Contacts of the strand formed by residues 315 - 324 (chain B) in PDB entry 3R2W
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 ILE 315 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70B PRO* 4.3 6.7 - - + -
75B ILE* 4.0 40.4 - - + -
271B VAL* 3.4 19.3 - - + -
272B THR 3.2 2.2 - - - -
274B LYS* 5.0 0.9 - - - +
283B THR* 2.9 33.1 - - - +
284B LEU* 3.1 51.4 - - + +
285B THR* 6.0 0.2 - - + -
313B PHE* 2.4 27.8 + - + +
314B LYS* 1.3 75.6 - - - +
316B PHE* 1.3 63.9 + - - +
375B ASN* 4.2 11.7 - - - +
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Residues in contact with PHE 316 (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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271B VAL* 3.3 7.6 - - - +
272B THR* 2.9 41.3 + - - +
273B ASN 3.7 18.2 - - - -
274B LYS* 4.5 12.3 - - + -
278B ASP* 3.4 36.3 - - + +
281B GLY* 4.1 24.2 - - - -
282B GLY 3.7 8.3 - - - +
283B THR* 4.8 2.2 - - + +
315B ILE* 1.3 75.7 - - - +
317B ASN* 1.3 82.2 + - + +
318B THR* 5.8 0.4 - - - -
378B ARG* 3.4 20.4 - - - -
381B PHE* 3.7 26.7 - + - -
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Residues in contact with ASN 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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269B MET* 3.1 38.9 - - + +
270B GLU 4.6 1.1 - - - -
282B GLY* 3.0 25.5 + - - +
293B LEU* 4.0 19.7 - - + +
295B GLU* 5.5 3.0 + - - +
316B PHE* 1.3 99.6 - - + +
318B THR* 1.3 76.7 + - - +
319B ASN* 2.5 34.7 + - - +
321B LEU* 6.0 0.2 - - - +
362B GLY* 4.8 3.6 - - - -
381B PHE* 4.7 1.4 - - - -
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Residues in contact with THR 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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240B ASN* 5.1 3.3 + - - -
243B ASN* 4.4 2.4 + - - +
270B GLU* 3.1 32.7 + - + +
271B VAL* 3.3 12.8 + - - -
272B THR* 3.8 7.3 + - - +
316B PHE* 5.6 0.7 - - - -
317B ASN* 1.3 79.2 + - - +
319B ASN* 1.3 67.2 + - - +
320B ASN* 3.3 32.7 + - + +
376B VAL* 4.5 2.1 - - + +
380B ARG 4.0 7.0 - - - +
381B PHE* 3.6 38.4 - - + -
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Residues in contact with ASN 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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102B LEU* 4.0 23.8 - - - +
212B HIS* 3.8 29.3 + - - -
238B VAL* 3.9 5.8 - - - +
239B SER* 4.0 7.3 - - - -
240B ASN* 4.2 19.1 + - - +
317B ASN* 2.5 34.3 + - - +
318B THR* 1.3 74.4 - - - +
320B ASN* 1.3 64.6 + - - +
321B LEU* 3.5 22.7 - - - +
361B VAL* 4.6 2.4 - - - +
362B GLY 4.5 6.9 + - - -
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Residues in contact with ASN 320 (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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237B PHE* 4.2 6.7 - - + -
238B VAL 3.5 3.4 - - - -
239B SER* 3.7 9.1 - - - -
240B ASN 4.8 1.2 - - - +
243B ASN* 3.8 7.3 - - - +
246B ALA* 3.5 30.2 - - - +
268B VAL 4.2 0.2 - - - +
269B MET* 3.6 0.5 - - - +
270B GLU* 3.0 59.1 + - + +
318B THR* 3.0 20.7 + - + +
319B ASN* 1.3 81.0 + - - +
321B LEU* 1.3 63.7 + - - +
380B ARG* 3.3 15.2 + - - +
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Residues in contact with LEU 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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237B PHE* 3.0 8.9 - - - -
238B VAL* 2.9 43.6 + - + -
267B PHE* 3.3 37.5 - - + -
268B VAL 3.4 5.2 - - - +
269B MET* 3.9 14.1 - - + -
317B ASN* 5.4 0.2 - - - +
319B ASN* 3.5 26.7 - - - +
320B ASN* 1.3 81.8 - - - +
322B TRP* 1.3 61.3 + - - +
323B ILE* 4.1 16.2 - - + -
361B VAL* 3.5 30.3 - - + -
362B GLY* 4.3 8.1 - - - -
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Residues in contact with TRP 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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97B LEU* 3.4 21.5 - - + -
235B TYR* 4.6 6.4 - - + -
236B ILE 3.3 6.7 - - - -
237B PHE* 3.6 39.6 - + + -
248B VAL* 4.1 20.2 - - + -
249B ASP 4.2 10.1 - - - -
252B ILE* 3.5 37.0 - - + +
253B LEU* 3.4 25.6 - - + -
256B LEU* 3.6 31.6 - - + -
267B PHE* 3.4 4.3 + - - -
268B VAL* 2.7 60.4 + - + +
270B GLU* 3.8 16.4 + - + -
321B LEU* 1.3 74.5 - - - +
323B ILE* 1.3 63.8 + - - +
380B ARG* 4.9 1.3 - - - -
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Residues in contact with ILE 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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215B ILE* 5.9 0.7 - - + -
216B TYR* 4.0 30.5 - - + +
235B TYR* 3.3 7.3 - - - -
236B ILE* 2.7 62.3 + - + +
238B VAL* 5.0 12.1 - - + -
266B GLU 3.5 11.9 - - - +
267B PHE* 3.6 17.7 - - + -
321B LEU* 4.2 16.8 - - + -
322B TRP* 1.3 79.9 - - - +
324B SER* 1.3 65.7 + - - +
328B VAL* 4.5 7.6 - - + -
361B VAL* 5.2 3.4 - - + -
368B PHE* 3.5 26.7 - - + -
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Residues in contact with SER 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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234B GLU 3.5 8.8 + - - -
235B TYR* 3.6 24.2 - - - -
266B GLU* 3.0 25.6 + - - +
323B ILE* 1.3 70.7 - - - +
325B LEU* 1.3 54.2 + - - +
326B ALA* 3.4 13.0 - - - +
327B ALA* 2.5 44.0 + - - +
328B VAL* 3.1 11.8 + - - +
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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