Contacts of the strand formed by residues 272 - 278 (chain B) in PDB entry 5N4D
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 TYR 272 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266B THR* 3.6 4.0 - - - -
267B SER* 3.0 30.5 + - - +
270B GLY 3.6 0.5 - - - -
271B LYS* 1.3 118.3 + - + +
273B LEU* 1.3 59.9 + - - +
274B TYR* 3.5 37.2 - + + +
289B VAL* 3.4 26.5 - - + -
290B ALA 3.3 6.7 - - - +
291B GLU* 3.7 25.1 + - + -
292B LEU* 4.0 9.2 - - - +
319B ASN* 3.8 13.0 - - - -
321B GLY 3.6 15.3 - - - -
322B SER* 3.4 16.6 + - - -
324B VAL* 4.5 7.6 - - + -
342B LEU* 3.9 17.4 - - + +
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Residues in contact with LEU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 3.7 23.8 - - + -
251B VAL* 4.3 14.4 - - + -
264B ALA* 4.7 2.7 - - + -
265B ASP 3.6 16.4 - - - +
266B THR* 3.7 16.2 - - + -
272B TYR* 1.3 72.8 - - - +
274B TYR* 1.3 67.9 + - - +
289B VAL* 3.6 2.3 - - - +
290B ALA* 2.8 45.0 + - + +
292B LEU* 4.0 28.4 - - + +
297B VAL* 4.9 12.1 - - + -
301B ILE* 5.0 5.6 - - + -
303B TRP* 3.7 27.7 - - + -
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Residues in contact with TYR 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B ALA* 3.2 11.4 - - - +
265B ASP* 2.8 57.2 + - + +
266B THR 4.5 0.4 - - - -
267B SER* 4.0 23.6 - - - -
272B TYR* 3.5 34.0 - + + +
273B LEU* 1.3 76.5 - - - +
275B LEU* 1.3 61.4 + - - +
276B TYR* 4.2 3.4 - - + -
287B LEU* 4.4 6.5 - - + -
288B TRP 3.5 4.0 - - - +
289B VAL* 3.9 30.5 - - + -
303B TRP* 4.5 1.5 - - - -
316B ILE* 3.7 45.7 - - + +
319B ASN* 3.9 16.5 + - - +
324B VAL* 3.9 13.2 - - + +
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B MET* 4.3 12.3 - - + -
251B VAL* 5.4 0.9 - - + -
252B TYR* 3.7 40.6 - - + -
262B TYR* 4.3 13.5 - - + -
263B GLY 3.6 13.9 - - - +
264B ALA* 5.4 0.9 - - + -
274B TYR* 1.3 75.1 - - - +
276B TYR* 1.3 72.6 + - - +
277B GLN* 3.8 21.2 - - + +
286B LEU 3.8 0.5 - - - +
287B LEU* 3.4 5.9 + - - +
288B TRP* 2.8 51.0 + - + +
303B TRP* 3.6 27.8 - - + -
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Residues in contact with TYR 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B TYR* 3.3 7.4 - - - +
263B GLY* 2.8 49.6 + - - +
264B ALA* 3.8 12.8 - - - -
265B ASP* 2.6 33.0 + - + -
274B TYR* 4.8 2.7 - - + -
275B LEU* 1.3 71.4 - - - +
277B GLN* 1.3 67.1 + - - +
278B PHE* 3.7 25.6 - + + -
285B ASN* 3.5 17.7 - - - +
286B LEU 3.3 4.9 - - - +
287B LEU* 3.6 26.5 - - + -
314B TYR 3.7 15.0 - - - -
315B ASN* 3.6 11.7 + - - -
316B ILE* 3.0 31.9 + - + +
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Residues in contact with GLN 277 (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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252B TYR* 3.6 16.8 + - - -
254B ASP* 4.7 0.2 - - - +
260B TRP* 3.3 26.3 - - + -
261B ILE 3.4 4.3 - - - -
262B TYR* 3.6 18.7 - - + -
275B LEU* 3.8 11.9 - - + +
276B TYR* 1.3 79.7 - - - +
278B PHE* 1.3 62.7 + - - +
285B ASN* 3.1 8.7 - - - -
286B LEU* 2.9 42.6 + - + +
288B TRP* 3.4 50.4 - - - +
310B TYR* 3.3 14.5 - - - +
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Residues in contact with PHE 278 (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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259B GLU 4.6 0.2 - - - +
260B TRP* 3.3 4.5 - - - +
261B ILE* 2.9 63.5 + - + +
262B TYR 4.3 2.2 - - - -
263B GLY* 4.0 13.5 - - - -
276B TYR* 3.7 34.5 - + + -
277B GLN* 1.3 74.7 - - - +
279B LYS* 1.3 61.7 + - - +
280B ASP 3.6 14.1 - - - +
282B SER 5.2 4.0 - - - -
283B LYS* 6.3 0.9 - - - -
284B LYS 4.1 9.0 - - - +
285B ASN* 3.6 25.8 - - + -
310B TYR* 3.7 5.4 - - - -
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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