 6.7 - - - +
342B ASN* 3.3 11.4 - - - +
343B VAL* 2.7 48.1 + - + +
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Residues in contact with ILE 324 (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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303B TYR* 3.3 4.0 - - - -
304B ILE* 2.8 56.0 + - + +
306B VAL* 4.1 29.8 - - + -
322B TYR* 3.9 24.0 - - + +
323B LYS* 1.3 72.5 - - - +
325B ASN* 1.3 65.1 + - - +
326B LEU* 3.5 16.7 + - + +
342B ASN* 3.6 12.6 - - - +
410B LDA 4.8 18.4 - - + +
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Residues in contact with ASN 325 (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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302B LYS 3.3 4.6 - - - +
303B TYR* 4.1 8.3 - - - +
323B LYS* 3.6 8.9 + - + +
324B ILE* 1.3 72.7 - - - +
326B LEU* 1.3 71.0 + - - +
327B LEU* 3.3 26.9 + - - +
339B ASN* 3.0 30.3 + - - +
340B THR* 3.2 20.3 - - - +
341B ASP 3.1 24.4 + - - +
342B ASN* 2.7 22.4 + - - +
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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